difference between journal and research articles

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Types of journal articles

It is helpful to familiarise yourself with the different types of articles published by journals. Although it may appear there are a large number of types of articles published due to the wide variety of names they are published under, most articles published are one of the following types; Original Research, Review Articles, Short reports or Letters, Case Studies, Methodologies.

Original Research:

This is the most common type of journal manuscript used to publish full reports of data from research. It may be called an  Original Article, Research Article, Research, or just  Article, depending on the journal. The Original Research format is suitable for many different fields and different types of studies. It includes full Introduction, Methods, Results, and Discussion sections.

Short reports or Letters:

These papers communicate brief reports of data from original research that editors believe will be interesting to many researchers, and that will likely stimulate further research in the field. As they are relatively short the format is useful for scientists with results that are time sensitive (for example, those in highly competitive or quickly-changing disciplines). This format often has strict length limits, so some experimental details may not be published until the authors write a full Original Research manuscript. These papers are also sometimes called Brief communications .

Review Articles:

Review Articles provide a comprehensive summary of research on a certain topic, and a perspective on the state of the field and where it is heading. They are often written by leaders in a particular discipline after invitation from the editors of a journal. Reviews are often widely read (for example, by researchers looking for a full introduction to a field) and highly cited. Reviews commonly cite approximately 100 primary research articles.

TIP: If you would like to write a Review but have not been invited by a journal, be sure to check the journal website as some journals to not consider unsolicited Reviews. If the website does not mention whether Reviews are commissioned it is wise to send a pre-submission enquiry letter to the journal editor to propose your Review manuscript before you spend time writing it.  

Case Studies:

These articles report specific instances of interesting phenomena. A goal of Case Studies is to make other researchers aware of the possibility that a specific phenomenon might occur. This type of study is often used in medicine to report the occurrence of previously unknown or emerging pathologies.

Methodologies or Methods

These articles present a new experimental method, test or procedure. The method described may either be completely new, or may offer a better version of an existing method. The article should describe a demonstrable advance on what is currently available.

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International Journal of Research (IJR)

IJR Journal is Multidisciplinary, high impact and indexed journal for research publication. IJR is a monthly journal for research publication.

DIFFERENCE BETWEEN RESEARCH PAPER AND JOURNAL ARTICLE

Difference between research paper and journal article.

Research Paper

Argumentative Research Paper

Analytical research paper, journal article, the differences, research paper:, journal article:.

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• Key Differences

Know the Differences & Comparisons

Difference Between Article and Journal

On the contrary, Journal is a periodical publication in a specific field of study, which is often reviewed by experts in the concerned area. Journal publications are regarded as one of the highly honoured forms of publications, because of its high standards in reviewing and publishing.

Come let’s discuss the differences between article and journal.

Content: Article Vs Journal

Comparison chart.

Definition of Article

The article implies an independently written composition, usually short and precise, which is traditionally included in the newspaper, magazines, websites, journals, etc. It is written for a large audience in an entertaining manner, so as to grab and retain their interest and attention. The name of the person who wrote the article is always mentioned.

An article not just integrates facts, but the thoughts and opinions of the writer and experts, and balanced arguments are also included. A well-drafted article often brings out topics of interest into the limelight.

An article may cover fascinating stories, reported speech, information, suggestions and other descriptions. It can also describe any event, experience, person or anything else. Articles are classified on the basis of need or preference:

• News Articles : Articles containing breaking news, information, happenings, events of public interest, what will happen in the near future or a trending topic. It may contain photographs, charts, interviews, debates, etc. Its objective is to report on when, how, where and why the event took place and who is involved in it.
• Feature Articles : One that is written creatively and descriptively so as to entertain, engage and influence the reader. The article can be based on anything, i.e. from people to place or from event to experience.
• Editorial Articles : These are commonly found in newspapers and magazines, which often showcase a new outlook or opinion, on a current issue. It often expresses a distinctive angle or approach about someone or something and provokes the reader to think that way.
• How-to Articles : Such articles are instructional in the sense that they offer complete guidelines on how-to-do something.
• Marketing Articles : A short piece of writing, which is actually an advertisement, written to catch the attention of the reader towards the company’s product or service.
• Question-Answer Articles : As the name suggest, these articles are in question-answer format, based upon an interview with the famous personality. It does not contain an introductory paragraph.
• Profile Articles : Profile articles are all about a specific person, which requires research and interview, to gather relevant information about that person.

Definition of Journal

Journal can be defined as a professional or academic publication, which features a number of educational articles, written by researchers, experts or someone having academic qualifications in the concerned subject, which presents original and new research, book reviews, feedback, review articles and so forth. It includes references and targets academic audience only.

A journal is always on a specific discipline, that targets a particular group of people, typically students pursuing that discipline and not the general public. It must be noted, the journals are usually peer-reviewed (refereed) and so they undergo an extensive editorial process. However, all the journals are not peer-reviewed.

They focus on current developments in the field of study. It is available in both offline (printed form) and online mode. One can use journal articles for the purpose of research as they are authoritative, up to date, topic-specific and understandable.

Journals are published periodically, i.e. weekly, bi-monthly, monthly, quarterly, semi-annually or annually. Each copy is termed as an issue, and a set of issues are called volume.

Key Differences Between Article and Journal

The points given below are noteworthy so far as the difference between article and journal is concerned:

• An article is a written composition on a topic of interest, which forms a separate part of a book, magazine or newspaper. On the other hand, Journal is a type of magazine which contains articles and other descriptions on a particular discipline or professional activities.
• While the article is a work of literature, the journal is a form of publication.
• An article is non-fictional and informative in nature. As against, the journal is educational and academic.
• The article can include news, stories, information, facts or writer’s experience, opinion, suggestion, facts, etc. Conversely, a journal contains articles, book reviews, editorial content, achievements, feedback, recent developments in the field of study and many more.
• An article is written on the topic of interest of the writer or any burning issue. In contrast, a journal is all about the specific field of study or professional course and developments thereon.
• The main objective of writing an article is to influence the reader and urging them to think. On the flip side, a journal aims to provide relevant information relating to the professional course.

In a nutshell, an article differs from a journal in the sense that an article is a written composition, which is just a small part of the journal, while the journal is itself a publication containing a number of articles and other relevant material.

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Understanding Scientific Journals and Articles: How to approach reading journal articles

by Anthony Carpi, Ph.D., Anne E. Egger, Ph.D., Natalie H. Kuldell

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Did you know that scientific literature goes all the way back to 600 BCE? Although scientific articles have changed some – for example, Isaac Newton wrote about the fun he had with prisms in a 1672 scientific article – the basics remain the same. This ensures that published research becomes part of the archive of scientific knowledge upon which other scientists can build.

Scientists make their research available to the community by publishing it in scientific journals.

In scientific papers, scientists explain the research that they are building on, their research methods, data and data analysis techniques, and their interpretation of the data.

Understanding how to read scientific papers is a critical skill for scientists and students of science.

We've all read the headlines at the supermarket checkout line: "Aliens Abduct New Jersey School Teacher" or "Quadruplets Born to 99-Year-Old Woman: Exclusive Photos Inside." Journals like the National Enquirer sell copies by publishing sensational headlines, and most readers believe only a fraction of what is printed. A person more interested in news than gossip could buy a publication like Time, Newsweek or Discover . These magazines publish information on current news and events, including recent scientific advances. These are not original reports of scientific research , however. In fact, most of these stories include phrases like, "A group of scientists recently published their findings on..." So where do scientists publish their findings?

Scientists publish their original research in scientific journals, which are fundamentally different from news magazines. The articles in scientific journals are not written by journalists – they are written by scientists. Scientific articles are not sensational stories intended to entertain the reader with an amazing discovery, nor are they news stories intended to summarize recent scientific events, nor even records of every successful and unsuccessful research venture. Instead, scientists write articles to describe their findings to the community in a transparent manner.

• Scientific journals vs. popular media

Within a scientific article, scientists present their research questions, the methods by which the question was approached, and the results they achieved using those methods. In addition, they present their analysis of the data and describe some of the interpretations and implications of their work. Because these articles report new work for the first time, they are called primary literature . In contrast, articles or news stories that review or report on scientific research already published elsewhere are referred to as secondary .

The articles in scientific journals are different from news articles in another way – they must undergo a process called peer review , in which other scientists (the professional peers of the authors) evaluate the quality and merit of research before recommending whether or not it should be published (see our Peer Review module). This is a much lengthier and more rigorous process than the editing and fact-checking that goes on at news organizations. The reason for this thorough evaluation by peers is that a scientific article is more than a snapshot of what is going on at a certain time in a scientist's research. Instead, it is a part of what is collectively called the scientific literature, a global archive of scientific knowledge. When published, each article expands the library of scientific literature available to all scientists and contributes to the overall knowledge base of the discipline of science.

Comprehension Checkpoint

• Scientific journals: Degrees of specialization

Figure 1: Nature : An example of a scientific journal.

There are thousands of scientific journals that publish research articles. These journals are diverse and can be distinguished according to their field of specialization. Among the most broadly targeted and competitive are journals like Cell , the New England Journal of Medicine (NEJM), Nature , and Science that all publish a wide variety of research articles (see Figure 1 for an example). Cell focuses on all areas of biology, NEJM on medicine, and both Science and Nature publish articles in all areas of science. Scientists submit manuscripts for publication in these journals when they feel their work deserves the broadest possible audience.

Just below these journals in terms of their reach are the top-tier disciplinary journals like Analytical Chemistry, Applied Geochemistry, Neuron, Journal of Geophysical Research , and many others. These journals tend to publish broad-based research focused on specific disciplines, such as chemistry, geology, neurology, nuclear physics, etc.

Next in line are highly specialized journals, such as the American Journal of Potato Research, Grass and Forage Science, the Journal of Shellfish Research, Neuropeptides, Paleolimnology , and many more. While the research published in various journals does not differ in terms of the quality or the rigor of the science described, it does differ in its degree of specialization: These journals tend to be more specialized, and thus appeal to a more limited audience.

All of these journals play a critical role in the advancement of science and dissemination of information (see our Utilizing the Scientific Literature module for more information). However, to understand how science is disseminated through these journals, you must first understand how the articles themselves are formatted and what information they contain. While some details about format vary between journals and even between articles in the same journal, there are broad characteristics that all scientific journal articles share.

• The standard format of journal articles

In June of 2005, the journal Science published a research report on a sighting of the ivory-billed woodpecker, a bird long considered extinct in North America (Fitzpatrick et al., 2005). The work was of such significance and broad interest that it was displayed prominently on the cover (Figure 2) and highlighted by an editorial at the front of the journal (Kennedy, 2005). The authors were aware that their findings were likely to be controversial, and they worked especially hard to make their writing clear. Although the article has no headings within the text, it can easily be divided into sections:

Figure 2: A picture of the cover of Science from June 3, 2005.

Title and authors: The title of a scientific article should concisely and accurately summarize the research . Here, the title used is "Ivory-billed Woodpecker ( Campephilus principalis ) Persists in North America." While it is meant to capture attention, journals avoid using misleading or overly sensational titles (you can imagine that a tabloid might use the headline "Long-dead Giant Bird Attacks Canoeists!"). The names of all scientific contributors are listed as authors immediately after the title. You may be used to seeing one or maybe two authors for a book or newspaper article, but this article has seventeen authors! It's unlikely that all seventeen of those authors sat down in a room and wrote the manuscript together. Instead, the authorship reflects the distribution of the workload and responsibility for the research, in addition to the writing. By convention, the scientist who performed most of the work described in the article is listed first, and it is likely that the first author did most of the writing. Other authors had different contributions; for example, Gene Sparling is the person who originally spotted the bird in Arkansas and was subsequently contacted by the scientists at the Cornell Laboratory of Ornithology. In some cases, but not in the woodpecker article, the last author listed is the senior researcher on the project, or the scientist from whose lab the project originated. Increasingly, journals are requesting that authors detail their exact contributions to the research and writing associated with a particular study.

Abstract: The abstract is the first part of the article that appears right after the listing of authors in an article. In it, the authors briefly describe the research question, the general methods , and the major findings and implications of the work. Providing a summary like this at the beginning of an article serves two purposes: First, it gives readers a way to decide whether the article in question discusses research that interests them, and second, it is entered into literature databases as a means of providing more information to people doing scientific literature searches. For both purposes, it is important to have a short version of the full story. In this case, all of the critical information about the timing of the study, the type of data collected, and the potential interpretations of the findings is captured in four straightforward sentences as seen below:

The ivory-billed woodpecker ( Campephilus principalis ), long suspected to be extinct, has been rediscovered in the Big Woods region of eastern Arkansas. Visual encounters during 2004 and 2005, and analysis of a video clip from April 2004, confirm the existence of at least one male. Acoustic signatures consistent with Campephilus display drums also have been heard from the region. Extensive efforts to find birds away from the primary encounter site remain unsuccessful, but potential habitat for a thinly distributed source population is vast (over 220,000 hectares).

Introduction: The central research question and important background information are presented in the introduction. Because science is a process that builds on previous findings, relevant and established scientific knowledge is cited in this section and then listed in the References section at the end of the article. In many articles, a heading is used to set this and subsequent sections apart, but in the woodpecker article the introduction consists of the first three paragraphs, in which the history of the decline of the woodpecker and previous studies are cited. The introduction is intended to lead the reader to understand the authors' hypothesis and means of testing it. In addition, the introduction provides an opportunity for the authors to show that they are aware of the work that scientists have done before them and how their results fit in, explicitly building on existing knowledge.

Materials and methods: In this section, the authors describe the research methods they used (see The Practice of Science module for more information on these methods). All procedures, equipment, measurement parameters , etc. are described in detail sufficient for another researcher to evaluate and/or reproduce the research. In addition, authors explain the sources of error and procedures employed to reduce and measure the uncertainty in their data (see our Uncertainty, Error, and Confidence module). The detail given here allows other scientists to evaluate the quality of the data collected. This section varies dramatically depending on the type of research done. In an experimental study, the experimental set-up and procedure would be described in detail, including the variables , controls , and treatment . The woodpecker study used a descriptive research approach, and the materials and methods section is quite short, including the means by which the bird was initially spotted (on a kayaking trip) and later photographed and videotaped.

Results: The data collected during the research are presented in this section, both in written form and using tables, graphs, and figures (see our Using Graphs and Visual Data module). In addition, all statistical and data analysis techniques used are presented (see our Statistics in Science module). Importantly, the data should be presented separately from any interpretation by the authors. This separation of data from interpretation serves two purposes: First, it gives other scientists the opportunity to evaluate the quality of the actual data, and second, it allows others to develop their own interpretations of the findings based on their background knowledge and experience. In the woodpecker article, the data consist largely of photographs and videos (see Figure 3 for an example). The authors include both the raw data (the photograph) and their analysis (the measurement of the tree trunk and inferred length of the bird perched on the trunk). The sketch of the bird on the right-hand side of the photograph is also a form of analysis, in which the authors have simplified the photograph to highlight the features of interest. Keeping the raw data (in the form of a photograph) facilitated reanalysis by other scientists: In early 2006, a team of researchers led by the American ornithologist David Sibley reanalyzed the photograph in Figure 3 and came to the conclusion that the bird was not an ivory-billed woodpecker after all (Sibley et al, 2006).

Figure 3: An example of the data presented in the Ivory-billed woodpecker article (Fitzpatrick et al ., 2005, Figure 1).

Discussion and conclusions: In this section, authors present their interpretation of the data , often including a model or idea they feel best explains their results. They also present the strengths and significance of their work. Naturally, this is the most subjective section of a scientific research article as it presents interpretation as opposed to strictly methods and data, but it is not speculation by the authors. Instead, this is where the authors combine their experience, background knowledge, and creativity to explain the data and use the data as evidence in their interpretation (see our Data Analysis and Interpretation module). Often, the discussion section includes several possible explanations or interpretations of the data; the authors may then describe why they support one particular interpretation over the others. This is not just a process of hedging their bets – this how scientists say to their peers that they have done their homework and that there is more than one possible explanation. In the woodpecker article, for example, the authors go to great lengths to describe why they believe the bird they saw is an ivory-billed woodpecker rather than a variant of the more common pileated woodpecker, knowing that this is a likely potential rebuttal to their initial findings. A final component of the conclusions involves placing the current work back into a larger context by discussing the implications of the work. The authors of the woodpecker article do so by discussing the nature of the woodpecker habitat and how it might be better preserved.

In many articles, the results and discussion sections are combined, but regardless, the data are initially presented without interpretation .

References: Scientific progress requires building on existing knowledge, and previous findings are recognized by directly citing them in any new work. The citations are collected in one list, commonly called "References," although the precise format for each journal varies considerably. The reference list may seem like something you don't actually read, but in fact it can provide a wealth of information about whether the authors are citing the most recent work in their field or whether they are biased in their citations towards certain institutions or authors. In addition, the reference section provides readers of the article with more information about the particular research topic discussed. The reference list for the woodpecker article includes a wide variety of sources that includes books, other journal articles, and personal accounts of bird sightings.

Supporting material: Increasingly, journals make supporting material that does not fit into the article itself – like extensive data tables, detailed descriptions of methods , figures, and animations – available online. In this case, the video footage shot by the authors is available online, along with several other resources.

• Reading the primary literature

The format of a scientific article may seem overly structured compared to many other things you read, but it serves a purpose by providing an archive of scientific research in the primary literature that we can build on. Though isolated examples of that archive go as far back as 600 BCE (see the Babylonian tablets in our Description in Scientific Research module), the first consistently published scientific journal was the Philosophical Transactions of the Royal Society of London , edited by Henry Oldenburg for the Royal Society beginning in 1666 (see our Scientific Institutions and Societies module). These early scientific writings include all of the components listed above, but the writing style is surprisingly different than a modern journal article. For example, Isaac Newton opened his 1672 article "New Theory About Light and Colours" with the following:

I shall without further ceremony acquaint you, that in the beginning of the Year 1666...I procured me a Triangular glass-Prisme, to try therewith the celebrated Phenomena of Colours . And in order thereto having darkened my chamber, and made a small hole in my window-shuts, to let in a convenient quantity of the Suns light, I placed my Prisme at his entrance, that it might be thereby refracted to the opposite wall. It was at first a very pleasing divertissement, to view the vivid and intense colours produced thereby; but after a while applying my self to consider them more circumspectly, I became surprised to see them in an oblong form; which, according to the received laws of Refraction, I expected should have been circular . (Newton, 1672)

Figure 4: Isaac Newton described the rainbow produced by a prism as a "pleasing divertissement."

Newton describes his materials and methods in the first few sentences ("... a small hole in my window-shuts"), describes his results ("an oblong form"), refers to the work that has come before him ("the received laws of Refraction"), and highlights how his results differ from his expectations. Today, however, Newton 's statement that the "colours" produced were a "very pleasing divertissement" would be out of place in a scientific article (Figure 4). Much more typically, modern scientific articles are written in an objective tone, typically without statements of personal opinion to avoid any appearance of bias in the interpretation of their results. Unfortunately, this tone often results in overuse of the passive voice, with statements like "a Triangular glass-Prisme was procured" instead of the wording Newton chose: "I procured me a Triangular glass-Prisme." The removal of the first person entirely from the articles reinforces the misconception that science is impersonal, boring, and void of creativity, lacking the enjoyment and surprise described by Newton. The tone can sometimes be misleading if the study involves many authors, making it unclear who did what work. The best scientific writers are able to both present their work in an objective tone and make their own contributions clear.

The scholarly vocabulary in scientific articles can be another obstacle to reading the primary literature. Materials and Methods sections often are highly technical in nature and can be confusing if you are not intimately familiar with the type of research being conducted. There is a reason for all of this vocabulary, however: An explicit, technical description of materials and methods provides a means for other scientists to evaluate the quality of the data presented and can often provide insight to scientists on how to replicate or extend the research described.

The tone and specialized vocabulary of the modern scientific article can make it hard to read, but understanding the purpose and requirements for each section can help you decipher the primary literature. Learning to read scientific articles is a skill, and like any other skill, it requires practice and experience to master. It is not, however, an impossible task.

Strange as it seems, the most efficient way to tackle a new article may be through a piecemeal approach, reading some but not all the sections and not necessarily in their order of appearance. For example, the abstract of an article will summarize its key points, but this section can often be dense and difficult to understand. Sometimes the end of the article may be a better place to start reading. In many cases, authors present a model that fits their data in this last section of the article. The discussion section may emphasize some themes or ideas that tie the story together, giving the reader some foundation for reading the article from the beginning. Even experienced scientists read articles this way – skimming the figures first, perhaps, or reading the discussion and then going back to the results. Often, it takes a scientist multiple readings to truly understand the authors' work and incorporate it into their personal knowledge base in order to build on that knowledge.

• Building knowledge and facilitating discussion

The process of science does not stop with the publication of the results of research in a scientific article. In fact, in some ways, publication is just the beginning. Scientific journals also provide a means for other scientists to respond to the work they publish; like many newspapers and magazines, most scientific journals publish letters from their readers.

Unlike the common "Letters to the Editor" of a newspaper, however, the letters in scientific journals are usually critical responses to the authors of a research study in which alternative interpretations are outlined. When such a letter is received by a journal editor, it is typically given to the original authors so that they can respond, and both the letter and response are published together. Nine months after the original publication of the woodpecker article, Science published a letter (called a "Comment") from David Sibley and three of his colleagues, who reinterpreted the Fitzpatrick team's data and concluded that the bird in question was a more common pileated woodpecker, not an ivory-billed woodpecker (Sibley et al., 2006). The team from the Cornell lab wrote a response supporting their initial conclusions, and Sibley's team followed that up with a response of their own in 2007 (Fitzpatrick et al., 2006; Sibley at al., 2007). As expected, the research has generated significant scientific controversy and, in addition, has captured the attention of the public, spreading the story of the controversy into the popular media.

For more information about this story see The Case of the Ivory-Billed Woodpecker module.

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Comparison of Types of Journals

The information below can help you understand the differences between scholarly journals, professional/trade journals, and popular periodicals. 

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• Insights blog

Different types of research articles

A guide for early career researchers.

In scholarly literature, there are many different kinds of articles published every year. Original research articles are often the first thing you think of when you hear the words ‘journal article’. In reality, research work often results in a whole mixture of different outputs and it’s not just the final research article that can be published.

Finding a home to publish supporting work in different formats can help you start publishing sooner, allowing you to build your publication record and research profile.

But before you do, it’s very important that you check the  instructions for authors  and the  aims and scope  of the journal(s) you’d like to submit to. These will tell you whether they accept the type of article you’re thinking of writing and what requirements they have around it.

Understanding the different kind of articles

There’s a huge variety of different types of articles – some unique to individual journals – so it’s important to explore your options carefully. While it would be impossible to cover every single article type here, below you’ll find a guide to the most common research articles and outputs you could consider submitting for publication.

Book review

Many academic journals publish book reviews, which aim to provide insight and opinion on recently published scholarly books. Writing book reviews is often a good way to begin academic writing. It can help you get your name known in your field and give you valuable experience of publishing before you write a full-length article.

If you’re keen to write a book review, a good place to start is looking for journals that publish or advertise the books they have available for review. Then it’s just a matter of putting yourself forward for one of them.

You can check whether a journal publishes book reviews by browsing previous issues or by seeing if a book review editor is listed on the editorial board. In addition, some journals publish other types of reviews, such as film, product, or exhibition reviews, so it’s worth bearing those in mind as options as well.

Get familiar with instructions for authors

Be prepared, speed up your submission, and make sure nothing is forgotten by understanding a journal’s individual requirements.

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Case report

A medical case report – also sometimes called a clinical case study – is an original short report that provides details of a single patient case.

Case reports include detailed information on the symptoms, signs, diagnosis, treatment, and follow-up of an individual patient. They remain one of the cornerstones of medical progress and provide many new ideas in medicine.

Depending on the journal, a case report doesn’t necessarily need to describe an especially novel or unusual case as there is benefit from collecting details of many standard cases.

Take a look at  F1000Research’s guidance on case reports , to understand more about what’s required in them. And don’t forget that for all studies involving human participants, informed written consent to take part in the research must be obtained from the participants –  find out more about consent to publish.

Clinical study

In medicine, a clinical study report is a type of article that provides in-depth detail on the methods and results of a clinical trial. They’re typically similar in length and format to original research articles.

Most journals now require that you register protocols for clinical trials you’re involved with in a publicly accessible registry. A list of eligible registries can be found on the  WHO International Clinical Trials Registry Platform (ICTRP) . Trials can also be registered at  clinicaltrials.gov  or the  EU Clinical Trials Register . Once registered, your trial will be assigned a clinical trial number (CTN).

Before you submit a clinical study, you’ll need to include clinical trial numbers and registration dates in the manuscript, usually in the abstract and methods sections.

Commentaries and letters to editors

Letters to editors, as well as ‘replies’ and ‘discussions’, are usually brief comments on topical issues of public and political interest (related to the research field of the journal), anecdotal material, or readers’ reactions to material published in the journal.

Commentaries are similar, though they may be slightly more in-depth, responding to articles recently published in the journal. There may be a ‘target article’ which various commentators are invited to respond to.

You’ll need to look through previous issues of any journal you’re interested in writing for and review the instructions for authors to see which types of these articles (if any) they accept.

Conference materials

Many of our medical journals  accept conference material supplements. These are open access peer-reviewed, permanent, and citable publications within the journal. Conference material supplements record research around a common thread, as presented at a workshop, congress, or conference, for the scientific record. They can include the following types of articles:

Poster extracts

Conference abstracts

Presentation extracts

Find out more about submitting conference materials.

Data notes  are a short peer-reviewed article type that concisely describe research data stored in a repository. Publishing a data note can help you to maximize the impact of your data and gain appropriate credit for your research.

Data notes promote the potential reuse of research data and include details of why and how the data were created. They do not include any analysis but they can be linked to a research article incorporating analysis of the published dataset, as well as the results and conclusions.

F1000Research  enables you to publish your data note rapidly and openly via an author-centric platform. There is also a growing range of options for publishing data notes in Taylor & Francis journals, including in  All Life  and  Big Earth Data .

Read our guide to data notes to find out more.

Letters or short reports

Letters or short reports (sometimes known as brief communications or rapid communications) are brief reports of data from original research.

Editors publish these reports where they believe the data will be interesting to many researchers and could stimulate further research in the field. There are even entire journals dedicated to publishing letters.

As they’re relatively short, the format is useful for researchers with results that are time sensitive (for example, those in highly competitive or quickly-changing disciplines). This format often has strict length limits, so some experimental details may not be published until the authors write a full original research article.

Brief reports  (previously called Research Notes) are a type of short report published by  F1000Research  – part of the Taylor & Francis Group. To find out more about the requirements for a brief report, take a look at  F1000Research’s guidance .

Method article

A method article is a medium length peer-reviewed, research-focused article type that aims to answer a specific question. It also describes an advancement or development of current methodological approaches and research procedures (akin to a research article), following the standard layout for research articles. This includes new study methods, substantive modifications to existing methods, or innovative applications of existing methods to new models or scientific questions. These should include adequate and appropriate validation to be considered, and any datasets associated with the paper must publish all experimental controls and make full datasets available.  

Posters and slides

With F1000Research, you can publish scholarly posters and slides covering basic scientific, translational, and clinical research within the life sciences and medicine. You can find out more about how to publish posters and slides  on the F1000Research website .

Registered report

A  Registered Report  consists of two different kinds of articles: a study protocol and an original research article.

This is because the review process for Registered Reports is divided into two stages. In Stage 1, reviewers assess study protocols before data is collected. In Stage 2, reviewers consider the full published study as an original research article, including results and interpretation.

Taking this approach, you can get an in-principle acceptance of your research article before you start collecting data. We’ve got  further guidance on Registered Reports here , and you can also  read F1000Research’s guidance on preparing a Registered Report .

Research article

Original research articles are the most common type of journal article. They’re detailed studies reporting new work and are classified as primary literature.

You may find them referred to as original articles, research articles, research, or even just articles, depending on the journal.

Typically, especially in STEM subjects, these articles will include Abstract, Introduction, Methods, Results, Discussion, and Conclusion sections. However, you should always check the instructions for authors of your chosen journal to see whether it specifies how your article should be structured. If you’re planning to write an original research article, take a look at our guidance on  writing a journal article .

Review article

Review articles provide critical and constructive analysis of existing published literature in a field. They’re usually structured to provide a summary of existing literature, analysis, and comparison. Often, they identify specific gaps or problems and provide recommendations for future research.

Unlike original research articles, review articles are considered as secondary literature. This means that they generally don’t present new data from the author’s experimental work, but instead provide analysis or interpretation of a body of primary research on a specific topic. Secondary literature is an important part of the academic ecosystem because it can help explain new or different positions and ideas about primary research, identify gaps in research around a topic, or spot important trends that one individual research article may not.

There are 3 main types of review article

Literature review

Presents the current knowledge including substantive findings as well as theoretical and methodological contributions to a particular topic.

Systematic review

Identifies, appraises and synthesizes all the empirical evidence that meets pre-specified eligibility criteria to answer a specific research question. Researchers conducting systematic reviews use explicit, systematic methods that are selected with a view aimed at minimizing bias, to produce more reliable findings to inform decision making.

Meta-analysis

A quantitative, formal, epidemiological study design used to systematically assess the results of previous research to derive conclusions about that body of research. Typically, but not necessarily, a meta-analysis study is based on randomized, controlled clinical trials.

Take a look at our guide to  writing a review article  for more guidance on what’s required.

Software tool articles

A  software tool article  – published by  F1000Research  – describes the rationale for the development of a new software tool and details of the code used for its construction.

The article should provide examples of suitable input data sets and include an example of the output that can be expected from the tool and how this output should be interpreted. Software tool articles submitted to F1000Research should be written in open access programming languages. Take a look at  their guidance  for more details on what’s required of a software tool article.

Further resources

Ready to write your article, but not sure where to start?

For more guidance on how to prepare and write an article for a journal you can download the  Writing your paper eBook .

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Q. What's the difference between an article, a journal, and a database?

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Answered By: Elizabeth Galoozis (she/her) Last Updated: Sep 27, 2019     Views: 74835

In assignments, or on the library website, you’ve probably seen the three words “article,” “journal,” and “database.” How do they relate to each other, and how do they relate to searching for sources?

When you search in the libraries’ home page, you’re searching across several databases , including collections of books, e-books, and films, along with individual databases  - for example, JSTOR or ProQuest Research Library. Each database includes sources such as articles, government documents, and many more. You can search for databases by name using the “Databases” search on the libraries’ home page.

One of the most common types of sources is a journal . This word may be used interchangeably in some places with periodical or serial , but basically a journal is a publication that comes out in issues on a regular basis - for example, four times a year. An example is Feminist Economics:

An issue of a journal contains individual articles . These are probably what you’re used to finding when you search for sources in the libraries or online, but you usually find them detached from their particular journal issue.

You can search for journals by title using the “Journals” search on the libraries’ home page.

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Answered By: Laura Marek Last Updated: Dec 07, 2023     Views: 4966

An article is a nonfiction writing that forms an independent part of a publication like a journal.

A journal is a collection of articles and is published periodically throughout the year.  Examples would be the  Journal of the American Medical Association  or American Journal of Public Health .  You would find articles in a journal.

Let's take a look at a citation to see where the article title and journal name appear:

Wright, C.V., Perez, S., Johnson, D.M. (2010). The mediating role of empowerment for African American women experiencing intimate partner violence.  Psychological Trauma: Theory, Research, Practice, and Policy, 2 (4), 266-272. 

The article is:  The mediating role of empowerment for African American women experiencing intimate partner violence.

The journal it is published in is:  Psychological Trauma: Theory, Research, Practice, and Policy

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Q. What's a scholarly journal, academic journal, or peer-reviewed journal?

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Answered By: Mary Ann Cullen Last Updated: Jul 29, 2020     Views: 22693

"Scholarly Journal" and "Academic Journal" are two words for the same thing. Scholarly journals publish articles—usually articles about research—written by experts (scholars) in the field of study.

Usually, articles in these publications go through a "peer-review" process, which means other experts (peers) on the topic of the article weigh in on the quality of the article and the research it presents as well as the article's importance in their field of study. ( This video explains more ). Many professors will require you to use scholarly sources because they are more credible than articles published in popular magazines or on most websites.

Many databases label articles as being published in either a scholarly journal or a popular magazine . What's the difference?

For more help,  ask a librarian.

updated 6/30/2020 kas

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Article Types: What's the Difference Between Newspapers, Magazines, and Journals?

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Article : Much shorter than a book, an article can be as short as a paragraph or two or as long as several dozen pages. Articles can address any topic that the author decides to explore and can reflect opinion, news, research, reviews, instruction, nearly any focus. Articles appear in newspapers, magazines, trade publication, journals, and even in books. Because of their relative brevity, articles typically are used to provide up-to-date information on a wide variety of topics.

Book Review : A usually brief article that provides an evaluation and appreciation of a book. A review might assess the importance of a book's contributions to a particular field of study or might make recommendations to potential readers of the book. Reviews of fiction will usually comment on originality, style, and readability. While an important tool for helping a researcher assess the value of a book to his or her research topic, a book review, by itself, is usually not sufficient for use as a source in a research project.

Issue : A single, regular publication of a journal, magazine, newspaper, newsletter, or trade publication. A magazine or journal that publishes monthly will have twelve issues in a year. News magazines like Time and Newsweek publish weekly and will have 52 issues in a year. Newspapers might publish daily or weekly. A daily will have 365 issues in a year. Issues are usually numbered, so a journal that publishes twelve issues in a year starting with January will number each issue sequentially (issue 1, January; issue 2, February; issue 3, March; etc.).

Journal : A regularly published collection of articles that focus on topics specific to a particular academic discipline or profession. Journals might be published monthly, bi-monthly, quarterly, semi-annually, or even annually. Probably the most common publication frequency is monthly and quarterly. Journal articles are typically of substantial length (often more than 10 pages) and usually reflect research, whether it be surveys of existing research or discussions of original research. Most journal articles will be prefaced with an abstract and will include extensive documentation within the article or at the end of the article. Most research begins with a survey of existing literature on a topic and proceeds with the development of new ideas or new research into a topic. Articles are usually written by experts in their fields, although journals might also publish letters from their readership commenting on articles that have been published in previous issues. Journals might also include opinion articles or editorials. Examples of journals include Journal of the American Medical Association, American Sociological Review, Psychological Reports, Publications of the Modern Language Association, Educational Research Quarterly, and Evolutionary Biology.

Literature Review : An important part of nearly any research project, a literature review consists of a survey of previously published or non-published materials that focus on a particular subject under investigation. For example, a researcher looking into whether there is a relationship between musical aptitude and academic achievement in elementary age students would begin by looking for articles, books, and other materials that reflected previous research into this topic. The function of the review is to identify what is already known about the topic and to provide a knowledge foundation for the current study.

Magazine : A regularly published collection of articles that might focus on any topic in general or on topics of interest to a specific group, such as sports fans or music fans or home decorators. Magazines might be published weekly, monthly, semi-monthly or only several times a year. More commonly, magazines are published weekly or monthly. Articles in magazines are typically written for the general reading public and don't reflect in-depth research (an exception might be an investigative report written in a news magazine that involved weeks or months of research and interviews to complete). Most magazine articles do not list references and are written by the magazine's own staff writers. In general, magazine articles are easy to read, are fairly brief in length, and may include illustrations or photographs. Magazines also rely heavily on advertisements targeted to consumers as a source of revenue. Examples of magazines include Time, Newsweek, Rolling Stone, Popular Mechanics, Car and Driver, Interview, Good Housekeeping, Elle, GQ, and Sports Illustrated.

Newsletter : A regularly published collection of brief news articles of interest to members of a particular community. Professional associations might issue newsletters to keep their membership up to date. Businesses and schools might issue newsletters to keep their constituents up to date. Nearly any type of organization or society might have its own newsletter. Articles in newsletters are typically brief, and the entire newsletter itself might be only half a dozen pages in length. These are usually internal publications that have interest mainly to people who participate in the activities of the issuing body. They are frequently used to inform members of an organization of upcoming events. Examples of newsletters include 401(k) Advisor, Adult Day Services Letter, Black History News & Notes, Credit Card Weekly, Education Business Weekly, Music Critics Association Newsletter, and Student Aid News.

Newspaper : A regularly published collection of fairly brief articles that provide updates on current events and interests. Newspapers are generally published daily, weekly, and bi-weekly, although they may have less regular publication schedules. Most major newspapers publish daily, with expanded coverage on the weekends. Newspapers can be national or international in focus or might be targeted strictly to a particular community or locality. Newspaper articles are written largely by newspaper staff and editors and often do not provide authors' names. Many of the articles appearing in national, international, and regional papers are written by various wire service writers and are nationally or internationally syndicated. Examples of wire services are Reuters and the Associated Press. Newspapers rely on advertising for a part of their income and might also include photographs and even full color illustrations of photos. A common feature of most newspapers is its editorial page, where the editors express opinions on timely topics and invite their readers to submit their opinions. Examples of newspapers include New York Times, Times of London, Florida Times-Union, Tampa Tribune, Denver Post, Guardian, and USA Today.

Peer Reviewed/Refereed Journal : Most academic/scholarly journals use subject experts or "peers" to review articles being considered for publication. Reviewers will carefully examine articles to ensure that they meet journal criteria for subject matter and style. The process ensures that articles are appropriate to a particular journal and that they are of the highest quality.

Trade Journal : A regularly published collection of articles that address topics of interest to members of a particular profession, such as law enforcement or advertising or banking. Articles tend to be brief and often report on developments and news within a field and might summarize current research being done in a particular area. Trade journals might also include editorials, letters to the editor, photo essays, and advertisements that target members of the profession. While trade journal articles might include references, the reference lists tend to be brief and don't reflect thorough reviews of the literature. Articles are usually written with the particular profession in mind, but are generally pretty accessible so that a person wishing to learn more about the profession would still be able to understand the articles. Examples of trade journals include Police Chief, Education Digest, Energy Weekly News, Aviation Week and Space Technology, Engineering News Record, Design News, and Traffic World.

Volume : Most journals and many magazines, newsletters, newspapers, and trade publications assign volume numbers to a year's worth or half a year's worth of issues. For example, a journal that publishes four times a year (quarterly) might assign each yearly collection of four issues a volume number to help identify which issues of the journal were published during a particular year. Publications that publish more frequently than monthly might also assign volume numbers, but they might change volume numbers mid year, so that there may be two volumes in any one publishing year.

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Articles, Books and . . . ? Understanding the Many Types of Information Found in Libraries

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Academic Journals

Magazines and trade journals, conference papers, technical reports, anthologies.

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Because of their short length, articles often exclude background info and explanations, so they're usually the last stop in your research process, after you've narrowed down your topic and need to find very specific information.

The main thing to remember about articles is that they're almost always published in some larger work , like a journal, a newspaper, or an anthology. It's those "article containers" that define the types of articles, how you use them, and how you find them.

Articles are also the main reason we have so many databases . The Library Catalog lists everything we own, but only at the level of whole books and journals. It will tell you we have the New York Times, and for what dates, but it doesn't know what articles are in it. Search in UC Library Search using the "Articles, books, and more" scope will search all the databases we subscribe to and some we don't. If you find something we do not own, you can request it on Interlibrary Loan.

Physical Media

While newer journals and magazines are usually online, many older issues are still only available in paper. In addition, many of our online subscriptions explicitly don't include the latest material, specifically to encourage sales of print subscriptions. Older newspapers are usually transferred to microfilm.

Scholarly Sources

The terms academic or scholarly journal are usually synonymous with peer-reviewed , but check the journal's publishing policies to be sure. Trade journals, magazines, and newspapers are rarely peer-reviewed.

Primary or Secondary Sources

In the social sciences and humanities, articles are usually secondary sources; the exceptions are articles reporting original research findings from field studies. Primary source articles are more common in the physical and life sciences, where many articles are reporting primary research results from experiments, case studies, and clinical trials.

Clues that you're reading an academic article

• Footnotes or endnotes
• Bilbliography or list of references

Articles in academic (peer-reviewed) journals are the primary forum for scholarly communication, where scholars introduce and debate new ideas and research. They're usually not written for laymen, and assume familiarity with other recent work in the field. Journal articles also tend to be narrowly focused, concentrating on analysis of one or two creative works or studies, though they may also contain review articles or literature reviews which summarize recent published work in a field.

In addition to regular articles, academic journals often include book reviews (of scholarly books ) and letters from readers commenting on recent articles.

Clues that you're reading a non -academic article

• Decorative photos
• Advertisements

Unlike scholarly journals, magazines are written for a mainstream audience and are not peer-reviewed. A handful of academic journals (like Science and Nature ) blur the line between these two categories; they publish peer-reviewed articles, but combine them with news, opinions, and full-color photos in a magazine-style presentation.

Trade journals are targeted toward a specific profession or industry. Despite the name, they are usually not peer-reviewed. However, they sometimes represent a gray area between popular magazines and scholarly journals. When in doubt, ask your professor or TA whether a specific source is acceptable.

Newspapers as Primary Sources

Though usually written by journalists who were not direct witnesses to events, newspapers and news broadcasts may include quotes or interviews from people who were. In the absence of first-person accounts, contemporary news reports may be the closest thing to a primary source available.

Of all the content types listed here, newspapers are the fastest to publish. Use newspaper articles to find information about recent events and contemporary reports of/reactions to historic events.

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Reviews are a type of article that can appear in any of the categories above. The type of publication will usually determine the type of review. Newspapers and magazines review movies, plays, general interest books, and consumer products. Academic journals review scholarly books.

Note that a review is not the same as scholarly analysis and criticism! Book reviews, even in scholarly journals, are usually not peer-reviewed.

Conference papers aren't always published and can be tricky to find . Recent conference papers are often online, along with the PowerPoint files or other materials used in the actual presentation. However, access may be limited to conference participants and/or members of the academic organization which sponsored the conference.

In paper formats, all of the papers from a certain conference may be re-printed in the conference proceedings . Search for Proceedings of the [name of conference] to find what's available, or ask for help from a librarian. But be aware that published proceedings may only include abstracts or even just the name of the presenter and the title of the presentation. This is especially true of poster presentations , which really are large graphic posters (which don't translate well to either printed books or computer monitors).

As the name implies, most technical reports are about research in the physical sciences or engineering. However, there are also technical reports produced in the life and social sciences,

Like conference papers , some technical reports are eventually transformed into academic journal articles , but they may also be released after a journal article to provide supplementary data that didn't fit within the article. Also like conference papers, technical reports can be hard to find , especially older reports which may only be available in microfiche . Ask for help from a librarian!

Anthologies are a cross-over example. They're books that contain articles (chapters). Anthologies may be collections of articles by a single author, or collections of articles on a theme from different authors chosen by an editor. Many anthologies reprint articles already published elsewhere, but some contain original works.

Anthologies are rarely peer-reviewed, but they still may be considered scholarly works, depending on the reputation of the authors and editors. Use the same criteria listed for scholarly books .

Of course, reprints of articles originally published in peer-reviewed journals retain their "scholarly" status. (Note that most style manuals have special rules for citing reprinted works.)

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Peer-Reviewed Journals

When it comes to scholarly journals, the terms peer-reviewed and refereed are interchangeable. Before publication, peer-reviewed/refereed journals go through a highly critical and rigorous review process by other scholars in the author's field or specialty. This review process ensures that the content being published is first being evaluated by the author's peers and also, reflect a solid scholarship in the their fields of study.

Scholarly Journals

Although peer-reviewed journals are always scholarly in nature, scholarly journals are not always peer-reviewed.  

Scholarly journals are research focused, reporting results of original research and experimentation. They are heavily cited in the form of either footnotes or bibliographies, and written by, and addressed to, experts in a discipline. However, whereas peer-reviewed journals require a strict "peer-approval" for publishing, a scholarly journal that is not peer-reviewed only requires the approval of an editorial board.

The quickest and easiest way to identify if a journal is peer-reviewed is to look it up in Ulrichsweb, a database that provides bibliographic and publisher information on all types of serials (journals, magazines, newspapers, etc.).

Provides bibliographic and publisher information on more than 300,000 periodicals of all types: academic and scholarly journals, Open Access publications, refereed (i.e. peer-reviewed) titles, popular magazines, newspapers, newsletters, and more, from around the world.

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Scholarly Journals and Popular Magazines: Differences in Research, Review, and Opinion Articles

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Research Articles, Reviews, and Opinion Pieces

Scholarly or research articles are written for experts in their fields. They are often peer-reviewed or reviewed by other experts in the field prior to publication. They often have terminology or jargon that is field specific. They are generally lengthy articles. Social science and science scholarly articles have similar structures as do arts and humanities scholarly articles. Not all items in a scholarly journal are peer reviewed. For example, an editorial opinion items can be published in a scholarly journal but the article itself is not scholarly. Scholarly journals may include book reviews or other content that have not been peer reviewed.

Empirical Study: (Original or Primary) based on observation, experimentation, or study. Clinical trials, clinical case studies, and most meta-analyses are empirical studies.

Review Article: (Secondary Sources) Article that summarizes the research in a particular subject, area, or topic. They often include a summary, an literature reviews, systematic reviews, and meta-analyses.

Clinical case study (Primary or Original sources): These articles provide real cases from medical or clinical practice. They often include symptoms and diagnosis.

Clinical trials ( Health Research): Th ese articles are often based on large groups of people. They often include methods and control studies. They tend to be lengthy articles.

Opinion Piece:  An opinion piece often includes personal thoughts, beliefs, or feelings or a judgement or conclusion based on facts. The goal may be to persuade or influence the reader that their position on this topic is the best.

Book review: Recent review of books in the field. They may be several pages but tend to be fairly short. 

Social Science and Science Research Articles

The majority of social science and physical science articles include

• Journal Title and Author
• Abstract 
• Introduction with a hypothesis or thesis
• Literature Review
• Methods/Methodology
• Results/Findings

Arts and Humanities Research Articles

In the Arts and Humanities, scholarly articles tend to be less formatted than in the social sciences and sciences. In the humanities, scholars are not conducting the same kinds of research experiments, but they are still using evidence to draw logical conclusions.  Common sections of these articles include:

• an Introduction
• Discussion/Conclusion
• works cited/References/Bibliography

Research versus Review Articles

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What's the Difference between Scholarly Journals and Popular Magazines?

Why does it matter.

• In your research project or paper, you need to show how your ideas relate to those of others.
• In most cases, you'll want to use articles from scholarly journals to support your arguments because these are written by experts, include references you can consult, and have been carefully edited.
• Sometimes, depending on your topic, you'll need to use articles from popular magazines. Be sure to check with your professor or instructor that the sources you're using are acceptable for the assignment's requirements.
• Does the author show bias and does it affect his/her conclusions?
• Is the information accurate?
• Does the author support his/her arguments with credible evidence?

A Quick Comparison

Determining whether a source is scholarly or popular is just one step in evaluating information. Learn more on this Source Evaluation page on the Start Your Research guide.

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What is the difference between letter, communication and journal paper?

Scientific literature has items called letters, communications and journal papers. They all seem quite similar in terms of format and content. What are the differences between them?

• publications

• 1 This may depend heavily on the specific journal (eg in some 'letters' are a short paper, in others, just an editorial leyter...) –  Andrew is gone Commented Nov 15, 2015 at 9:49

2 Answers 2

In physics, each category has a different length limit. Often "paper" has no limit. Typically the shorter the length limit, the more prestigious it is and the tougher the acceptance criteria. The subject matter covered by the journal is the same for all categories. Some journals also have a "review" category which includes papers which are not original research. Often a review is by invitation only.

• 1 short publications such as "letters" are also peer reviewed? –  Sparkler Commented Nov 14, 2015 at 20:56
• 1 Yes, they are: see for example link.springer.com/journal/11005 . –  gented Commented Nov 14, 2015 at 21:52

This will depend wildly on the field and journal in question. In my experience, the main differentiators are the allowable length and the amount of peer review. For example, in my field (Epidemiology):

• Journal Article (of which there are several categories): Word limit in the several thousands of words, full on peer review.
• Communication (often also called 'Brief Report'): A smaller <2000 word word limit with further restrictions on the number of tables and figures. Goes out for full peer review. This is intended to report a single, small finding that may not warrant a full publication.
• Letters: This is a very ambiguous category, primarily defined by being short, often <1000 words. They may be used to report a single piece of information, often from part of a larger study, or may be used to respond to another paper. These may or may not go out for peer review - for example, I recently had a paper accepted where the decision was made entirely by the editor.

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Open Access

Peer-reviewed

Research Article

Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections

Roles Conceptualization, Data curation, Formal analysis, Methodology, Visualization, Writing – original draft, Writing – review & editing

* E-mail: [email protected] (KL); [email protected] (NDG)

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America

Roles Conceptualization, Methodology, Writing – review & editing

Roles Methodology, Software, Writing – review & editing

Affiliation Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America

Roles Visualization, Writing – review & editing

Roles Data curation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

Roles Data curation, Investigation

Affiliations Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America, Yale School of Medicine Biorepository, Yale University, New Haven, Connecticut, United States of America

¶ Membership of the Termite Genome Working Group is listed in the Acknowledgments.

Roles Methodology, Writing – review & editing

Affiliations Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America, Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America, Santa Fe Institute, Santa Fe, New Mexico, United States of America

Roles Supervision, Writing – review & editing

Affiliations Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America, Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America, Microsoft Research, Cambridge, Massachusetts, United States of America

•  [ ... ],

Roles Funding acquisition, Supervision, Writing – review & editing

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America, Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America

• [ view all ]
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• Ke Li, 
• Chrispin Chaguza, 
• Julian Stamp, 
• Yi Ting Chew, 
• Nicholas F. G. Chen, 
• David Ferguson, 
• Sameer Pandya, 
• Nick Kerantzas, 
• Wade Schulz, 

• Published: September 17, 2024
• https://doi.org/10.1371/journal.pcbi.1012469
• Reader Comments

This is an uncorrected proof.

Significant variations have been observed in viral copies generated during SARS-CoV-2 infections. However, the factors that impact viral copies and infection dynamics are not fully understood, and may be inherently dependent upon different viral and host factors. Here, we conducted virus whole genome sequencing and measured viral copies using RT-qPCR from 9,902 SARS-CoV-2 infections over a 2-year period to examine the impact of virus genetic variation on changes in viral copies adjusted for host age and vaccination status. Using a genome-wide association study (GWAS) approach, we identified multiple single-nucleotide polymorphisms (SNPs) corresponding to amino acid changes in the SARS-CoV-2 genome associated with variations in viral copies. We further applied a marginal epistasis test to detect interactions among SNPs and identified multiple pairs of substitutions located in the spike gene that have non-linear effects on viral copies. We also analyzed the temporal patterns and found that SNPs associated with increased viral copies were predominantly observed in Delta and Omicron BA.2/BA.4/BA.5/XBB infections, whereas those associated with decreased viral copies were only observed in infections with Omicron BA.1 variants. Our work showcases how GWAS can be a useful tool for probing phenotypes related to SNPs in viral genomes that are worth further exploration. We argue that this approach can be used more broadly across pathogens to characterize emerging variants and monitor therapeutic interventions.

Author summary

Our study explores why viral load (copies measured by RT-qPCR) varies during SARS-CoV-2 infections by analyzing viral mutations and measuring viral copies in 9,902 individuals over two years. We aimed to understand how genetic differences in SARS-CoV-2 influence viral copies, considering host age and vaccination status. Using a genome-wide association study (GWAS), we identified several single-nucleotide polymorphisms (SNPs) in the virus linked to variations in viral levels. Notably, interactions between certain SNPs in the spike gene had non-linear effects on viral copies. Our analysis revealed that SNPs associated with higher viral copies were common in Delta and Omicron BA.2/BA.4/BA.5/XBB variants, while those linked to lower levels were mainly found in Omicron BA.1. This research highlights GWAS as a powerful tool for exploring virus genetics and suggests it can be broadly applied to monitor new variants of COVID-19 and other infectious diseases.

Citation: Li K, Chaguza C, Stamp J, Chew YT, Chen NFG, Ferguson D, et al. (2024) Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLoS Comput Biol 20(9): e1012469. https://doi.org/10.1371/journal.pcbi.1012469

Editor: Thomas Leitner, Los Alamos National Laboratory, UNITED STATES OF AMERICA

Received: March 3, 2024; Accepted: September 6, 2024; Published: September 17, 2024

Copyright: © 2024 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: We used the R statistical software (v4.0.2) for all statistical analyses and visualization. Data and code used in this study are publicly available on Github: https://github.com/grubaughlab/2024_paper_GWAS . All genome sequences used for the GWAS analysis and a subset of the associated metadata (accession number, virus name, collection date, originating lab and submitting lab, and the list of authors) in this dataset are published in GISAID’s EpiCoV database: https://doi.org/10.55876/gis8.240219fh . The de-identified and coded clinical metadata associated with the sequenced samples are available on Github: https://github.com/grubaughlab/2024_paper_GWAS .

Funding: This project is supported by the Centers for Disease Control and Prevention (CDC) Broad Agency Announcement Contract 75D30122C14697 (to NDG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: NDG is a paid consultant for BioNTech, DMW has received consulting fees from Pfizer, Merck, and GSK, unrelated to this manuscript, and has been PI on research grants from Pfizer and Merck to Yale, unrelated to this manuscript.

Introduction

Continued SARS-CoV-2 transmission and evolution has propelled the COVID-19 pandemic. Peak viral replication in the upper respiratory tract occurs during the first few days of infection [ 1 ]. The viral load (or copies measured by RT-qPCR) in patient samples are valuable data to understand infection dynamics, such as inferring the likelihood of disease transmission [ 2 ]. However, it is challenging to use viral load data, and the challenge often arises from significant variations in viral load dynamics among sampled cases, which can be associated with 1) host heterogeneity, e.g., age [ 3 ] and vaccination status [ 4 – 6 ]; 2) distinct inherent properties of virus variants or sublineages [ 7 ], and 3) different sampling times [ 8 ]. For example, sampling during the early stages of infection may yield higher viral loads compared to later stages after viral replication has reached its peak. Nevertheless, the relative importance of these factors influencing viral load has not been completely explored [ 9 , 10 ].

Genome-wide association studies (GWAS) have emerged as a useful tool in the field of genetics, providing an approach to unraveling the complex interplay between genetic variations and observable traits, including diseases and drug resistance, as reviewed in [ 11 ]. Several studies have employed GWAS analysis to identify and investigate the association between human genetic variations across different individuals and the severity of COVID-19, shedding light on genetic variations that are related to severe infections [ 12 – 14 ]. However, few studies have utilized a GWAS method to study associations between the viral genome and viral traits [ 15 – 18 ]. The confluence of the extensive existing research on SARS-CoV-2 mutations and the millions of infections that have been sequenced provides us the opportunity to evaluate the application of GWAS for viral genomics. The hypothesis-free approach has the potential to enhance our understanding of genetic determinants influencing viral fitness and evolution and further inform effective public health strategies aimed at mitigating the spread and impact of SARS-CoV-2.

In this work, we aim to investigate the impact of intrinsic viral genetic substitutions (i.e., single nucleotide polymorphisms [SNPs]) on the changes in viral copies, adjusted for host age and vaccination status. For this, we apply a viral GWAS analysis to SARS-CoV-2 genomic sequencing and standardized RT-qPCR data collected from the Yale New Haven Hospital from February 2021 to March 2023. Using whole genome sequencing data on SARS-CoV-2 infections, along with relevant laboratory and patient metadata, we identify associations between viral SNPs and viral copies for different variants of concern (VOCs). We then examine the temporal pattern of identified SNPs by constructing a phylogenetic tree, drawing upon subsamples, and analyzing the time series of the fraction of SNPs occurring in the sequences. This multifaceted analysis contributes to unraveling the complex dynamics of SARS-CoV-2 infections, providing valuable insights into the underlying viral SNPs that influence viral copies in different VOCs.

Viral copies vary in SARS-CoV-2 infections

To better understand how SARS-CoV-2 viral load varies in infected individuals, we analyzed the viral copy data, along with associated host metadata (i.e., age and vaccination status), and genome sequencing data from a cohort of patients tested at the Yale New Haven Hospital (YNHH) located in Connecticut, US. We selected 9902 whole genome sequences with available viral copy data generated from remnant SARS-CoV-2 diagnostic samples over a 2-year period, from 03-Feb-2021 to 21-Mar-2023 ( Fig 1A ). The VOCs that we identified in our dataset during the sampling period included Alpha (n = 809), Delta (n = 1278), Gamma (n = 36), BA.1 (n = 1818), BA.2 (n = 2432), BA.4 (n = 293), BA.5 (n = 1992), XBB (n = 698), and the pre-VOC variant (named ‘Other’, n = 546). We conducted RT-qPCR using a standardized assay targeting the nucleocapsid (CDC ‘N1’ primers) for each sample to allow for cross-sample comparisons [ 19 ], except for a period during October 2021 when the PCR data were not generated. Across all samples, the viral copies, expressed as log 10 (viral copies per milliliter (Genome Equivalents/ml)), exhibited variations, ranging from 3.60 to 10.55, with a median value of 7.26 ( Fig 1B ). The variations in viral copies could be attributed either to the introduction and/or replacement of different VOCs, each with its own epidemic curve, or to the stochasticity from the sampling process. To reduce stochastic effects, we aggregated the viral copies by month and still observed large variations in the viral copies across the months, albeit with no consistent trend ( Fig 1C ). Notably, we observed the lowest median value of viral copies (median = 6.49) in February 2022, during which 96.3% of the sampled sequences tested positive for BA.1 infections. By contrast, we observed the highest median value of viral copies (median = 7.70) in June 2022, during which the sampled sequences tested positive for BA.2 (64.9%), BA.4 (6%), or BA.5 (29.1%) infections. Taken together, we showed a wide range of viral copies in the sampled SARS-CoV-2 infections with different VOCs, utilizing data from genomic surveillance and standardized RT-qPCR tests.

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• PNG larger image
• TIFF original image

(A) The daily number of genomic sequences of SARS-CoV-2 VOCs from February 2021 to March 2023. (B) The summary of viral copies of all samples, expressed as log 10(viral copies per milliliter). (C) The summary of viral copies aggregated by month. The data gap in October 2021 is because we were unable to conduct PCR to obtain viral copies during this time.

https://doi.org/10.1371/journal.pcbi.1012469.g001

Viral copies correlate with age and variants, but not with vaccination status

Having uncovered a large variability in the observed viral copies from the samples, we next assessed the factors associated with these changes. To do this, we first summarized and compared viral copies in various age groups ( Fig 2A ). A positive correlation has been previously reported between age and SARS-CoV-2 viral copies, showing that younger age groups had lower viral copies independent of gender and/or symptom duration [ 20 ]. We observed a similar result in our dataset and found that the oldest age group (i.e., >70 years old) had the highest viral copies compared with other age groups (mean = 7.47, 95% confidence interval (CI): [5.12, 9.49], p < 0.001, Wilcoxon signed-rank test). For the effect of vaccination on viral copies, some studies have demonstrated that although vaccination reduced the risk of infections with the Delta variant, no significant difference in peak viral copies was found between fully vaccinated and unvaccinated individuals [ 4 , 5 , 21 ]. In contrast, other studies have shown that vaccination reduced viral copies in BA.1 infections among boosted individuals compared to unvaccinated ones [ 6 ]. These results suggest the effect of vaccination on viral copies may depend on the characteristics of the infecting SARS-CoV-2 variant. We compared viral copies among groups with different vaccination statuses to assess the impact of vaccination on viral copies ( Fig 2B ), and no statistically significant differences were detected between the groups in our data ( p > 0.05, Wilcoxon signed-rank test). Finally, we compared viral copies stratified by variant category ( Fig 2C ). Combining samples collected from all age and vaccination status groups for each variant, we found that the overall mean values of viral copies were lowest for infections with BA.1 (mean = 6.83, 95% CI: [4.87, 8.87], p < 0.001, Wilcoxon signed-rank test) compared to infections with other all non-BA.1 variants.

Comparison of viral copies stratified by (A) age groups, (B) vaccination statuses, (C) variant of concerns. (D) Association of age, vaccination status, and VOCs with viral copies, expressed as log 10 (viral copies per milliliter (Genome Equivalents/ml)). The reference groups (in gray) are Age <18 years old, 0 doses of vaccination, and the Other variant, respectively. The positive coefficients indicate the covariate is associated with higher viral copies value compared to the reference group, and vice versa. 0 Vax, 1 Vax, 2 Vax, 2 Vax 1 booster, and 2 vax 2 boosters denote vaccination statuses of 0 doses, 1 dose, 2 doses, 2 doses, and 1 booster, and 2 doses and 2 boosters, respectively, corresponding to the labels in (B). Results are shown as means with 95% confidence intervals. *** p < 0.001.

https://doi.org/10.1371/journal.pcbi.1012469.g002

Since several factors may simultaneously impact the SARS-CoV-2 viral load, next, we sought to quantify the combined impact of age, vaccination status, and VOCs on the observed viral copies. To achieve this, we fitted a multivariate linear regression model, with viral copies as the outcome variable and age, vaccination, and VOCs as covariates ( Fig 2D ). We found that the older age group (i.e., age >70 years old) had a positive association with viral copies (mean = 0.17, 95% CI: [0.09, 0.25], p < 0.001) compared with the reference group (i.e., age <18 years old). We also found that vaccination status was not associated with viral copies (i.e., 95% CIs of the vaccination coefficients span 0, p > 0.05). Notably, we showed that infections with BA.1 were associated with reduced viral copies, with a mean effect size of -0.34 (95% CI: [-0.44, -0.24], p < 0.001) in the same age group and vaccination status, compared to the Other variant. We also showed that infections with BA.2 (mean = 0.19, 95% CI: [0.09, 0.28], p < 0.001), BA.4, or BA.5 (mean = 0.17, 95% CI: [0.07, 0.26], p < 0.001) were associated with increased viral copies. Among them, infections with BA.4 were associated with the largest positive effect size (mean = 0.27, 95% CI: [0.12, 0.41], p < 0.001). Our findings demonstrated that variations in viral copies were associated with infections caused by different SARS-CoV-2 variants and the older age group. This implies that intrinsic factors of the viruses, such as genetic mutations among distinct VOCs, are key determinants impacting viral copies.

Viral GWAS reveals SARS-CoV-2 SNPs associated with viral copies

Having demonstrated that changes in SARS-CoV-2 viral copies are associated with infections caused by different viral variants or strains, especially Omicron BA.1/BA.2/BA.4/BA.5 variants ( Fig 2D ), we then sought to identify potential genetic mutations—specifically, SNPs—that contributed to these changes in viral copies. For this, we performed a GWAS analysis using high-quality genome sequences (i.e., genome coverage > 95%). We conducted whole-genome sequencing on the 9902 SARS-CoV-2 positive specimens collected from February 2021 to March 2023. Firstly, using Wuhan-Hu-1 (GenBank MN908937.3) as the reference genome, we identified 10,697 SNPs for further testing associated with viral copies as covariates. We then checked for the population structure of the 9902 genome sequences using a multidimensional scaling (MDS) method [ 22 ] ( S1 Fig ). We observed that Delta was an outgroup to other pre-Omicron variants (i.e., pre-VOC variant (Other), Alpha, and Gamma), and BA.1 was an outgroup to the BA.2/BA.4/BA.5/XBB cluster. In our model, we included the inferred four clusters based on the MDS-computed distance to capture the viral population structure. Clusters were defined using a k-means clustering method ( S1 Fig ). The host ages and vaccination status were also included in the model as covariates.

Using the linear regression model on viral copies for each SNP, adjusted for viral population structure and host factors, we identified 31 SNPs exceeding the permuted threshold for genome-wide significance ( p = 4.67×10 −6 , dashed line, Fig 3A ). The threshold value was calculated as 0.05 divided by 10,697 SNPs [ 23 ]. We found that the observed distribution of p -values closely matches the expected distribution under the null hypothesis of no association ( S2A Fig ). To ascertain whether those SNPs have a negative or positive impact on viral copies and evaluate their effect size, we extracted the coefficients ( β ) of the SNPs with p <1×10 −10 and their standard deviations ( σ ) from the regression model (dashed box, Fig 3B ). We then annotated the SNPs to identify the associated amino acids, and among them, 14 SNPs were non-synonymous (i.e., changed the amino acid; Fig 3C ). We found that a non-synonymous change N:R203M, located on the N gene, had the most significant association with increased viral copies ( p = 2.68×10 −22 , β = 1.65, σ = 0.16). By contrast, the amino acid change most strongly associated with a negative effect on viral copies was ORF1ab:L5086I ( p = 9.20×10 −20 , β = -1.20, σ = 0.13). We further conducted a marginal epistasis test [ 24 – 26 ] to detect the epistatic effects of SNPs on viral copies. We discovered multiple pairs of SNPs that exhibit positive epistatic effects on viral copies, with most interactions occurring in the S gene ( S3 Fig ).

(A) Genome-wide association results of the impact of identified SNPs on viral copies during SARS-CoV-2 infection. The dashed line indicates the permuted threshold for genome-wide significance p = 4.67 × 10 −6 (0.05/10697 SNPs). Significant SNPs are shown with solid colors. (B) SNPs (with p < 1 × 10 −10 ) that have positive (blue) or negative (red) effects on viral copies. (C) The corresponding synonymous (triangles) and non-synonymous (circles) amino acid changes that associate with increased or decreased viral copies. Data shown as means with 95% confidence intervals. The estimated effective sizes and associated standard deviations are given S1 Table .

https://doi.org/10.1371/journal.pcbi.1012469.g003

To assess the impact of adjusting for the population structure of the SARS-CoV-2 strains using the MDS components on the regression results, we conducted a sensitivity analysis on the genome sequences using the inferred MDS components from the pairwise SNP distance matrix of SARS-CoV-2 sequences as covariates. By doing this, we identified 113 SNPs exceeding the permuted threshold ( S4 Fig ). The observed distribution of p -values also closely matched the expected distribution under the null hypothesis of no association ( S2B Fig ). The results may be more likely to reflect the SNPs that influence the viral copies dependent on lineage. We also examined the association between viral copies and SNPs after adjusting for the population structure based on the VOCs themselves, which broadly correspond to the identified sequence clusters. We showed that only a few SNPs were found ( S5 – S8 Figs), mostly within the Omicron BA.2/BA.4/BA.5/XBB cluster ( S8 Fig ).

The impact of amino acid changes on viral copies is dependent on the variant

Having identified the 14 non-synonymous SNPs with statistically significant effects on viral copies in our primary analysis, we next sought to understand the temporal patterns of the emergence of these amino acid changes ( Fig 4 ). To investigate the clustering of these SNPs, we randomly sampled approximately 120 genome sequences from each VOC category (only 36 sequences were available for Gamma in our dataset) and generated a phylogenetic tree drawing upon the subsamples ( Fig 4A ). We found a clear pattern in how these mutations emerged by VOC ( Fig 4A heatmap). We found that all amino acid changes associated with a positive effect on viral copies were found in Delta and Omicron BA.2/BA.4/BA.5/XBB infections. Often, more than one amino acid change was observed in each sampled sequence, suggesting genetic linkage between these SNPs, as also shown in the epistasis test ( S3 Fig ), such as S:Q954H and N969K. In particular, we identified that the amino acid changes S:L452Q ( p = 3.91×10 −25 , β = 0.34, σ = 0.03) and S704L ( p = 1.35×10 −24 , β = 0.34, σ = 0.03) associated with a positive effect on viral copies were typically observed in combination with BA.2 infections—specifically, lineage BA.2.12.1. We also observed that the amino acid changes with negative effects on viral copies (ORF1ab:L5086I, S:N856K and L981F) were only associated with BA.1 infections.

The results are based on the multivariate regression analysis using the sequence clusters (i.e., a categorical variable) inferred from the MDS components. (A) The phylogenetic tree estimated from a representative set of 996 genome sequences showing variant assignments and the locations of amino acid changes that increase (blue) or decrease (red) viral copies. (B) The temporal dynamics of the SNPs from February 2021 to March 2023. The transparency of the color corresponds to the mutation fraction in the daily sequence count: transparent color indicates low fractions, and opaque color indicates high fractions. The temporal dynamics of the SNPs, using MDS-inferred distance as a population control, are shown in S9 – S11 Figs.

https://doi.org/10.1371/journal.pcbi.1012469.g004

To explore the temporal dynamics of these amino acid changes, we calculated the fraction of SNPs occurring in the sequences for each day, thereby accounting for the number of introductions to the population ( Fig 4B ). We observed most SNPs with a positive impact on viral copies emerging in sequences sampled from February 2022, when BA.2 was first detected in Connecticut. These SNPs were consistently observed in almost every sequence thereafter. By contrast, we found that the other two amino acid changes (S:L452Q and S704L) that had a positive effect on viral copies were only in the samples from BA.2 infections and did not arise again in sublineages of BA.4 or BA.5. S:G252V was associated with higher viral copies; however, we found that the SNP only appeared in a few sequences associated with XBB infections. Notably, the N:R203M mutation was only associated with Delta infections. For the SNPs (ORF1ab:L5086I, S:N856K and L981F) that had a negative association with viral copies, we observed that they were present in samples associated with BA.1 infections and did not persist when BA.1 was replaced by BA.2.

We conducted a GWAS analysis on 9,902 high-quality SARS-CoV-2 genome sequences generated from two years of genomic surveillance in Connecticut, US to identify and evaluate SNPs that were associated with variations in viral copies during infections. Using a GWAS approach, we were able to identify and examine virus-related factors that were associated with the observed variations in viral copies independent of host factors. This was achieved by combining data from a large cohort of individuals infected with different VOCs and employing a regression model for viral copies that accounted for virus-level factors (i.e., specific SNPs and genetic background), adjusted for individual factors (i.e., age and vaccination status). We identified several SNPs corresponding to non-synonymous amino acid changes in the SARS-CoV-2 genome that were individually or jointly associated with the variations in viral copies. In particular, temporal patterns of the SNPs revealed that SNPs associated with increased viral copies were predominantly observed in Delta and Omicron BA.2/BA.4/BA.5/XBB infections, whereas those associated with decreased viral copies were mostly observed in infections with Omicron BA.1 variants.

Using a GWAS approach, we successfully identified a subset of variant-defining amino acid changes in Delta and Omicron variants ( S12 Fig ). Note that we did not detect any substitutions in the Alpha and Gamma variants (likely due to the low sample size for Gamma). We also identified SNPs that did not define any major variant category, including S:L452Q and S704L that were specifically associated with BA.2.12.1, a sublineage of BA.2 that briefly dominated during the pandemic (i.e., dominated mainly in the US between March and May 2022). This highlights the application of GWAS for identifying SNPs associated with important phenotypic effects without requiring a set of lineage-defining mutations to be defined a priori. Nevertheless, there are several reasons why we only detected a subset of the SNPs that defined different VOCs. Firstly, SNPs with small effect sizes may not be detected due to the stringent statistical significance thresholds applied in GWAS. Secondly, lineage-defining SNPs that are in low linkage disequilibrium with the causal mutations may not be detected [ 27 ], even if they may be functionally relevant. Our results showcase how GWAS can help to narrow the focus of SNPs associated with specific phenotypes, generating hypotheses for further investigation.

A key result from our analysis is that SNPs associated with viral copies did not exhibit the same temporal dynamics, even though they could have similar (either positive or negative) effects on viral copies, suggesting they may have independent effects on viral copies. Some amino acid changes, for example, ORF1ab:I4915T (positive effects), were only present in samples with BA.2 infections and disappeared when new Omicron variants emerged. Other SNPs (e.g., S:T19R), while also associated with higher viral copies, were observed and persisted in all BA.2/BA.4/BA.5/XBB infections. The distinct temporal pattern of SNPs, dependent on VOCs, may help explain the different fitness levels (e.g., intrinsic transmissibility or immune escape) of each variant [ 28 , 29 ]. Notably, we found three SNPs, ORF1ab:L5086I, S:N856K and L981F, were associated with decreased viral copies in BA.1 infections. The negative impact on viral copies should be interpreted with caution. Although the possibility that these SNPs have a direct impact on reducing viral copies cannot be ruled out, it is also likely that the estimated negative effects are due to a synthetic association with other SNPs. Further study may be required to disentangle the direct effects of these SNPs from the confounding influences of other genetic variations and to confirm their functional impact on viral copies.

In this study, we employed a series of single SNP regression models to identify the underlying SNPs associated with the changes in viral copies without accounting for potential interactions between SNPs. We noted that several synonymous SNPs located in the ORF1ab gene were identified to have an impact on viral copies. The synonymous SNPs were likely linked to non-synonymous SNPs that were under positive selection. In such cases, the synonymous SNPs can be carried along with the non-synonymous SNPs, resulting in their significance in the GWAS analysis, as shown in the subsequent epistasis test ( S3 Fig ). The epistasis test provided evidence that the synonymous mutations identified through GWAS analysis are likely the result of synthetic associations with other non-synonymous mutations. Nevertheless, the method provided an initial set of SNPs that are worth further exploration, pinpointing important mutations associated with viral copies and providing valuable insights into the overall genetic landscape of the viral population. The method, thus, represented an important first step towards understanding detailed epistatic effects among these mutations on viral copies. A paired or higher-order SNP regression study could be conducted as a subsequent step to test potential interactions or joint effects among different SNPs.

There are limitations to our study. First, we assumed that the distribution of times between infection and sample collection was similar through time and across variants as these data were not available. Given our samples were taken frequently over a 2-year period, we do not anticipate that this assumption will qualitatively impact our results. Second, our study primarily focuses on the genetic variants in VOCs, neglecting other factors such as host immune responses or environmental influences, partially captured by the host-associated covariates, including age and vaccination status in this study, that may also contribute to the changes in viral copies. Further study will be needed to address the impact of these factors on viral copies, for example, genome-to-genome analysis to reveal the impact of host-viral genetic interactions in SARS-CoV-2 infections [ 18 , 30 ]. Third, our data were obtained from a specific geographic region, whose population diversity may not necessarily be similar to other settings; therefore, extrapolating these findings to a broader population may require caution. Additionally, focusing solely on consensus genomic changes in the analysis could overlook the genetic diversity within the sample, which may also influence variations in viral load. Despite these constraints, our study highlights the importance of sustained genomic surveillance and the need for comprehensive analyses to understand the nuanced impact of specific genetic variations on viral copies at the within-host level, and its implications for viral transmissibility and immune escape at the population level. Further work and collaborative efforts are essential to elucidate the complex interplay between viral genetics, host factors, and the dynamics of transmission associated with emerging variants. Such studies could inform predictive early warning public health systems regarding the emergence of potentially highly transmissible viral strains based on their constellation of mutations.

Recently, Duesterwald et al. [ 10 ] used genome sequence data and a machine-learning approach to predict cycle threshold (Ct) values of SARS-CoV-2 infections based on the k -mers. Similar to our findings, they suggested that S:L452 and P681 were hallmarks of VOCs, implying impacts on the observed Ct values in clinical samples. Although the machine-learning approach may capture broader patterns and interactions within the genome on Ct values, they lack interpretability compared to regression models. For example, regression-based models could offer insights into the direct association between specific genetic variants and viral copies. In addition, regression-based models may perform well even with limited sample sizes [ 16 ], provided that the assumptions of the model are met and the predictors are informative, whereas using machine-learning methods with small sample sizes can be challenging. However, the viral GWAS method may not be appropriate in situations where there is insufficient genetic diversity in the viral population under study, as this can limit the power to detect meaningful associations between mutations and viral traits. Additionally, it may not be suitable when the phenotypic traits of interest are not well-defined or accurately measured.

With the availability of high-quality whole-genome sequences for SARS-CoV-2, we demonstrated that GWAS analysis of the viral genome can identify SNPs that associate with positive or negative impacts on viral copies in VOCs, revealing important biological insights and enhancing our understanding of within-host viral dynamics. We argue that the application of GWAS analyses to study viral genomes provides a particularly tractable tool to identify potential SNPs of interest for further evaluation across different viral pathogens. It is particularly useful to understand the genetic basis of viral virulence, transmission, resistance to antiviral treatments, and host-virus interactions for several reasons. First, the small genome size of viruses and high evolutionary rates make it easier to perform comprehensive genome-wide scans for SNPs and to experimentally test the impacts of SNPs on specific traits. Second, significant phenotypic variations (e.g., viral loads and antibody responses) are often observed in viral infections, despite limited changes in the viral genome. GWAS can help to identify SNPs that correlate with these phenotypic variations, providing insights into the genetic basis of these traits. Third, the increasing accessibility to sequence viral genomes makes it possible to perform GWAS on rich datasets, enabling in-depth analysis of the temporal dynamics of viral evolution. Together, the applicability of GWAS analyses to study viral genomes can provide a new approach for exploring the intricate interplay between genetic mutations and phenotypes, informing strategies for managing and mitigating the impact of emerging viral variants, and contributing to the development of potential therapeutic interventions.

Materials & methods

Ethics statement.

The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).

Clinical sample collection and measurement of viral copies by RT-qPCR

SARS-CoV-2 positive samples (nasal swabs in viral transport media) were collected through the Yale New Haven Hospital (YNHH) System as a part of routine inpatient and outpatient testing and sent to the Yale SARS-CoV-2 Genomic Surveillance Initiative. Using the MagMAX viral/pathogen nucleic acid isolation kit, nucleic acid was extracted from 300μl of each clinical sample and eluted into 75μl of elution buffer. Extracted nucleic acid was then used as template for a “research use only” (RUO) RT-qPCR assay [ 19 ] to test for presence of SARS-CoV-2 RNA. Ct values from the nucleocapsid target (CDC-N1 primer-probe set [ 31 ]) were used to derive viral copy numbers using a previously determined standard curve for this primer set [ 32 ]. A positive RNA control with defined viral copy number (1000/μl) was used to standardize results across individual runs.

Whole genome sequencing

Libraries were prepared for sequencing using the Illumina COVIDSeq Test (RUO version) and quantified using the Qubit High Sensitivity dsDNA kit. Negative controls were included for RNA extraction, cDNA synthesis, and amplicon generation. Prepared libraries were sequenced at the Yale Center for Genomic Analysis on the Illumina NovaSeq with a 2x150 approach and at least 1 million reads per sample.

Reads were then aligned to the Wuhan-Hu-1 reference genome (GenBank MN908937.3) using BWA-MEM v.0.7.15 [ 33 ]. Adaptor sequences were then trimmed, primer sequences masked, and consensus genomes called (simple majority >60% frequency) using iVar v1.3.133 [ 34 ] and SAMtools v1.11 [ 35 ]. When <20 reads were present at a site an ambiguous “N” was used, with negative controls consisting of ≥99% Ns. The Pangolin lineage assignment tool [ 36 ] was used for assigning viral lineages.

Clinical metadata

We obtained patient metadata and vaccination records from the YNHH system and the Center for Outcomes Research and Evaluation (CORE) and matched these records to sequencing data through unique sample identifiers. Duplicate patient records or those with missing or inconsistent metadata and vaccination date were removed from the GWAS analysis. We also removed patient records with persistent infections (>28 days since first positive test).

We determined vaccination status at time of infection by comparing the sample collection date to the patient’s vaccination record dates. We categorized vaccine statuses based on the number of vaccine doses received at least 14 days before the collection date. Patient vaccination statuses at the time of infection were categorized as follows: non-vaccine, one-dose vaccine, two-dose vaccine, two-dose vaccine with one booster, or two-dose vaccine with two boosters. We calculated the age of each patient as the difference between the date of birth and the sampling date.

Single nucleotide polymorphisms

To identify single nucleotide polymorphisms (SNPs), we first aligned the 9902 genome sequences using nextalign (v3.2.1) [ 37 ] with the reference genome of the Wuhan-Hu-1 genome (GenBank accession: MN908937.3). Then, SNPs were identified using snp-sites (v2.4.1) [ 38 ], with the reference genome of the Wuhan-Hu-1 genome (GenBank accession: MN908937.3). We also normalized the SNPs in the generated VCF file, such that multiallelic SNPs were separated into different rows. Normalizing the SNPs ensured that each SNP was one-hot encoded and analyzed separately. Note that we did not include ambiguous SNPs, deletions and insertions in our GWAS analysis. We used vcf-annotator (v0.7) to annotate SNPs to corresponding amino acid changes.

Multidimensional scaling and population control

To reveal the underlying structure of the 9902 genome sequences. We first used snp-dists (v0.7.0) [ 39 ] to convert the aligned sequences (a FASTA alignment) to a SNP distance matrix. We then applied a multidimensional scaling (MDS) method [ 22 ] to transform the SNP distance matrix into a geometric configuration while preserving the original pairwise relationships. The scaling was conducted using cmdscale function in an R package stats (v3.6.2). We set the maximal dimensional parameter k = 2.

To measure the goodness of the transformation, we calculated the distance between the original genome sequencing data and compared it with the new distances determined by MDS. This involved arranging the two matrices of distances into two columns and computing the correlation coefficient (i.e., r ) between them. Finally, we used r 2 to measure the proportion of variance in the original distance matrix explained by the new computed distance matrix.

To determine the clusters (i.e., categorical variables) from MDS, we applied the k-means clustering method using the kmeans function implemented in R statistical software (v4.0.2). We set the number of centroids k = 4.

Testing for associations between viral copies and SNPs

Marginal epistasis test

We applied the marginal epistasis test method to explore the interactions between SNPs on viral copies, using an R package mvMAPIT (v.2.0.3) [ 24 – 26 ]. This method maps SNPs with non-zero marginal epistatic effects—the combined pairwise interaction effects between a given SNP and all other SNPs—identifying candidate variants involved in epistasis without needing to identify the exact partners with which the variants interact.

The key takeaway from MAPIT is that the variance component σ 2 represents a measure of the marginal epistatic effect for each SNP in the data. Therefore, to identify variants that have significant nonzero marginal epistatic effects, the model assesses the null hypothesis H 0 : σ 2 = 0 for each variant in the data set. The mvMAPIT software uses a method of moments algorithm to estimate model parameters and then uses a calibrated two-sided z-score (i.e., normal) test to derive p -values.

Phylogenetic tree construction and comparison to variant-defining substitutions

We employed iq-tree (v2.2.2.6) [ 40 ] of a representative set using 996 of our 9902 genome sequences for tree construction, using Wuhan-Hu-1 (GenBank MN908937.3) as the reference genome. We specified the HKY substitution model and set the number of bootstrap replicates to 1,000. To visualize the phylogenetic tree, we used the ggtree (v1.4.11) implemented in the R statistical software (v4.0.2). The variant-defining amino acid changes were defined as those mutations with >75% prevalence in at least one lineage, as estimated on outbreak.info website [ 41 ]. Note that we did not include deletions in variant-defining substitutions.

Supporting information

S1 fig. results of multidimensional scaling. the population structure of the 9902 genome sequences using a multidimensional scaling (mds) method..

Clusters are defined using a k -means clustering method, as demonstrated on the bottom right corner.

https://doi.org/10.1371/journal.pcbi.1012469.s001

S2 Fig. Q-Q plots of GWAS p-values.

Q-Q plots (quantile-quantile plots) showing the p-values from GWAS analysis using (A) two MDS-computed components, or (B) MDS-inferred four clusters as covariates in the regression model.

https://doi.org/10.1371/journal.pcbi.1012469.s002

S3 Fig. Marginal epistasis tests identify single nucleotide polymorphisms (SNPs) that have epistatic interactions with others and are associated with the changes in viral copies.

(A) Marginal epistasis test results of the SNPs (annotated as amino acid changes) that have marginal epistatic effects on viral copies. The dashed line indicates the permuted threshold for genome-wide significance p = 0.05/171 = 2.74 × 10 −4 . Significant mutations are shown with solid colors. (B) The p -values and (C) the effect size of pairwise interaction tests among the significant mutations.

https://doi.org/10.1371/journal.pcbi.1012469.s003

S4 Fig. GWAS analysis identifies several single nucleotide polymorphisms (SNPs) that are associated with the changes in viral copies.

(A) Genome-wide association results of the impact of identified SNPs on viral copies during SARS-CoV-2 infection. The dashed line indicates the permuted threshold for genome-wide significance p = 4.67 × 10 −6 . Significant SNPs are shown with solid colors. (B) SNPs (with p < 1 × 10 −10 ) that have positive (blue) or negative (red) effects on viral copies. (C) The corresponding synonymous (triangles) and non-synonymous (circles) amino acid changes that associate with increased or decreased viral copies. Data is shown as means with 95% confidence intervals. The estimated effective sizes and associated standard deviations are given in S1 Table . A Q-Q plot showing the observed distribution of p-value and the expected distribution is given in S2 Fig .

https://doi.org/10.1371/journal.pcbi.1012469.s004

S5 Fig. GWAS analysis using only Cluster 1 data (shown in S1 Fig ).

(A) Genome-wide association results of the impact of identified SNPs on viral copies during SARS-CoV-2 infection. The dashed line indicates the permuted threshold for genome-wide significance p = 4.03 × 10 −5 (0.05/1242 SNPs). Significant SNPs are shown with solid colors. (B) SNPs (with p <1×10 −10 ) that have positive (blue) or negative (red) effects on viral copies. (C) The corresponding synonymous (triangles) amino acid changes that associate with increased or decreased viral copies. Data shown as means with 95% confidence intervals.

https://doi.org/10.1371/journal.pcbi.1012469.s005

S6 Fig. GWAS analysis using Cluster 2 data (shown in S1 Fig ).

(A) Genome-wide association results of the impact of identified SNPs on viral copies during SARS-CoV-2 infection. The dashed line indicates the permuted threshold for genome-wide significance p = 3.68 × 10 −5 (0.05/1357 SNPs). Significant SNPs are shown with solid colors. (B) SNPs (with p <1×10 −10 ) that have positive (blue) or negative (red) effects on viral copies. (C) The corresponding synonymous (triangles) amino acid changes that associate with increased or decreased viral copies. Data shown as means with 95% confidence intervals.

https://doi.org/10.1371/journal.pcbi.1012469.s006

S7 Fig. GWAS analysis using Cluster 3 data (shown in S1 Fig ).

(A) Genome-wide association results of the impact of identified SNPs on viral copies during SARS-CoV-2 infection. The dashed line indicates the permuted threshold for genome-wide significance p = 2 .80 × 10 −5 (0.05/1784 SNPs). Significant SNPs are shown with solid colors. (B) SNPs (with p < 1 × 10 −10 ) that have positive (blue) or negative (red) effects on viral copies. (C) The corresponding non-synonymous (circles) amino acid changes that associate with increased or decreased viral copies. Data shown as means with 95% confidence intervals.

https://doi.org/10.1371/journal.pcbi.1012469.s007

S8 Fig. GWAS analysis using Cluster 4 data (shown in S1 Fig ).

(A) Genome-wide association results of the impact of identified SNPs on viral copies during SARS-CoV-2 infection. The dashed line indicates the permuted threshold for genome-wide significance p = 7.91 × 10 −6 (0.05/6314 SNPs). Significant SNPs are shown with solid colors. (B) SNPs (with p < 1 × 10 −10 ) that have positive (blue) or negative (red) effects on viral copies. (C) The corresponding synonymous (triangles) and non-synonymous (circles) amino acid changes that associate with increased or decreased viral copies. Data shown as means with 95% confidence intervals.

https://doi.org/10.1371/journal.pcbi.1012469.s008

S9 Fig. The temporal dynamics of amino acid changes in the S gene associated with changes in viral copies.

The results are based on the multivariate regression analysis using the two MDS components as covariates. (A) The phylogenetic tree estimated from a representative set of 996 genome sequences showing variant assignments and the locations of amino acid changes that increase (blue) or decrease (red) viral copies. (B) The temporal dynamics of the SNPs from February 2021 to March 2023. The transparency of the color corresponds to the mutation fraction in the daily sequence count: transparent color indicates low fractions, and opaque color indicates high fractions.

https://doi.org/10.1371/journal.pcbi.1012469.s009

S10 Fig. The temporal dynamics of amino acid changes in the ORF1ab gene associated with changes in viral copies.

https://doi.org/10.1371/journal.pcbi.1012469.s010

S11 Fig. The temporal dynamics of amino acid changes in the ORF3a gene (S26L and T223I), M gene (D3G and I82T), ORF7b gene (T40I) and N gene (D63G and S413R) associated with changes in viral copies.

https://doi.org/10.1371/journal.pcbi.1012469.s011

S12 Fig. Comparison of key variant-defining amino acid changes with GWAS-identified substitutions.

The comparison of the key amino acid changes (dark purple) in each variant, with GWAS-identified SNPs that were associated with negative (red) or positive (blue) effects on viral copies in the (A) S gene and (B) ORF1ab gene. The results of GWAS analysis using the two dimensions computed by MDS as covariates are shown as “GWAS 1”, and the results of the analysis using the categorical clusters as covariates are shown as “GWAS 2”. The effective sizes of identified SNPs using different population control methods are given in S1 and S2 Tables.

https://doi.org/10.1371/journal.pcbi.1012469.s012

S1 Table. The identified amino acid changes associated estimated effective sizes and standard deviations using the multivariate linear regression model with categorical clusters as covariates.

https://doi.org/10.1371/journal.pcbi.1012469.s013

S2 Table. The identified amino acid changes associated estimated effective sizes and standard deviations using the multivariate linear regression model with MDS-computed dimensions as covariates.

https://doi.org/10.1371/journal.pcbi.1012469.s014

Acknowledgments

We would like to thank Verity Hill, Seth Redmond, Jiye Kwon, Rafael Lopes, Sophie Taylor, and Philip Jack for their helpful conversations and feedback on this work.

• View Article
• PubMed/NCBI
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• 10. Duesterwald L, Nguyen M,Christensen P, Wesley Long, Olsen R, Musser JM, et al. Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values. https://doi.org/10.1101/2022.11.14.22282297
• 39. Creators Seemann, Torsten1 Show affiliations 1. The University of Melbourne. Source code for snp-dists software. https://doi.org/10.5281/zenodo.1411986

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• Published: 20 September 2024

Is smokeless tobacco a healthier option in patients with AUD? A follow-up study during treatment

• Lars Lien 1 , 2 ,
• Ingeborg Bolstad 1 , 2 &
• Jørgen G. Bramness 1 , 3 , 4  

Harm Reduction Journal volume  21 , Article number:  173 ( 2024 ) Cite this article

Metrics details

Introduction

Smoking is negatively related to mental health, but there is a paucity of research on the relationship between the use of smokeless tobacco, such as snus, and mental health outcomes, especially in people with alcohol use disorders (AUD). The aim of the present study was to examine the development of mental distress and quality of life (QoL) among AUD patients in treatment who did or did not use snus.

The study included 128 AUD patients (27% female) from three rehabilitation clinics in Eastern Norway who were interviewed at admission, at 6 weeks, and after 6 months. Patients were asked about their mental health-related problems, alcohol, and substance use, QoL, and physical activity. Information about tobacco use was gathered with the questions “Do you smoke cigarettes?” and “Do you use snus?”, with follow-up questions “How often?”.

There were 39 current snus users (31%), of which 20 were also current smokers (dual users). Seventy-five patients (59%) were smokers only, and only 14 (11%) patients were abstainers. Those who used snus only had a lower severity of dependence score than the other groups ( p  < 0.05). The dual use group reported lower QoL than the no tobacco use group. In a regression model adjusted for sex and age, smokers and dual users, but not users of snus, had higher levels of mental distress and poorer QoL compared to nontobacco users ( p  < 0.05). There were no differences between tobacco groups at follow-ups.

In this study, among AUD patients, snus users reported QoL and mental distress close to that of non-smokers, indicating a lower problem load among snus users compared to smokers.

Implications

Previous studies have shown conflicting results regarding the potential harm reduction effect of snus use among patients with AUD who smoke regarding their tobacco use, quality of life and mental health problems. This study suggests that snus use could also be a viable alternative to smoking for patients with addictions.

The Scandinavian smokeless tobacco product “snus” is a moist oral tobacco product that is placed behind the upper lip, mostly in portioned sachets. The composition of smokeless oral tobacco products may differ between geographical regions and contain different ingredients in addition to tobacco [ 12 , 30 ]. Snus is air-cured tobacco mixed with salt and water and processed using techniques resembling pasteurization. Sale of snus is prohibited in all EU countries except Sweden, but it is available in non-EU countries such as Norway and Switzerland. In Norway, snus is now more prevalent in use than smoking and is used by approximately 15% of the population aged 16 to 74 years, approximately twice the number of smokers [ 31 ].

In contrast to the steeply declining smoking rates in the general population, 75% of people with substance use disorders (SUD) are still smokers [ 18 ]. Together with other unhealthy lifestyle factors, this may contribute to the large increase in death rates, mainly due to cardiovascular diseases [ 1 , 2 ]. It is of interest to reduce smoking among people with SUD [ 22 ], as this may also increase the success of SUD treatment [ 23 ].

Studies have shown considerably lower health risks associated with snus smoking than with cigarette smoking [ 3 , 4 , 12 , 34 ]. In countries with higher use of alternative nicotine products, a lower smoking prevalence has been observed, indicating that alternative nicotine products may reduce smoking [ 8 , 27 ]. Sweden is a country with a high prevalence of snus use and simultaneously one of the countries within the EU with the lowest prevalence of tobacco-related disease and is especially low in lung cancer among men [ 4 ].

Snus and alternative tobacco and nicotine products may even have a role in assisting smoking reduction and cessation [ 28 ]. A study following former smokers over seven years found that approximately 80% reported snus to be of great importance to succeed with smoking cessation [ 21 ], and even in randomized smoking cessation trials, snus has shown efficacy [ 14 ]. However, a meta-analysis showed little effect, possibly due to poor quality studies [ 32 ].

We know from general population studies that there seems to be a close relationship between smoking and alcohol use [ 36 ]. However, even snus users have 60% higher estimated yearly excess consumption of alcohol and another drinking style than tobacco nonusers [ 38 ]. Another follow-up study found that snus use was associated with an increased risk of alcohol use disorders (AUD) with a dose–response relationship independent of smoking status [ 25 ].

Additionally, from several population studies, we know that smoking and the use of alcohol independently and together increase the risk of poor mental health [ 9 , 15 ]. In an earlier article, we were able to show that compared to smokers, non-smokers had a lower drop-out rate, were less distressed and had a higher quality of life [ 18 ].

Few studies have examined the use of snus and the possible relationships to mental health symptoms and quality of life among people with AUD. A follow-up study of alcohol-dependent individuals in alcohol treatment facilities found that both smokers and those who used snus had an earlier alcohol debut than tobacco never-users, but there was no difference in treatment outcome between the groups [ 29 ].

The aim of this study is thus to examine the effects of snus, cigarette smoking and dual use on mental distress and quality of life among AUD patients in treatment and to further study longitudinal effects on the same parameters, including drop-out rates.

Materials and methods

Study participants.

Participants were recruited from three inpatient rehabilitation clinics located in Eastern Norway, as previously detailed by (Bolstad et al., 2023). The study included patients diagnosed with AUD (n = 113) and/or other SUD (n = 37) according to the International Classification of Diseases, 10th Revision (ICD-10). Patients were excluded if they had psychosis, cognitive impairments, severe physical illnesses, or lacked proficiency in a Scandinavian language. Eligible patients were informed about the study, and 128 individuals provided written informed consent. Data were collected at one week post-admission, at six weeks, and at six months. Information on mental health, substance dependence, and tobacco use was gathered through interviews by trained staff, while data on mental distress, physical activity, and alcohol dependence were obtained via self-report questionnaires.

Ethical considerations

The study was approved by the Norwegian Regional Ethics Committee (ref. no. 2017/1314). We ensured that all methods were used in accordance with relevant guidelines and regulations.

Background variables

Information about age, sex and educational level was collected initially when meeting the participant. Waist circumference, weight and height were measured, and body mass index (BMI) was calculated.

The International Physical Activity Questionnaire short version (IPAQ-S) was used to measure the level of physical activity [ 6 , 17 ]. Time spent walking or doing moderate or vigorous exercise weekly was reported in a seven-item questionnaire, and the participants were placed in categories of low, moderate, or high physical activity level. The variable was dichotomized as low vs. moderate/high for the purpose of this study.

AUD severity was measured using the Norwegian version of the Severity of Dependence Scale (SDS) [ 10 , 16 ]. The SDS consists of five four-level (0–3) Likert items mapping impaired control over drinking, anxiety, and preoccupation with drinking the past year. Item responses are summed into a score where a higher score indicates more severe AUD. Cronbach’s alpha for SDS in our study was 0.86.

The Mini International Neuropsychiatric Interview (MINI) version 6.0 was used to identify substance use disorder. Module I (alcohol use/addiction) and J (substance use/addiction) were performed according to the manual by trained personnel.

Tobacco habits

Tobacco use habits were assessed through questions during an interview. Study participants were asked, "Do you smoke cigarettes?" and "Do you use snus?" Those who responded positively were then asked how often they used cigarettes/snus (“daily”/”occasionally”). Individuals who reported daily use of cigarettes or snus were classified as smokers or snus users, respectively, while those who reported no or occasional use were categorized as non-smokers or nonusers of snus.

Outcome measures

Mental distress was assessed using the 10-item version of the Hopkins Symptom Checklist (HSCL-10) [ 7 ], a widely recognized self-report tool that measures common symptoms of depression and anxiety experienced over the past week. The HSCL-10 includes ten items rated on a four-point Likert scale, ranging from "not at all" (1) to "extremely" (4). The responses are summed and then divided by the number of items to generate an individual score between 1 and 4, with higher scores indicating higher level of mental distress. The Cronbach’s alpha for the scale was 0.91.

Quality of life was measured by the five-item Quality of Life (QoL-5) instrument to measure patient satisfaction with life in general [ 19 ]. This taps into self-perceived quality of mental and physical health and relationship to oneself and to significant others. There are five ordinal response alternatives ranging from (1) ‘Very good’ to (5) ‘Very poor’. The raw scores are transposed and inverted into a total score between 10 and 90, where a higher score indicates better quality of life. Chronbach’s alpha was 0.60.

Statistical analyses

Due to non-normal distributions of the variables, medians and percentiles are used for descriptive statistics, and nonparametric tests are used to assess group differences. Bivariate linear regression models were built to examine the effect of snus and cigarette smoking on mental distress and quality of life. Analyses are performed using Stata 17.0.

There were 39 (31%) current snus users at admission, 20 of whom were also current smokers. Seventy-five (59%) patients were smokers only, and only 14 (11%) patients abstained from both (Table  1 ).

More men than women were dual users of snus and tobacco compared to the no tobacco use group ( p  = 0.002), and the dual users ( p  = 0.009) and snus only users ( p  = 0.018) were younger. Among the smokers, fewer had education at the upper secondary level ( p  = 0.006) (Table  1 ). Approximately one-third of both non-smokers and snus users reported smoking earlier in their life. Those who used snus only had a lower SDS score than the non-tobacco users ( p  = 0.002). There were more patients among the dual users than nontobacco users with an SUD other than AUD ( p  = 0.016).

Table 2 shows the development in self-reported mental distress (HSCL-10) from baseline through the 6-week to six-month follow-up. At baseline, the dual use group reported poorer QoL than nontobacco users ( p  = 0.015). Overall, the snus users reported QoL scores intermediate to those seen for smokers and abstainers. The treatment drop-out was higher for smokers and dual users. However, none of these differences were statistically significant.

In the bivariate regression with self-reported mental distress and quality of life at baseline as outcome variables, we controlled for age and sex (Table  3 ). Smokers and dual users reported significantly higher mental distress and significantly poorer quality of life than those not currently using tobacco (all p  < 0.05). Users of snus did not differ from those with no tobacco use.

The aim of this study was to examine cross sectional and longitudinal effects of snus, cigarette smoking and dual use on mental distress and quality of life. The main finding from this study is that smokers, either those just smoking or those using snus in addition, reported higher mental distress and lower quality of life than those abstaining from tobacco products. Those using snus only did not report higher mental distress or lower quality of life compared to tobacco abstainers. There was a non-significant tendency for more drop-out among smokers with or without simultaneous snus use.

Several earlier studies have shown that smokers have worse mental health with a higher risk of several mental health outcomes compared to non-smokers in the general population [ 40 , 42 ]. Most studies also show a close relationship between poor mental health and smoking in AUD patients [ 18 ], but some studies end up with an opposite finding [ 33 ].

Even if the snus user group did not differ from the tobacco abstainers, they seemed to place themselves in a middle position concerning mental health and quality of life. Even other studies have shown an increased risk for depression and anxiety among snus users, but less so than for smokers [ 3 , 35 ]. Additionally, for health-related quality of life, a cross-sectional study found that snus use was associated with a lower quality of life, but less so than for smokers [ 37 ].

Smokers had lower educational levels than nontobacco users and snus users. This reflects findings from general population studies where smoking is associated with lower socioeconomic status [ 5 ]. The lower age found among snus users might reflect changes in society, where young people use snus more often than the elderly [ 26 ]. There was also a trend towards a higher level of physical activity among snus users. A positive association between snus use and sport and exercise has been described by others [ 13 , 41 ].

Another interesting finding was that those who only used snus, but not smokers or dual users, had a lower severity of dependence score than nontobacco users. This is in contrast to a Swedish study that did not find any difference in different parameters of severity of dependence according to smoking status either at baseline or follow-up according to smoking status [ 29 ].

The question remains whether the current results can be used as an argument for snus being a harm reduction measure for smokers. Despite small numbers in the present study, more than 30% of both non-tobacco users and snus users were previous smokers, which might indicate that snus might be used as a quitting strategy in this population. A Norwegian repeated cross-sectional representative survey found that 26% of those quitting smoking used snus as their preferred method and that snus was also the method with the highest success rate [ 21 ]. In 2019 the US Food and Drug Administration (FDA) granted a modified risk orders to Swedish Match USA, Inc. for eight snus smokeless tobacco products that may be advertised with specific information about the lower risks of certain health effects using the products compared to smoking cigarettes ( https://www.fda.gov/tobacco-products/advertising-and-promotion/fda-authorizes-modified-risk-tobacco-products ).

In the present study, a relatively high proportion both smoked and used snacks. This was related to lower quality of life and higher severity of dependence. This could be used as an argument against introducing snus as a harm reduction measure. Previous studies have shown that such dual use hampers smoking cessation and might result in high smoking rates even among young adults [ 11 ]. However, other studies have found that snus use is associated with a higher likelihood of quitting smoking within the first 5 years of using snus [ 20 ].

Last, the question remains regarding how snus use may contribute to addiction. We know from other research that continued smoking hampers addiction treatment [ 39 ]. We still lack research on the implications of snus usage. One study indicated that other mechanisms of addiction may contribute to the maintenance of snus use than other addictive substances [ 24 ].

There are some limitations of this study. First, we have no measures to validate the self-reported level of smoking and snus use. Second, most of the results are based on cross-sectional data, limiting the possibility of drawing conclusions on the directions of our findings. Third, the sample size is small, and we cannot rule out whether our sample is representative of all people entering AUD treatment facilities. A small sample size also restricts the number of variables we can use and increases the risk of type II errors.

The conclusion from this study is that snus users have levels of mental health problems and quality of life closer to those seen for current non-smokers in an AUD treatment population. A possible implication from this study is that snus might be a safe smoking cessation tool in this group of patients. Specific attention should be given to patients with dual use of snus and tobacco.

Availability of data and materials

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Abebe DS, Lien L, Bramness JG. Effects of age and gender on the relationship between alcohol use disorder and somatic diseases: a national register study in Norway. BMJ Open. 2021;11(11): e050608. https://doi.org/10.1136/bmjopen-2021-050608 .

Article   PubMed   PubMed Central   Google Scholar  

Bandiera FC, Anteneh B, Le T, Delucchi K, Guydish J. Tobacco-related mortality among persons with mental health and substance abuse problems. PLoS ONE. 2015;10(3): e0120581. https://doi.org/10.1371/journal.pone.0120581 .

Article   CAS   PubMed   PubMed Central   Google Scholar  

Bondø P, Høye A, Løchen ML, Bramness JG. The relationship between smokeless tobacco (snus) and anxiety and depression among adults and elderly people A comparison to smoking in the Tromsø Study. Addiction. 2022;117(10):2695–706. https://doi.org/10.1111/add.15950 .

Clarke E, Thompson K, Weaver S, Thompson J, O’Connell G. Snus: a compelling harm reduction alternative to cigarettes. Harm Reduct J. 2019;16(1):62. https://doi.org/10.1186/s12954-019-0335-1 .

Corsi DJ, Lear SA, Chow CK, Subramanian SV, Boyle MH, Teo KK. Socioeconomic and geographic patterning of smoking behaviour in Canada: a cross-sectional multilevel analysis. PLoS ONE. 2013;8(2): e57646. https://doi.org/10.1371/journal.pone.0057646 .

Craig CL, Marshall AL, Sjöström M, Bauman AE, Booth ML, Ainsworth BE, Pratt M, Ekelund U, Yngve A, Sallis JF, Oja P. International physical activity questionnaire: 12-country reliability and validity. Med Sci Sports Exerc. 2003;35(8):1381–95. https://doi.org/10.1249/01.Mss.0000078924.61453.Fb .

Article   PubMed   Google Scholar  

Derogatis LR, Lipman RS, Rickels K, Uhlenhuth EH, Covi L. The Hopkins Symptom Checklist (HSCL): a self-report symptom inventory. Behav Sci. 1974;19(1):1–15. https://doi.org/10.1002/bs.3830190102 .

Article   CAS   PubMed   Google Scholar  

Fagerström K. Can alternative nicotine products put the final nail in the smoking coffin? Harm Reduct J. 2022;19(1):131. https://doi.org/10.1186/s12954-022-00722-5 .

Ferreira VR, Jardim TV, Sousa ALL, Rosa BMC, Jardim PCV. Smoking, alcohol consumption and mental health: Data from the Brazilian study of Cardiovascular Risks in Adolescents (ERICA). Addictive behaviors reports. 2019;9: 100147. https://doi.org/10.1016/j.abrep.2018.100147 .

Gossop M, Darke S, Griffiths P, Hando J, Powis B, Hall W, Strang J. The Severity of Dependence Scale (SDS): psychometric properties of the SDS in English and Australian samples of heroin, cocaine and amphetamine users. Addiction. 1995;90(5):607–14. https://doi.org/10.1046/j.1360-0443.1995.9056072.x .

Grøtvedt L, Forsén L, Ariansen I, Graff-Iversen S, Lingaas Holmen T. Impact of snus use in teenage boys on tobacco use in young adulthood; a cohort from the HUNT Study Norway. BMC Public Health. 2019;19(1):1265. https://doi.org/10.1186/s12889-019-7584-5 .

Hajat C, Stein E, Ramstrom L, Shantikumar S, Polosa R. The health impact of smokeless tobacco products: a systematic review. Harm Reduct J. 2021;18(1):123. https://doi.org/10.1186/s12954-021-00557-6 .

Henninger S, Fischer R, Cornuz J, Studer J, Gmel G. Physical activity and snus: Is there a link? Int J Environ Res Public Health. 2015;12(7):7185–98. https://doi.org/10.3390/ijerph120707185 .

Joksić G, Spasojević-Tišma V, Antić R, Nilsson R, Rutqvist LE. Randomized, placebo-controlled, double-blind trial of Swedish snus for smoking reduction and cessation. Harm Reduct J. 2011;8:25. https://doi.org/10.1186/1477-7517-8-25 .

Kim HO, Jeon M. The Relationship Between Smoking, Drinking and the Mental Health in Adolescents. Journal of Korean Public Health Nursing. 2007;21:217–29.

Google Scholar  

Kristoffersen ES, Benth J, Straand J, Russell MB, Lundqvist C. Validity of self-reported assessment of Severity of Dependence Scale in Medication-Overuse Headache. Scand J Pain. 2019;19(4):837–41. https://doi.org/10.1515/sjpain-2019-0022 .

Kurtze N, Rangul V, Hustvedt BE, Flanders WD. Reliability and validity of self-reported physical activity in the Nord-Trøndelag Health Study: HUNT 1. Scand J Public Health. 2008;36(1):52–61. https://doi.org/10.1177/1403494807085373 .

Lien L, Bolstad I, Bramness JG. Smoking among inpatients in treatment for substance use disorders: prevalence and effect on mental health and quality of life. BMC Psychiatry. 2021;21(1):244. https://doi.org/10.1186/s12888-021-03252-9 .

Lindholt JS, Ventegodt S, Henneberg EW. Development and validation of QoL5 for clinical databases a short, global and generic questionnaire based on an integrated theory of the quality of life. Eur J Surg. 2002;168(2):107–13. https://doi.org/10.1080/11024150252884331 .

Lund I, Christiansen SG. Association between snus use over time and smoking cessation in Norwegian smokers. Addiction. 2020;115(1):170–4. https://doi.org/10.1111/add.14809 .

Lund M, Lund I. Smoking cessation aids and strategies: a population-based survey of former and current smokers in Norway. BMC Public Health. 2022;22(1):631. https://doi.org/10.1186/s12889-022-13032-z .

McCuistian C, Kapiteni K, Le T, Safier J, Delucchi K, Guydish J. Reducing tobacco use in substance use treatment: An intervention to promote tobacco-free grounds. J Subst Abuse Treat. 2022;135: 108640. https://doi.org/10.1016/j.jsat.2021.108640 .

McKelvey K, Thrul J, Ramo D. Impact of quitting smoking and smoking cessation treatment on substance use outcomes: An updated and narrative review. Addict Behav. 2017;65:161–70. https://doi.org/10.1016/j.addbeh.2016.10.012 .

Mentzoni RA, Sætrevik B, Molde H, Wiium N, Hetland J, Fagerland I, Nordnes LT, Storemark SS, Fossum IN, Pallesen S. Attentional bias in snus users: an experimental study. PLoS ONE. 2014;9(10): e108897. https://doi.org/10.1371/journal.pone.0108897 .

Norberg M, Malmberg G, Ng N, Broström G. Use of moist smokeless tobacco (snus) and the risk of development of alcohol dependence: a cohort study in a middle-aged population in Sweden. Drug Alcohol Depend. 2015;149:151–7. https://doi.org/10.1016/j.drugalcdep.2015.01.042 .

Pedersen W, von Soest T. Tobacco use among Norwegian adolescents: from cigarettes to snus. Addiction. 2014;109(7):1154–62. https://doi.org/10.1111/add.12509 .

Ramström L, Borland R, Wikmans T. Patterns of Smoking and Snus Use in Sweden: Implications for Public Health. Int J Environ Res Public Health. 2016. https://doi.org/10.3390/ijerph13111110 .

Ramström L, Wikmans T. Mortality attributable to tobacco among men in Sweden and other European countries: an analysis of data in a WHO report. Tob Induc Dis. 2014;12(1):14. https://doi.org/10.1186/1617-9625-12-14 .

Rauwolf KK, Berglund KJ, Berggren U, Balldin J, Fahlke C. The Influence of Smoking and Smokeless Tobacco on the Progression, Severity and Treatment Outcome in Alcohol-Dependent Individuals. Alcohol Alcohol. 2017;52(4):477–82. https://doi.org/10.1093/alcalc/agx031 .

Siddiqi K, Husain S, Vidyasagaran A, Readshaw A, Mishu MP, Sheikh A. Global burden of disease due to smokeless tobacco consumption in adults: an updated analysis of data from 127 countries. BMC Med. 2020;18(1):222. https://doi.org/10.1186/s12916-020-01677-9 .

Statistics Norway. Tobacco, alcohol and other drugs. 2022. https://www.ssb.no/en/helse/helseforhold-og-levevaner/statistikk/royk-alkohol-og-andre-rusmidler

Stjepanović D, Phartiyal P, Leung J, Lim CCW, Sun T, Chung JYC, Gartner CE, Hall WD, Chan GCK. Efficacy of smokeless tobacco for smoking cessation: a systematic review and meta-analysis. Tob Control. 2022. https://doi.org/10.1136/tobaccocontrol-2021-057019 .

Saatçioğlu O, Celikel FC, Çakmak D. Depression and anxiety in alcohol dependent inpatients who smoke. Isr J Psychiatry Relat Sci. 2008;45(1):33–8.

PubMed   Google Scholar  

Titova OE, Baron JA, Michaëlsson K, Larsson SC. Swedish snuff (snus) and risk of cardiovascular disease and mortality: prospective cohort study of middle-aged and older individuals. BMC Med. 2021;19(1):111. https://doi.org/10.1186/s12916-021-01979-6 .

Tjora T, Skogen JC, Sivertsen B. Establishing the Association Between Snus Use and Mental Health Problems: A Study of Norwegian College and University Students. Nicotine Tob Res. 2023;25(1):135–42. https://doi.org/10.1093/ntr/ntac208 .

Vallée A. Associations between smoking and alcohol consumption with blood pressure in a middle-aged population. Tobacco Induc Dis. 2023;21:61. https://doi.org/10.18332/tid/162440 .

Article   Google Scholar  

Wachsmann S, Nordeman L, Billhult A, Rembeck G. Tobacco impact on quality of life, a cross-sectional study of smokers, snuff-users and non-users of tobacco. BMC Public Health. 2023;23(1):886. https://doi.org/10.1186/s12889-023-15844-z .

Watten RG, Watten VP. Snus and alcohol: Mutually rewarding effects in the brain? A matched controlled population study. Subst Abuse. 2021;15:11782218211027124. https://doi.org/10.1177/11782218211027124 .

Weinberger AH, Platt J, Jiang B, Goodwin RD. Cigarette smoking and risk of alcohol use relapse among adults in recovery from alcohol use disorders. Alcohol Clin Exp Res. 2015;39(10):1989–96. https://doi.org/10.1111/acer.12840 .

Wilson N, Weerasekera D, Collings SC, Edwards R, van der Deen FS. Poorer mental health in many New Zealand smokers: national survey data from the ITC Project. N Z Med J. 2010;123(1326):129–32.

Zandonai T, Tam E, Bruseghini P, Pizzolato F, Franceschi L, Baraldo M, Capelli C, Cesari P, Chiamulera C. The effects of oral smokeless tobacco administration on endurance performance. J Sport Health Sci. 2018;7(4):465–72. https://doi.org/10.1016/j.jshs.2016.12.006 .

Zvolensky MJ, Jardin C, Wall MM, Gbedemah M, Hasin D, Shankman SA, Gallagher MW, Bakhshaie J, Goodwin RD. Psychological distress among smokers in the United States: 2008–2014. Nicotine Tob Res. 2017;20(6):707–13. https://doi.org/10.1093/ntr/ntx099 .

Article   PubMed Central   Google Scholar  

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Acknowledgements

The following treatment facilities took part in the study; Blå Kors Eina, Riisby and Trasopp. We would like to thank all patients and staff for their valuable support.

The study was funded under the FRIPRO program of the Norwegian Research Council, and the funding body did not take part in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

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LL wrote the main manuscript text and IB did the analysis and prepared tables 1–3. JGB had the idea and provided the data. All authors reviewed the manuscript.

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Lien, L., Bolstad, I. & Bramness, J.G. Is smokeless tobacco a healthier option in patients with AUD? A follow-up study during treatment. Harm Reduct J 21 , 173 (2024). https://doi.org/10.1186/s12954-024-01077-9

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Real Estate Automated Valuation Model with Explainable Artificial Intelligence Based on Shapley Values

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• Dieudonné Tchuente   ORCID: orcid.org/0000-0002-6752-4269 1  

The literature on the use of machine learning (ML) models for the estimation of real estate prices is increasing at a high rate. However, the black-box nature of the proposed models hinders their adoption by market players such as appraisers, assessors, mortgage lenders, fund managers, real estate agents or investors. Explaining the outputs of those ML models can thus boost their adoption by these domain-field experts. However, very few studies in the literature focus on exploiting the transparency of eXplainable Artificial Intelligence (XAI) approaches in this context. This paper fills this research gap and presents an experiment on the French real estate market using ML models coupled with Shapley values to explain the models. The used dataset contains 1,505,033 transactions (in 7 years) from nine major French cities. All the processing steps for preparing, building, and explaining the ML models are presented in a transparent way. At a global level, beyond the predictive capacity of the models, the results show the similarities and the differences between these nine real estate submarkets in terms of the most important predictors of property prices (e.g., living area, land area, location variables, number of dwellings in a condominium), trends over years, the differences between the markets of apartments and houses, and the impact of sales before completion. At the local level, the results show how one can easily interpret and evaluate the contribution of each feature value for any single prediction, thereby providing essential support for the understanding and adoption by domain-field experts. The results are discussed with respect to the existing literature in the real estate field, and many future research avenues are proposed.

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The dataset used in this study is publicly available at https://www.data.gouv.fr/fr/datasets/5c4ae55a634f4117716d5656/ .

https://geo.api.gouv.fr .

Aas, K., Jullum, M., & Løland, A. (2021). Explaining individual predictions when features are dependent: More accurate approximations to Shapley values. Artificial Intelligence , 298 , 103502.

Article   Google Scholar  

Adadi, A., & Berrada, M. (2018). Peeking inside the black-box: A survey on explainable artificial intelligence (XAI). Ieee Access: Practical Innovations, Open Solutions , 6 , 52138–52160.

Agarwal, C., Krishna, S., Saxena, E., Pawelczyk, M., Johnson, N., Puri, I., Zitnik, M., & Lakkaraju, H. (2022). Openxai: Towards a transparent evaluation of model explanations. Advances in Neural Information Processing Systems , 35 , 15784–15799.

Google Scholar  

Amparore, E., Perotti, A., & Bajardi, P. (2021). To trust or not to trust an explanation: Using LEAF to evaluate local linear XAI methods. PeerJ Computer Science , 7 , e479.

Anselin, L. (2013). Spatial econometrics: Methods and models (Vol. 4). Springer Science & Business Media.

Apley, D. W., & Zhu, J. (2020). Visualizing the effects of predictor variables in black box supervised learning models. Journal of the Royal Statistical Society: Series B (Statistical Methodology) , 82 (4), 1059–1086.

Arrieta, A. B., Díaz-Rodríguez, N., Del Ser, J., Bennetot, A., Tabik, S., Barbado, A., García, S., Gil-López, S., Molina, D., & Benjamins, R. (2020). Explainable Artificial Intelligence (XAI): Concepts, taxonomies, opportunities and challenges toward responsible AI. Information Fusion , 58 , 82–115.

Basu, S., & Thibodeau, T. G. (1998). Analysis of spatial autocorrelation in house prices. The Journal of Real Estate Finance and Economics , 17 (1), 61–85.

Bauer, K., von Zahn, M., & Hinz, O. (2023). Expl (AI) ned: The impact of explainable artificial intelligence on users’ information processing. Information Systems Research , 34 (4), 1582–1602.

Binoy, B. V., Naseer, M. A., Kumar, P. P. A., & Lazar, N. (2021). A bibliometric analysis of property valuation research. International Journal of Housing Markets and Analysis .

Bitter, C., Mulligan, G. F., & Dall’erba, S. (2007). Incorporating spatial variation in housing attribute prices: A comparison of geographically weighted regression and the spatial expansion method. Journal of Geographical Systems , 9 (1), 7–27.

Bogin, A. N., & Shui, J. (2020). Appraisal Accuracy and Automated Valuation models in Rural Areas. The Journal of Real Estate Finance and Economics , 60 (1), 40–52. https://doi.org/10.1007/s11146-019-09712-0

Bourassa, S. C., Hoesli, M., & Peng, V. S. (2003). Do housing submarkets really matter? Journal of Housing Economics , 12 (1), 12–28.

Bourassa, S. C., Cantoni, E., & Hoesli, M. (2007). Spatial dependence, housing submarkets, and house price prediction. The Journal of Real Estate Finance and Economics , 35 (2), 143–160.

Breiman, L. (2001). Random forests. Machine Learning , 45 (1), 5–32.

Bücker, M., Szepannek, G., Gosiewska, A., & Biecek, P. (2022). Transparency, auditability, and explainability of machine learning models in credit scoring. Journal of the Operational Research Society , 73 (1), 70–90.

Cajias, M. (2020). Artificial intelligence and real estate-not just an evolution, a real game changer! Journal of Property Investment & Finance .

Cajias, M., & Wins, A. (2021). Data intelligence and real estate–machines are the real game changer. Journal of Property Investment & Finance .

Chakraborty, S., Tomsett, R., Raghavendra, R., Harborne, D., Alzantot, M., Cerutti, F., Srivastava, M., Preece, A., Julier, S., & Rao, R. M. (2017). Interpretability of deep learning models: A survey of results. 2017 IEEE Smartworld, Ubiquitous Intelligence & Computing, Advanced & Trusted Computed, Scalable Computing & Communications, Cloud & Big Data Computing, Internet of People and Smart City Innovation (Smartworld/SCALCOM/UIC/ATC/CBDcom/IOP/SCI ), 1–6.

Charlier, C. (2022). Revised EBA guidelines: How banks and financial institutions can leverage data in loan origination and monitoring processes .

Chen, L., Yao, X., Liu, Y., Zhu, Y., Chen, W., Zhao, X., & Chi, T. (2020). Measuring impacts of urban environmental elements on housing prices based on multisource data—a case study of Shanghai, China. ISPRS International Journal of Geo-Information , 9 (2), 106.

Chen, M., Liu, Y., Arribas-Bel, D., & Singleton, A. (2022b). Assessing the value of user-generated images of urban surroundings for house price estimation. Landscape and Urban Planning , 226 , 104486.

Chen, C., Lin, K., Rudin, C., Shaposhnik, Y., Wang, S., & Wang, T. (2022a). A holistic approach to interpretability in financial lending: Models, visualizations, and summary-explanations. Decision Support Systems , 152 , 113647.

Chou, Y. L., Moreira, C., Bruza, P., Ouyang, C., & Jorge, J. (2022). Counterfactuals and causability in explainable artificial intelligence: Theory, algorithms, and applications. Information Fusion , 81 , 59–83.

Clapp, J. M. (2003). A semiparametric method for valuing residential locations: Application to automated valuation. The Journal of Real Estate Finance and Economics , 27 (3), 303–320.

Cordera, R., Coppola, P., dell’Olio, L., & Ibeas, Á. (2019). The impact of accessibility by public transport on real estate values: A comparison between the cities of Rome and Santander. Transportation Research Part A: Policy and Practice , 125 , 308–319.

D’Amato, V., Di Lorenzo, E., Haberman, S. (2019). Pension schemes versus real estate. Annals of Operations Research , 1–13.

Deppner, J., von Ahlefeldt-Dehn, B., Beracha, E., & Schaefers, W. (2023). Boosting the accuracy of commercial real estate appraisals: An interpretable machine learning approach. The Journal of Real Estate Finance and Economics , 1–38.

Dimopoulos, T., & Bakas, N. (2019). Sensitivity analysis of machine learning models for the mass appraisal of real estate. Case study of residential units in Nicosia, Cyprus. Remote Sensing , 11 (24), 3047.

European Banking Authority (2020). Guidelines on Loan Origination and Monitoring .

Ferrettini, G., Escriva, E., Aligon, J., Excoffier, J. B., & Soulé-Dupuy, C. (2022). Coalitional strategies for efficient individual prediction explanation. Information Systems Frontiers , 24 (1), 49–75.

Francke, M., & van de Minne, A. (2024). Combining machine learning and econometrics: Application to commercial real estate prices. Real Estate Economics .

Frayne, C., Szczypińska, A., Vašíček, B., & Zeugner, S. (2022). Housing Market Developments in the Euro Area: Focus on Housing Affordability . Publications Office of the European Union.

Friedman, J. H. (2001). Greedy function approximation: A gradient boosting machine. Annals of Statistics , 1189–1232.

Gevrey, M., Dimopoulos, I., & Lek, S. (2003). Review and comparison of methods to study the contribution of variables in artificial neural network models. Ecological Modelling , 160 (3), 249–264.

Gibilaro, L., & Mattarocci, G. (2018). Peer-to-peer lending and real estate mortgages: Evidence from United Kingdom. Journal of European Real Estate Research .

Guliker, E., Folmer, E., & van Sinderen, M. (2022). Spatial determinants of Real Estate appraisals in the Netherlands: A Machine Learning Approach. ISPRS International Journal of Geo-Information , 11 (2), 125.

Gupta, R., Marfatia, H. A., Pierdzioch, C., & Salisu, A. A. (2022). Machine learning predictions of Housing Market synchronization across US States: The role of uncertainty. The Journal of Real Estate Finance and Economics , 64 (4), 523–545. https://doi.org/10.1007/s11146-020-09813-1

Hjort, A., Pensar, J., Scheel, I., & Sommervoll, D. E. (2022). House price prediction with gradient boosted trees under different loss functions. Journal of Property Research , 39 (4), 338–364.

Holstein, K., De-Arteaga, M., Tumati, L., & Cheng, Y. (2023). Toward supporting perceptual complementarity in human-AI collaboration via reflection on unobservables. Proceedings of the ACM on Human-Computer Interaction , 7 (CSCW1), 1–20.

Hurley, A. K., & Sweeney, J. (2022). Irish property price estimation using a flexible Geo-spatial Smoothing Approach: What is the impact of an address? The Journal of Real Estate Finance and Economics . https://doi.org/10.1007/s11146-022-09888-y

Iban, M. C. (2022). An explainable model for the mass appraisal of residences: The application of tree-based machine learning algorithms and interpretation of value determinants. Habitat International , 128 , 102660.

Ibrahim, H., Salama, A. M., Wiedmann, F., & Awwaad, R. (2016). A comparative assessment of housing dynamics In Abu Dhabi and Doha .

Kauko, T. O. M., Hooimeijer, P., & Hakfoort, J. (2002). Capturing housing market segmentation: An alternative approach based on neural network modelling. Housing Studies , 17 (6), 875–894.

Koetter, M., & Poghosyan, T. (2010). Real estate prices and bank stability. Journal of Banking & Finance , 34 (6), 1129–1138.

Kumar, S., Talasila, V., & Pasumarthy, R. (2019). A novel architecture to identify locations for real Estate Investment. International Journal of Information Management , 102012.

Lee, C. (2022). Training and interpreting machine learning models: Application in Property Tax Assessment. Real Estate Management and Valuation , 30 (1), 13–22.

Li, L., & Chau, K. W. (2019). What motivates a developer to sell before completion? The Journal of Real Estate Finance and Economics , 59 , 209–232.

Li, S., Jiang, Y., Ke, S., Nie, K., & Wu, C. (2021). Understanding the effects of influential factors on housing prices by combining extreme gradient boosting and a hedonic price model (XGBoost-HPM). Land , 10 (5), 533.

Lorenz, F., Willwersch, J., Cajias, M., & Fuerst, F. (2023). Interpretable machine learning for real estate market analysis. Real Estate Economics , 51 (5), 1178–1208.

Lundberg, S. M., & Lee, S. I. (2017). A unified approach to interpreting model predictions. Advances in Neural Information Processing Systems , 30 .

Mayer, M., Bourassa, S. C., Hoesli, M., & Scognamiglio, D. F. (2018). Estimation and updating methods for hedonic valuation. Swiss Finance Institute Research Paper , 18 – 76 .

Mayer, M., Bourassa, S. C., Hoesli, M., & Scognamiglio, D. (2022). Machine learning applications to land and structure valuation. Journal of Risk and Financial Management , 15 (5), 193.

McCluskey, W. J., & Borst, R. A. (2011). Detecting and validating residential housing submarkets. International Journal of Housing Markets and Analysis .

Murdoch, W. J., Singh, C., Kumbier, K., Abbasi-Asl, R., & Yu, B. (2019). Definitions, methods, and applications in interpretable machine learning. Proceedings of the National Academy of Sciences , 116 (44), 22071–22080.

Nyawa, S., Gnekpe, C., & Tchuente, D. (2023). Transparent machine learning models for predicting decisions to undertake energy retrofits in residential buildings. Annals of Operations Research , 1–29.

Oust, A., Westgaard, S., Waage, J. E., & Yemane, N. K. (2023). Assessing the explanatory power of dwelling condition in automated valuation models. Journal of Real Estate Research , 1–27.

Ozhegov, E. M., & Ozhegova, A. (2022). Distance in geographic and characteristics space for real estate pricing. International Journal of Housing Markets and Analysis , 15 (5), 938–952.

Pan, K. L., Teng, H. J., Lin, S. Y., & Cheng, Y. E. (2021). An empirical method for decomposing the contributions of Land and Building values to Housing Value. International Real Estate Review , 24 (3).

Park, S., & Yang, J. S. (2022). Interpretable deep learning LSTM model for intelligent economic decision-making. Knowledge-Based Systems , 248 , 108907.

Pavlov, A., & Wachter, S. (2011). Subprime lending and real estate prices. Real Estate Economics , 39 (1), 1–17.

Pedersen, A. M. B., Weissensteiner, A., & Poulsen, R. (2013). Financial planning for young households. Annals of Operations Research , 205 , 55–73.

Pérez-Rave, J. I., Correa-Morales, J. C., & González-Echavarría, F. (2019). A machine learning approach to big data regression analysis of real estate prices for inferential and predictive purposes. Journal of Property Research , 36 (1), 59–96.

Rampini, L., & Cecconi, F. R. (2021). Artificial intelligence algorithms to predict Italian real estate market prices. Journal of Property Investment & Finance .

Renigier-Biłozor, M., Źróbek, S., & Walacik, M. (2022). Modern technologies in the real estate market—opponents vs. proponents of their use: Does New Category of Value solve the Problem? Sustainability , 14 (20), 13403.

Ribeiro, M. T., Singh, S., & Guestrin, C. (2016). Why should i trust you? Explaining the predictions of any classifier. Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining , 1135–1144.

Rico-Juan, J. R., & de La Paz, P. T. (2021). Machine learning with explainability or spatial hedonics tools? An analysis of the asking prices in the housing market in Alicante, Spain. Expert Systems with Applications , 171 , 114590.

Senoner, J., Netland, T., & Feuerriegel, S. (2022). Using explainable artificial intelligence to improve process quality: Evidence from semiconductor manufacturing. Management Science , 68 (8), 5704–5723.

Sing, T. F., Yang, J. J., & Yu, S. M. (2022). Boosted tree ensembles for Artificial Intelligence Based Automated Valuation models (AI-AVM). The Journal of Real Estate Finance and Economics , 65 (4), 649–674. https://doi.org/10.1007/s11146-021-09861-1

Sisman, S., & Aydinoglu, A. C. (2022). A modelling approach with geographically weighted regression methods for determining geographic variation and influencing factors in housing price: A case in Istanbul. Land Use Policy , 119 , 106183.

Steurer, M., Hill, R. J., & Pfeifer, N. (2021). Metrics for evaluating the performance of machine learning based automated valuation models. Journal of Property Research , 38 (2), 99–129.

Tchuente, D., & Nyawa, S. (2022). Real estate price estimation in French cities using geocoding and machine learning. Annals of Operations Research , 308 (1), 571–608.

Tchuente, D., Lonlac, J., & Kamsu-Foguem, B. (2024). A methodological and theoretical framework for implementing explainable artificial intelligence (XAI) in business applications. Computers in Industry , 155 , 104044.

Tyvimaa, T., & Kamruzzaman, M. (2019). The effect of young, single person households on apartment prices: An instrument variable approach. Journal of Housing and the Built Environment , 34 , 91–109.

Valier, A. (2020). Who performs better? AVMs vs hedonic models. Journal of Property Investment & Finance .

Wan, W. X., & Lindenthal, T. (2023). Testing machine learning systems in real estate. Real Estate Economics , 51 (3), 754–778.

Wang, D., & Li, V. J. (2019). Mass Appraisal models of Real Estate in the 21st Century: A systematic literature review. Sustainability , 11 (24), 7006.

Wang, L., Gopal, R., Shankar, R., & Pancras, J. (2022). Forecasting venue popularity on location-based services using interpretable machine learning. Production and Operations Management .

Yoshida, T., Murakami, D., & Seya, H. (2022). Spatial prediction of apartment Rent using regression-based and machine learning-based approaches with a large dataset. The Journal of Real Estate Finance and Economics . https://doi.org/10.1007/s11146-022-09929-6

Zhang, P. (2019). A novel feature selection method based on global sensitivity analysis with application in machine learning-based prediction model. Applied Soft Computing , 85 , 105859.

Zhang, S., Zhang, C., & Yang, Q. (2003). Data preparation for data mining. Applied Artificial Intelligence , 17 (5–6), 375–381.

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Tchuente, D. Real Estate Automated Valuation Model with Explainable Artificial Intelligence Based on Shapley Values. J Real Estate Finan Econ (2024). https://doi.org/10.1007/s11146-024-09998-9

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Distinguishing between different types of journal articles

When writing a paper or conducting academic research, you’ll come across many different types of sources, including periodical articles. Periodical articles can be comprised of news accounts, opinion, commentary, scholarly analysis, and/or reports of research findings. There are three main types of periodicals that you will encounter: scholarly/academic, trade, and popular.  The chart below will help you identify which type of periodical your article comes from.

Text and chart adapted from the WSU University Libraries' How to Distinguish Between Types of Periodicals  and Types of Periodicals guides

What makes information peer-reviewed vs. scholarly vs. non-scholarly? Which type of source should I use?

• What makes information peer-reviewed vs. scholarly vs. non-scholarly?
• Which type of source should I use?

There is a nuanced distinction between peer-review and scholarship, which typically doesn't matter when evaluating sources for possible citation in your own work.  Peer-review is a process through which editors of a journal have other experts in the field evaluate articles submitted to the journal for possible publication.  Different journals have different ways of defining an expert in the field.  Scholarly works, by contrast have an editorial process, but this process does not involve expert peer-reviewers.  Rather, one or more editors, who are themselves often highly decorated scholars in a field, evaluate submissions for possible publication.  This editorial process can be more economically driven than a peer-review process, with a greater emphasis on marketing and selling the published material, but as a general rule this distinction is trivial with regard to evaluating information for possible citation in your own work.

What is perhaps a more salient way of thinking about the peer-review / scholarship distinction is to recognize that while peer-reviewed information is typically highly authoritative, and is generally considered "good" information, the absence of a peer-review process doesn't automatically make information "bad."  More specifically, the only thing the absence of a peer-review process means is that information published in this manner is not peer-reviewed.  Nothing more.  Information that falls into this category is sometimes referred to as "non-scholarly" information -- but again, that doesn't mean this information is somehow necessarily problematic.

Where does that leave you in terms of deciding what type of information to use in producing your own work?  That is a highly individual decision that you must make.  The Which type of source should I use?  tab in this box offers further guidance on answering this question, though it is important to be aware that many WSU instructors will only consider peer-reviewed sources to be acceptable in the coursework you turn in .  You can ask your instructor for his or her thoughts on the types of sources s/he will accept in student work.

Image:  Martin Grater. (2017, Nov. 1). Deep Thought. Retrieved from https://www.flickr.com/photos/152721954@N05/24304490568/. Used under the Creative Commons License.

Your topic and research question or thesis statement will guide you on which resources are best.  Sources can be defined as primary, secondary and tertiary levels away from an event or original idea. Researchers may want to start with tertiary or secondary source for background information. Learning more about a topic will help most researchers make better use of primary sources.

While articles from scholarly journals are often the most prominent of the sources you will consider incorporating into your coursework, they are not the only sources available to you.  Which sources are most appropriate to your research is a direct consequence of they type of research question you decide to address.  In other words, while most university-level papers will require you to reference scholarly sources, not all will.  A student in an English course writing a paper analyzing Bob Dylan's lyrics, for example, may find an interview with Dylan published in Rolling Stone magazine a useful source to cite alongside other scholarly works of literary criticism.

The WSU University Libraries' What Sources Should I Use? handout, as well as the other sub-tabs under the  Evaluating information  section of this guide (which is indeed the section you are currently viewing) offer further guidance on understanding and identifying scholarly resources, and comparing them against different criteria to evaluate if they will be of value to your research.  How many non-scholarly works (if any) you are at liberty to cite alongside scholarly ones is often a question to ask of your professor.  Some may not want you to cite any, whereas others may be ok with some non-scholarly works cited alongside scholarly ones.

Image:  Brett Woods. (2006, Jan. 6). Deep Thoughts. Retrieved from https://www.flickr.com/photos/brettanicus/87653641/. Used under the Creative Commons License.

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