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DOI Help: Digital Object Identifiers (DOIs)

Introduction.

For APA 7, you need to provide the digital object identifier (DOI) number for articles and ebooks when available. If an item does not have a DOI, the citation will look like the citation for a print resource. You no longer need to locate a journal homepage as part of your citation. 

The goal of this guide is to help you find the DOI for your reference citations. Specifically, this guide will cover:

• what DOIs are
• how to find DOIs

This guide will not cover how to correctly cite articles using APA style. For help with citation questions, please contact the Writing Center or refer to the Writing Center's resources on their website:

• Writing Center: Reference List: Electronic Source References
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What is a Digital Object Identifier (DOI)?

What is a doi.

Digital Object Identifiers, commonly shortened to DOIs, were invented to give each electronic, or digital, item a unique, persistent identifier. Any digital object can be assigned a DOI number, for example:

• academic journal articles 
• research reports 
• governmental reports
• conference proceedings
• media 

Who assigns DOIs?

The DOI creation process is governed and managed by the International DOI Foundation . DOI Registration agencies under the International DOI Foundation provide services and registration of DOI numbers. They are typically focused on specific geographic areas or types of content. For example, EIDR provides DOI numbers for movie and television content.

Crossref is one of the registration agencies for the International DOI Foundation. It assigns DOIs to scholarly research publications. These publications include journal articles, books, and conference proceedings.

What do DOIs look like?

All DOIs start with the number 10 followed by a period. This is an example:

10.1111/dome.12082

In APA 7, you format the DOIs as a URL, with "https://doi.org/" before the number. For example:

https://doi.org/ 10.1111/dome.12082

Things to know

There are a couple of important things to know about DOIs.

• Not every article or resources has a DOI .
• Both peer-reviewed and non-peer-reviewed articles can have DOIs.
• Quick Answer: What is peer review?

Look at the article

The first place to look for a DOI is the article itself. Many publishers will include the DOI somewhere on the first page of the article. Here are a few examples:

Journal of Social Issues, Vol. 71, No. 3, 2015, pp. 441-452 doi: 10.1111/josi.12122

DOI: 10.111/dome.12082 Digest of Middle East Student - Volume 25, Number 1 - Pages 36-51 © 2016 Policy Studies Organization. Published by Wiley Periodicals, Inc.  

Look at information about the article

Library databases include information about an article. If an article has a DOI, you may find it listed in the information about the article.

Different databases call these article information sections different things. They may be called Detailed Record, Abstract, Abstract/Details, or you may need to click on the article title to see more information about the article. 

If you don't see the DOI on the article itself, look around the page in the database to see if the DOI is listed.

Search Crossref

You can look for a DOI using the Crossref website. Crossref is one of the organizations that assigns DOIs, with a focus on research articles. If Crossref doesn't have a DOI for an article, you can safely assume that the article doesn't have one. 

Follow these steps to search Crossref for an article's DOI: 

• Go to the Crossref.org website .

• Press the Enter key to run your search.

Note: The actual DOI begins with 10. For APA 7, include "https://doi.org/" in front of the number. To learn more about what form of the DOI to use in a reference citation, please see these Quick Answers from the Writing Center:

• Quick Answer: Should I include a hyperlink in a DOI?
• Quick Answer: Can I use the DOI format provided by library databases?

Searches in Crossref always bring back results, even if the article you are looking for isn't there. If you don't see your article in the first page of results, here are a few things to try.

• For example:  "Storytelling for social change" AND Winskell
• Use the  Year  limiter in the left column to limit results to only the year in which your item was published.

If you still don't find the article you are looking for in Crossref, you can safely assume that it does not have a DOI.

More information

• DOI, Other URL, or No Retrieval Information? clickable flowchart
• Quick Answer: How do I cite an article with a DOI?
• Quick Answer: How do I cite an article without a DOI?
• Quick Answer: How do I find an article by DOI using Google Scholar?
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Articles Web of Science: Digital Object Identifier (DOI) search

Web of science: digital object identifier (doi) search, may 20, 2022 • knowledge, information.

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What is a DOI (digital object identifier)?

A DOI is a character string that can be assigned to an online article, book, or other source. If the location of the source changes, the DOI remains stable, which allows readers to locate the source. When you use the APA citation style, you should always include the DOI if one has been assigned to the source you are citing.

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Digital Object Identifiers Digital Object Identifiers

A Digital Object Identifier (DOI) is a number used to identify an electronic journal article or other online intellectual property. Because DOIs remain stable even if an article’s host publication changes platforms, names, or publishers, they provide permanent and reliable links for citation, sharing, and discovery. When properly implemented in citations and references, DOIs can provide readers and researchers instant access to the sources they’re looking for.

DOIs are designated and administered by the  CrossRef  organization, which is operated by the independent, nonprofit Publishers International Linking Association (PILA). Since their first implementation in 1999, DOIs have quickly become the backbone of CrossRef’s mandate to provide a “digital switchboard” that links all scholarly information in electronic form. Implementing DOIs for your journals and other online publications is an effective and respected way to increase access and exposure.

Citing with DOIs

In order for the digital switchboard to work, DOIs in URL format need to be included in citations and references. In fact, CrossRef requires journals that use DOIs for their own articles to include DOIs in their footnotes and bibliographies. This requirement applies only to content published after the publisher or journal has joined CrossRef. Below are common examples.

Chicago Manual of Style:

Kossinets, Gueorgi, and Duncan J. Watts. “Origins of Homophily in an Evolving Social Network.”  American Journal of Sociology  115 (2009): 405–50. Accessed February 28, 2010. https://doi.org/10.1086/599247.

Wooldridge, M.B., & Shapka, J. (2012). Playing with technology: Mother-toddler interaction scores lower during play with electronic toys.  Journal of Applied Developmental Psychology, 33 (5), 211-218. https://doi.org/10.1016/j.appdev.2012.05.005

Note that the full URL, not simply the digits of the DOI, should be included in the reference. Most style guides now recommend inclusion of DOIs in citations wherever they’re available, and authors should be instructed to follow this recommendation. If your journal is a member of CrossRef, then by extension, authors are members as well. Ultimately, however, it is the editors’ responsibility to ensure that DOIs are included in references and citations to any article that has a DOI. Fortunately, CrossRef provides strong tools to help authors and editors to meet these requirements.

Adding DOIs to Journals in Digital Commons

If a Digital Commons journal would like to include DOIs with its content, please ask your consultant about the latest options.

CrossRef offers a wealth of information and technical resources on DOIs. We particularly recommend the following:

• See the CrossRef DOI Display Guidelines ( https://www.crossref.org/display-guidelines/ ) for more details, examples, and instructions on displaying your own content’s DOIs and citing DOIs in your footnotes and references
• The Simple Text Query Form retrieves DOIs for single bibliographic entries or a complete reference list:  https://doi.crossref.org/simpleTextQuery

Resource for transforming Digital Commons XML to Crossref XML:

• Mortimore, Jeffrey M., “XSL File for Transformation of bepress Digital Commons Issue-Level Journal XML to Crossref 4.4.2 XML” (2020).  Faculty Datasets . 7.  https://digitalcommons.georgiasouthern.edu/data/7 )

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How to find a DOI?

Location of DOIs

How to include a doi in your citation, frequently asked questions about finding dois, related articles.

A digital object identifier , or DOI, refers to a handle that recognizes a unique object in the digital world. This label is assigned by the International Organization for Standardization (ISO) to different types of scholarly material, such as papers, journal articles, books, data sets, reports, government publications, and even videos.

A DOI should always be easily available in any source. Usually, you will find it on the first page, either in the header or somewhere close to the title.

Alternatively, you can also find it in the "About this article" or "Cite this article" sections.

If the DOI isn’t available, you can look it up on CrossRef.org by using the “Search Metadata” option. You just have to type in the source's title or author, and it will direct you to its DOI.

The correct format for adding a DOI to your citations will depend on the citation style you use. Here is a list of citation examples with DOIs in major formatting styles:

Hofman, C. A., & Rick, T. C. (2018). Ancient Biological Invasions and Island Ecosystems: Tracking Translocations of Wild Plants and Animals. Journal of Archeological Research , 26 (1), 65–115. https://doi.org/10.1007/s10814-017-9105-3

Hofman, Courtney A., and Torben C. Rick. “Ancient Biological Invasions and Island Ecosystems: Tracking Translocations of Wild Plants and Animals.”  Journal of Archaeological Research , vol. 26, no. 1, 2018, pp. 65–115, doi:10.1007/s10814-017-9105-3.

Hofman, Courtney A., and Torben C. Rick. 2018. “Ancient Biological Invasions and Island Ecosystems: Tracking Translocations of Wild Plants and Animals.”  Journal of Archaeological Research  26 (1): 65–115. https://doi.org/10.1007/s10814-017-9105-3.

The preferred format of a DOI in a citation is using https://doi.org/ followed by the alphanumeric string. It also depends on the style; as you can see that MLA prefers using doi:xxx. Make sure to double-check the citation style you use before adding the DOI.

Tip: Instead of manually adding citations with DOIs to your documents, which is error-prone and strenuous, consider using a reference manager like Paperpile to format and organize your citations. Paperpile allows you to save and organize your citations for later use and cite them in thousands of citation styles directly in Google Docs, Microsoft Word, or LaTeX, including the DOI:

The preferred format of a DOI in a citation is using https://doi.org/ followed by the alphanumeric string. Of course, it depends on the style, as MLA prefers using doi:xxx. Make sure to double check the citation style you use before adding the DOI.

The International Organization for Standardization (ISO) is responsible for assigning DOIs to different types of scholarly material, such as papers, journal articles, books, data sets, reports, government publications, and even videos.

URLs and DOIs are not the same. A DOI is a unique alphanumeric identifier that labels digital material and pinpoints its location on the internet, whereas a URL is a digital locator.

DOIs were invented for a reason. These alphanumeric identifiers allow readers to locate specific material in the digital world. They also add credibility to your sources.

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How to find an article's DOI to include in a citation

A DOI (Digital Object Identifier) is a unique identifier that identifies digital objects. The object may change physical locations, but the DOI assigned to that object will never change. Journal publishers often assign DOIs to electronic copies of individual articles in their journals. Because the DOI insures findability for the e-journal article, many citation styles (APA, MLA, Chicago Manual of Style, Turabian, etc.) require the use of a DOI in a citation for e-journal content. Below are some methods that can be used to obtain DOIs:

• Go to http://www.crossref.org/ and follow the instructions provided there to search for a DOI using the article title and author's last name. If this method doesn't yield a DOI, don't assume that a DOI doesn't exist. Follow up with the next two options.  
• If a journal publisher uses DOIs, they will usually print the DOI somewhere on the first page of the article. Open the full-text source and look for the DOI on the article's first page, usually in the header or footer.  
• Some online resources, such as EBSCO databases, will supply DOIs in their citation formatter. View the full citation to see if a DOI is included.

DOI Pro Tip:

• Some articles won't have a DOI. The International DOI Foundation was created in 1998 but not all publishers immediately started assigning DOIs. The publisher Elsevier, for example, appears to have started using DOIs on all of their journal articles around 2003. So unless a publisher has retrospectively assigned DOIs to articles, articles published prior to 1998 are less likely to have DOIs. So, if you have tried all the suggestions above, but you still cannot find the DOI, it may be that your article does not have one.

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• What's a DOI?
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What is a DOI?

"doi" is an acronym that stands for "digital object identifier.".

Functionally, a DOI is a lengthy "sentence" of letters and numbers that serves to identify the unique online location of a particular journal article. This alphanumeric string of characters serves as a digital fingerprint for an article's life online, similar to a URL for a particular webpage.

Much like its title, author, and publication information, an article's DOI can be used to identify both a particular article  and  its set location on the internet. Although access to an article may change over time, its DOI will remain constant - so you'll always be able to find it as it lives out its digital lifespan. This is why it's important to include an article's DOI when citing it, so people reviewing your work can access your sources if they so choose.

For more information, please visit DOI.org and review the DOI Handbook - Introduction 1.5 (ISO 26324) .

How do i find an article's doi, i need to include a article's doi in my citation. where should i look.

Depending on the citation style you're using, you may be asked to include a DOI when making reference to, or citing, a specific item. If the item was published prior to 2000, it may not have a DOI attached to it (see the next tab). However, all current digitally-available items have an associated DOI that will be included in the item's catalog record, as well as on the publication itself.

As an example, this is a journal article published in the online edition of the  BMJ: British Medical Journal.  The publication is available to us through ProQuest, and you can see the article's catalog record below. The DOI is listed at the top of the record (red box).

The DOI will also be listed in the article's publication details, which should be available in the catalog record as well (you may need to scroll down the record to find the DOI; red box).

If the DOI is hyperlinked, this will serve as the main access point for the article's existence online. Clicking the hyperlink will automatically redirect you to a webpage where the article is available online.

Finally, the DOI is also listed on the published copy of the article (both for physical and electronic items). This is typically printed at the top or bottom of the article's first page, and will be preceded by the acronym "DOI" (red box).

What if my article doesn't have a DOI?

The short answer is, it may not..

Not all articles have associated DOIs, because many of them were published long before the digital age began. Although a good number of pre-digital scholarship has been made available in electronic format, this doesn't negate the fact that those items were originally published before DOIs were routinely assigned to scholarly articles (let alone created in the first place).

Sometimes, publishers, databases, and distributors will assign a retroactive DOI to an article wasn't originally published with one - meaning that the article's online "edition" will be given a DOI to demarcate its life online. But this isn't always the case. Some articles, regardless of their availability online, never receive a DOI.

But that's okay! If you come across an item that lacks a DOI, chances are it was published prior to the early 2000s, and was likely never assigned a DOI (retroactively or otherwise). Therefore, you can omit that information from your citation in good conscience.

So what do I do if my article doesn't have a DOI? Or what I'm just not sure?

There are two ways you can check for an article's DOI if you're not able to find it (or you're not sure it even has one).

You can visit Crossref.org , a website devoted to assisting scholars with research and reference efforts, including those related to publication and citation issues. Searching for the article by title, author, publication, etc. should provide specific publication information about the item in question. If a DOI is not included, you can confirm that there was no DOI ever assigned to the item, so you won't need to include it bibliographically.

If you're not sure about an item's DOI, try searching it in DOI.org . This website is the main hub of all things DOI, and maintains records of all items that have associated DOIs. Searching for an item by DOI should confirm that you have the correct identifier for the title in question.

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DOI stands for Document Object Identifier . This is a unique identifier that is assigned to an online journal article, online book or online book chapter. Most publishers assign these to their online content. A DOI can take you directly to an online resource, but the Library does not always have access at a publisher site. The DOI lookup links to any online access we have.

PMID is a unique identifier used in the PubMed database and can be used to look up abstracts in PubMed. The PMID lookup links to online access through the Library.

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Type or paste a DOI name, e.g., 10.10000/IJLMH.XXXXX, into the text box below. (Be sure to enter all of the characters before and after the slash. Do not include extra characters, or sentence punctuation marks.)

Clicking on a DOI link (try this one: https://doij.org/10.10000/IJLMH.12345) takes you to one or more current URLs or other services related to a single resource. If the URLs or services change over time, e.g., the resource moves, this same DOI will continue to resolve to the correct resources or services at their new locations.

DOIJ.ORG is established under the aegis of VidhiAagaz - India's Leading Journals Publisher, and provides the technical framework for generating Digital Object Identifiers to the Manuscripts published in the Subsidiary Journals. It generates a unique URLs and metadata for manuscripts published in the journals, and resolves the resource location. It is a permanent link to the published Object. Authors can resolve the DOI's generated by DOIJ on this website to check the details of Published Manuscript and verify the DOI's generated.

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CrossRef – the DOI search tool

Looking for the DOIs (Digital Object Identifiers) for your citations?  Crossref offers a DOI search for journal articles, books, and chapters.  Simply cut and paste the reference list into their search box.  The form will take any reference style, although it works most reliably with standard styles.

DOIs are used to provide a stable source for information about a digital object, including where they  can be found on the Internet. Information about a digital object may change over time, including where to find it, but its DOI name does not change.

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The DOI Handbook is the main source of information about the DOI System (DOI https://doi.org/10.1000/182 identifies the latest current version of the handbook). It describes the DOI System at business and technical levels and assists the community in understanding the system and Registration Agencies (RA) in providing services based on the system.

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• 29 April 2024

How reliable is this research? Tool flags papers discussed on PubPeer

• Dalmeet Singh Chawla

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RedacTek’s tool alerts users to PubPeer discussions, and indicates when a study, or the papers that it cites, has been retracted. Credit: deepblue4you/Getty

A free online tool released earlier this month alerts researchers if a paper cites studies that are mentioned on the website PubPeer , a forum scientists often use to raise integrity concerns surrounding published papers.

Studies are usually flagged on PubPeer when readers have suspicions, for example about image manipulation , plagiarism , data fabrication or artificial intelligence (AI)-generated text . PubPeer already offers its own browser plug-in that alerts users if a study that they are reading has been posted on the site. The new tool, a plug-in released on 13 April by RedacTek , based in Oakland, California, goes further — it searches through reference lists for papers that have been flagged. The software pulls information from many sources, including PubPeer’s database; data from the digital-infrastructure organization Crossref, which assigns digital object identifiers to articles; and OpenAlex , a free index of hundreds of millions of scientific documents.

It’s important to track mentions of referenced articles on PubPeer, says Jodi Schneider, an information scientist at the University of Illinois Urbana-Champaign, who has tried out the RedacTek plug-in. “Not every single reference that’s in the bibliography matters, but some of them do,” she adds. “When you see a large number of problems in somebody’s bibliography, that just calls everything into question.”

The aim of the tool is to flag potential problems with studies to researchers early on, to reduce the circulation of poor-quality science, says RedacTek founder Rick Meyler, who is based in Emeryville, California. Future versions might also use AI to automatically clarify whether the PubPeer comments on a paper are positive or negative, he adds.

Third-generation retractions

As well as flagging PubPeer discussions, the plug-in alerts users if a study, or a paper that it cites, has been retracted. There are existing tools that alert academics about retracted citations ; some can do this during the writing process, so that researchers are aware of the publication status of studies when constructing bibliographies. But with the new tool, users can opt in to receive notifications about further ‘generations’ of retractions — alerts cover not only the study that they are reading, but also the papers it cites, articles cited by those references and even papers cited by the secondary references.

The software also calculates a ‘retraction association value’ for studies, a metric that measures the extent to which the paper is associated with science that has been withdrawn from the literature. As well as informing individual researchers, the plug-in could help scholarly publishers to keep tabs on their own journals, Meyler says, because it allows users to filter by publication.

In its ‘paper scorecard’, the tool also flags any papers in the three generations of referenced studies in which more than 25% of papers in the bibliography are self-citations — references by authors to their previous works.

Future versions could highlight whether papers cited retracted studies before or after the retraction was issued, notes Meyler, or whether mentions of such studies acknowledge the retraction. That would be useful, says Schneider, who co-authored a 2020 analysis that found that as little as 4% of citations to retracted studies note that the referenced paper has been retracted 1 .

Meyler says that RedacTek is currently in talks with the scholarly-services firm Cabell’s International in Beaumont, Texas, which maintains pay-to-view lists of suspected predatory journals . These publish articles without running proper quality checks for issues such as plagiarism, but still collect authors’ fees. The plan is to use these lists to improve the tool so that it can also automatically flag any cited papers that are published in such journals.

Nature 629 , 271-272 (2024)

doi: https://doi.org/10.1038/d41586-024-01247-6

Schneider, J., Ye, D., Hill, A. M. & Whitehorn, A. S. Scientometrics 125 , 2877–2913 (2020).

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We report highly pathogenic avian influenza A(H5N1) virus in dairy cattle and cats in Kansas and Texas, United States, which reflects the continued spread of clade 2.3.4.4b viruses that entered the country in late 2021. Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows. Cow-to-cow transmission appears to have occurred because infections were observed in cattle on Michigan, Idaho, and Ohio farms where avian influenza virus–infected cows were transported. Although the US Food and Drug Administration has indicated the commercial milk supply remains safe, the detection of influenza virus in unpasteurized bovine milk is a concern because of potential cross-species transmission. Continued surveillance of highly pathogenic avian influenza viruses in domestic production animals is needed to prevent cross-species and mammal-to-mammal transmission.

Highly pathogenic avian influenza (HPAI) viruses pose a threat to wild birds and poultry globally, and HPAI H5N1 viruses are of even greater concern because of their frequent spillover into mammals. In late 2021, the Eurasian strain of H5N1 (clade 2.3.4.4b) was detected in North America ( 1 , 2 ) and initiated an outbreak that continued into 2024. Spillover detections and deaths from this clade have been reported in both terrestrial and marine mammals in the United States ( 3 , 4 ). The detection of HPAI H5N1 clade 2.3.4.4b virus in severe cases of human disease in Ecuador ( 5 ) and Chile ( 6 ) raises further concerns regarding the pandemic potential of specific HPAI viruses.

In February 2024, veterinarians were alerted to a syndrome occurring in lactating dairy cattle in the panhandle region of northern Texas. Nonspecific illness accompanied by reduced feed intake and rumination and an abrupt drop in milk production developed in affected animals. The milk from most affected cows had a thickened, creamy yellow appearance similar to colostrum. On affected farms, incidence appeared to peak 4–6 days after the first animals were affected and then tapered off within 10–14 days; afterward, most animals were slowly returned to regular milking. Clinical signs were commonly reported in multiparous cows during middle to late lactation; ≈10%–15% illness and minimal death of cattle were observed on affected farms. Initial submissions of blood, urine, feces, milk, and nasal swab samples and postmortem tissues to regional diagnostic laboratories did not reveal a consistent, specific cause for reduced milk production. Milk cultures were often negative, and serum chemistry testing showed mildly increased aspartate aminotransferase, gamma-glutamyl transferase, creatinine kinase, and bilirubin values, whereas complete blood counts showed variable anemia and leukocytopenia.

In early March 2024, similar clinical cases were reported in dairy cattle in southwestern Kansas and northeastern New Mexico; deaths of wild birds and domestic cats were also observed within affected sites in the Texas panhandle. In > 1 dairy farms in Texas, deaths occurred in domestic cats fed raw colostrum and milk from sick cows that were in the hospital parlor. Antemortem clinical signs in affected cats were depressed mental state, stiff body movements, ataxia, blindness, circling, and copious oculonasal discharge. Neurologic exams of affected cats revealed the absence of menace reflexes and pupillary light responses with a weak blink response.

On March 21, 2024, milk, serum, and fresh and fixed tissue samples from cattle located in affected dairies in Texas and 2 deceased cats from an affected Texas dairy farm were received at the Iowa State University Veterinary Diagnostic Laboratory (ISUVDL; Ames, IA, USA). The next day, similar sets of samples were received from cattle located in affected dairies in Kansas. Milk and tissue samples from cattle and tissue samples from the cats tested positive for influenza A virus (IAV) by screening PCR, which was confirmed and characterized as HPAI H5N1 virus by the US Department of Agriculture National Veterinary Services Laboratory. Detection led to an initial press release by the US Department of Agriculture Animal and Plant Health Inspection Service on March 25, 2024, confirming HPAI virus in dairy cattle ( 7 ). We report the characterizations performed at the ISUVDL for HPAI H5N1 viruses infecting cattle and cats in Kansas and Texas.

Materials and Methods

Milk samples (cases 2–5) and fresh and formalin-fixed tissues (cases 1, 3–5) from dairy cattle were received at the ISUVDL from Texas on March 21 and from Kansas on March 22, 2024. The cattle exhibited nonspecific illness and reduced lactation, as described previously. The tissue samples for diagnostic testing came from 3 cows that were euthanized and 3 that died naturally; all postmortem examinations were performed on the premises of affected farms.

The bodies of 2 adult domestic shorthaired cats from a north Texas dairy farm were received at the ISUVDL for a complete postmortem examination on March 21, 2024. The cats were found dead with no apparent signs of injury and were from a resident population of ≈24 domestic cats that had been fed milk from sick cows. Clinical disease in cows on that farm was first noted on March 16; the cats became sick on March 17, and several cats died in a cluster during March 19–20. In total, >50% of the cats at that dairy became ill and died. We collected cerebrum, cerebellum, eye, lung, heart, spleen, liver, lymph node, and kidney tissue samples from the cats and placed them in 10% neutral-buffered formalin for histopathology.

At ISUVDL, we trimmed, embedded in paraffin, and processed formalin-fixed tissues from affected cattle and cats for hematoxylin/eosin staining and histologic evaluation. For immunohistochemistry (IHC), we prepared 4-µm–thick sections from paraffin-embedded tissues, placed them on Superfrost Plus slides (VWR, https://www.vwr.com ), and dried them for 20 minutes at 60°C. We used a Ventana Discovery Ultra IHC/ISH research platform (Roche, https://www.roche.com ) for deparaffinization until and including counterstaining. We obtained all products except the primary antibody from Roche. Automated deparaffination was followed by enzymatic digestion with protease 1 for 8 minutes at 37°C and endogenous peroxidase blocking. We obtained the primary influenza A virus antibody from the hybridoma cell line H16-L10–4R5 (ATCC, https://www.atcc.org ) and diluted at 1:100 in Discovery PSS diluent; we incubated sections with antibody for 32 minutes at room temperature. Next, we incubated the sections with a hapten-labeled conjugate, Discovery anti-mouse HQ, for 16 minutes at 37°C followed by a 16-minute incubation with the horse radish peroxidase conjugate, Discovery anti-HQ HRP. We used a ChromoMap DAB kit for antigen visualization, followed by counterstaining with hematoxylin and then bluing. Positive controls were sections of IAV-positive swine lung. Negative controls were sections of brain, lung, and eyes from cats not infected with IAV.

We diluted milk samples 1:3 vol/vol in phosphate buffered saline, pH 7.4 (Gibco/Thermo Fisher Scientific, https://www.thermofisher.com ) by mixing 1 unit volume of milk and 3 unit volumes of phosphate buffered saline. We prepared 10% homogenates of mammary glands, brains, lungs, spleens, and lymph nodes in Earle’s balanced salt solution (Sigma-Aldrich, https://www.sigmaaldrich.com ). Processing was not necessary for ocular fluid, rumen content, or serum samples. After processing, we extracted samples according to a National Animal Health Laboratory Network (NAHLN) protocol that had 2 NAHLN-approved deviations for ISUVDL consisting of the MagMax Viral RNA Isolation Kit for 100 µL sample volumes and a Kingfisher Flex instrument (both Thermo Fisher Scientific).

We performed real-time reverse transcription PCR (rRT-PCR) by using an NAHLN-approved assay with 1 deviation, which was the VetMAX-Gold SIV Detection kit (Thermo Fisher Scientific), to screen for the presence of IAV RNA. We tested samples along with the VetMAX XENO Internal Positive Control to monitor the possible presence of PCR inhibitors. Each rRT-PCR 96-well plate had 2 positive amplification controls, 2 negative amplification controls, 1 positive extraction control, and 1 negative extraction control. We ran the rRT-PCR on an ABI 7500 Fast thermocycler and analyzed data with Design and Analysis Software 2.7.0 (both Thermo Fisher Scientific). We considered samples with cycle threshold (Ct) values <40.0 to be positive for virus.

After the screening rRT-PCR, we analyzed IAV RNA–positive samples for the H5 subtype and H5 clade 2.3.4.4b by using the same RNA extraction and NAHLN-approved rRT-PCR protocols as described previously, according to standard operating procedures. We performed PCR on the ABI 7500 Fast thermocycler by using appropriate controls to detect H5-specific IAV. We considered samples with Ct values <40.0 to be positive for the IAV H5 subtype.

We conducted genomic sequencing of 2 milk samples from infected dairy cattle from Texas and 2 tissue samples (lung and brain) from cats that died at a different Texas dairy. We subjected the whole-genome sequencing data to bioinformatics analysis to assemble the 8 different IAV segment sequences according to previously described methods ( 8 ). We used the hemagglutinin (HA) and neuraminidase (NA) sequences for phylogenetic analysis. We obtained reference sequences for the HA and NA segments of IAV H5 clade 2.3.4.4 from publicly available databases, including GISAID ( https://www.gisaid.org ) and GenBank. We aligned the sequences by using MAFFT version 7.520 software ( https://mafft.cbrc.jp/alignment/server/index.html ) to create multiple sequence alignments for subsequent phylogenetic analysis. We used IQTree2 ( https://github.com/iqtree/iqtree2 ) to construct the phylogenetic tree from the aligned sequences. The software was configured to automatically identify the optimal substitution model by using the ModelFinder Plus option, ensuring the selection of the most suitable model for the dataset and, thereby, improving the accuracy of the reconstructed tree. We visualized the resulting phylogenetic tree by using iTOL ( https://itol.embl.de ), a web-based platform for interactive tree exploration and annotation.

Gross Lesions in Cows and Cats

All cows were in good body condition with adequate rumen fill and no external indications of disease. Postmortem examinations of the affected dairy cows revealed firm mammary glands typical of mastitis; however, mammary gland lesions were not consistent. Two cows that were acutely ill before postmortem examination had grossly normal milk and no abnormal mammary gland lesions. The gastrointestinal tract of some cows had small abomasal ulcers and shallow linear erosions of the intestines, but those observations were also not consistent in all animals. The colon contents were brown and sticky, suggesting moderate dehydration. The feces contained feed particles that appeared to have undergone minimal ruminal fermentation. The rumen contents had normal color and appearance but appeared to have undergone minimal fermentation.

The 2 adult cats (1 intact male, 1 intact female) received at the ISUVDL were in adequate body and postmortem condition. External examination was unremarkable. Mild hemorrhages were observed in the subcutaneous tissues over the dorsal skull, and multifocal meningeal hemorrhages were observed in the cerebrums of both cats. The gastrointestinal tracts were empty, and no other gross lesions were observed.

Microscopic Lesions in Cows and Cats

Figure 1 . Mammary gland lesions in cattle in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. A, B) Mammary gland...

The chief microscopic lesion observed in affected cows was moderate acute multifocal neutrophilic mastitis ( Figure 1 ); however, mammary glands were not received from every cow. Three cows had mild neutrophilic or lymphocytic hepatitis. Because they were adult cattle, other observed microscopic lesions (e.g., mild lymphoplasmacytic interstitial nephritis and mild to moderate lymphocytic abomasitis) were presumed to be nonspecific, age-related changes. We did not observe major lesions in the other evaluated tissues. We performed IHC for IAV antigen on all evaluated tissues; the only tissues with positive immunoreactivity were mastitic mammary glands from 2 cows that showed nuclear and cytoplasmic labeling of alveolar epithelial cells and cells within lumina ( Figure 1 ) and multifocal germinal centers within a lymph node from 1 cow ( Table 1 ).

Figure 2 . Lesions in cat tissues in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Tissue sections were stained with...

Both cats had microscopic lesions consistent with severe systemic virus infection, including severe subacute multifocal necrotizing and lymphocytic meningoencephalitis with vasculitis and neuronal necrosis, moderate subacute multifocal necrotizing and lymphocytic interstitial pneumonia, moderate to severe subacute multifocal necrotizing and lymphohistiocytic myocarditis, and moderate subacute multifocal lymphoplasmacytic chorioretinitis with ganglion cell necrosis and attenuation of the internal plexiform and nuclear layers ( Table 2 ; Figure 2 ). We performed IHC for IAV antigen on multiple tissues (brain, eye, lung, heart, spleen, liver, and kidney). We detected positive IAV immunoreactivity in brain (intracytoplasmic, intranuclear, and axonal immunolabeling of neurons), lung, and heart, and multifocal and segmental immunoreactivity within all layers of the retina ( Figure 2 ).

PCR Data from Cows and Cats

We tested various samples from 8 clinically affected mature dairy cows by IAV screening and H5 subtype-specific PCR ( Table 3 ). Milk and mammary gland homogenates consistently showed low Ct values: 12.3–16.9 by IAV screening PCR, 17.6–23.1 by H5 subtype PCR, and 14.7–20.0 by H5 2.3.4.4 clade PCR (case 1, cow 1; case 2, cows 1 and 2; case 3, cow 1; and case 4, cow 1). We forwarded the samples to the National Veterinary Services Laboratory, which confirmed the virus was an HPAI H5N1 virus strain.

When available, we also tested tissue homogenates (e.g., lung, spleen, and lymph nodes), ocular fluid, and rumen contents from 6 cows by IAV and H5 subtype-specific PCR ( Table 3 ). However, the PCR findings were not consistent. For example, the tissue homogenates and ocular fluid tested positive in some but not all cows. In case 5, cow 1, the milk sample tested negative by IAV screening PCR, but the spleen homogenate tested positive by IAV screening, H5 subtype, and H5 2.3.4.4 PCR. For 2 cows (case 3, cow 1; and case 4, cow 1) that had both milk and rumen contents available, both samples tested positive for IAV. Nevertheless, all IAV-positive nonmammary gland tissue homogenates, ocular fluid, and rumen contents had markedly elevated Ct values in contrast to the low Ct values for milk and mammary gland homogenate samples.

We tested brain and lung samples from the 2 cats (case 6, cats 1 and 2) by IAV screening and H5 subtype-specific PCR ( Table 3 ). Both sample types were positive by IAV screening PCR; Ct values were 9.9–13.5 for brain and 17.4–24.4 for lung samples, indicating high amounts of virus nucleic acid in those samples. The H5 subtype and H5 2.3.4.4 PCR results were also positive for the brain and lung samples; Ct values were consistent with the IAV screening PCR ( Table 3 ).

Phylogenetic Analyses

We assembled the sequences of all 8 segments of the HPAI viruses from both cow milk and cat tissue samples. We used the hemagglutinin (HA) and neuraminidase (NA) sequences specifically for phylogenetic analysis to delineate the clade of the HA gene and subtype of the NA gene.

Figure 3 . Phylogenetic analysis of hemagglutinin gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate different...

For HA gene analysis, both HA sequences derived from cow milk samples exhibited a high degree of similarity, sharing 99.88% nucleotide identity, whereas the 2 HA sequences from cat tissue samples showed complete identity at 100%. The HA sequences from the milk samples had 99.94% nucleotide identities with HA sequences from the cat tissues, resulting in a distinct subcluster comprising all 4 HA sequences, which clustered together with other H5N1 viruses belonging to clade 2.3.4.4b ( Figure 3 ). The HA sequences were deposited in GenBank (accession nos. PP599465 [case 2, cow 1], PP599473 [case 2, cow 2], PP692142 [case 6, cat 1], and PP692195 [case 6, cat 2]).

Figure 4 . Phylogenetic analysis of neuraminidase gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate different...

For NA gene analysis, the 2 NA sequences obtained from cow milk samples showed 99.93% nucleotide identity. Moreover, the NA sequences derived from the milk samples exhibited complete nucleotide identities (100%) with those from the cat tissues. The 4 NA sequences were grouped within the N1 subtype of HPAI viruses ( Figure 4 ). The NA sequences were deposited in GenBank (accession nos. PP599467 [case 2, cow 1], PP599475 [case 2, cow 2], PP692144 [case 6, cat 1], and PP692197 [case 6, cat 2]).

This case series differs from most previous reports of IAV infection in bovids, which indicated cattle were inapparently infected or resistant to infection ( 9 ). We describe an H5N1 strain of IAV in dairy cattle that resulted in apparent systemic illness, reduced milk production, and abundant virus shedding in milk. The magnitude of this finding is further emphasized by the high death rate (≈50%) of cats on farm premises that were fed raw colostrum and milk from affected cows; clinical disease and lesions developed that were consistent with previous reports of H5N1 infection in cats presumably derived from consuming infected wild birds ( 10 – 12 ). Although exposure to and consumption of dead wild birds cannot be completely ruled out for the cats described in this report, the known consumption of unpasteurized milk and colostrum from infected cows and the high amount of virus nucleic acid within the milk make milk and colostrum consumption a likely route of exposure. Therefore, our findings suggest cross-species mammal-to-mammal transmission of HPAI H5N1 virus and raise new concerns regarding the potential for virus spread within mammal populations. Horizontal transmission of HPAI H5N1 virus has been previously demonstrated in experimentally infected cats ( 13 ) and ferrets ( 14 ) and is suspected to account for large dieoffs observed during natural outbreaks in mink ( 15 ) and sea lions ( 16 ). Future experimental studies of HPAI H5N1 virus in dairy cattle should seek to confirm cross-species transmission to cats and potentially other mammals.

Clinical IAV infection in cattle has been infrequently reported in the published literature. The first report occurred in Japan in 1949, where a short course of disease with pyrexia, anorexia, nasal discharge, pneumonia, and decreased lactation developed in cattle ( 17 ). In 1997, a similar condition occurred in dairy cows in southwest England leading to a sporadic drop in milk production ( 18 ), and IAV seroconversion was later associated with reduced milk yield and respiratory disease ( 19 – 21 ). Rising antibody titers against human-origin influenza A viruses (H1N1 and H3N2) were later again reported in dairy cattle in England, which led to an acute fall in milk production during October 2005–March 2006 ( 22 ). Limited reports of IAV isolation from cattle exist; most reports occurred during the 1960s and 1970s in Hungary and in the former Soviet Union, where H3N2 was recovered from cattle experiencing respiratory disease ( 9 , 23 ). Direct detection of IAV in milk and the potential transmission from cattle to cats through feeding of unpasteurized milk has not been previously reported.

An IAV-associated drop in milk production in dairy cattle appears to have occurred during > 4 distinct periods and within 3 widely separated geographic areas: 1949 in Japan ( 17 ), 1997–1998 and 2005–2006 in Europe ( 19 , 21 ), and 2024 in the United States (this report). The sporadic occurrence of clinical disease in dairy cattle worldwide might be the result of changes in subclinical infection rates and the presence or absence of sufficient baseline IAV antibodies in cattle to prevent infection. Milk IgG, lactoferrin, and conglutinin have also been suggested as host factors that might reduce susceptibility of bovids to IAV infection ( 9 ). Contemporary estimates of the seroprevalence of IAV antibodies in US cattle are not well described in the published literature. One retrospective serologic survey in the United States in the late 1990s showed 27% of serum samples had positive antibody titers and 31% had low-positive titers for IAV H1 subtype-specific antigen in cattle with no evidence of clinical infections ( 24 ). Antibody titers for H5 subtype-specific antigen have not been reported in US cattle.

The susceptibility of domestic cats to HPAI H5N1 is well-documented globally ( 10 – 12 , 25 – 28 ), and infection often results in neurologic signs in affected felids and other terrestrial mammals ( 4 ). Most cases in cats result from consuming infected wild birds or contaminated poultry products ( 12 , 27 ). The incubation period in cats is short; clinical disease is often observed 2–3 days after infection ( 28 ). Brain tissue has been suggested as the best diagnostic sample to confirm HPAI virus infection in cats ( 10 ), and our results support that finding. One unique finding in the cats from this report is the presence of blindness and microscopic lesions of chorioretinitis. Those results suggest that further investigation into potential ocular manifestations of HPAI H5N1 virus infection in cats might be warranted.

The genomic sequencing and subsequent analysis of clinical samples from both bovine and feline sources provided considerable insights. The HA and NA sequences derived from both bovine milk and cat tissue samples from different Texas farms had a notable degree of similarity. Those findings strongly suggest a shared origin for the viruses detected in the dairy cattle and cat tissues. Further research, case series investigations, and surveillance data are needed to better understand and inform measures to curtail the clinical effects, shedding, and spread of HPAI viruses among mammals. Although pasteurization of commercial milk mitigates risks for transmission to humans, a 2019 US consumer study showed that 4.4% of adults consumed raw milk > 1 time during the previous year ( 29 ), indicating a need for public awareness of the potential presence of HPAI H5N1 viruses in raw milk.

Ingestion of feed contaminated with feces from wild birds infected with HPAI virus is presumed to be the most likely initial source of infection in the dairy farms. Although the exact source of the virus is unknown, migratory birds (Anseriformes and Charadriiformes) are likely sources because the Texas panhandle region lies in the Central Flyway, and those birds are the main natural reservoir for avian influenza viruses ( 30 ). HPAI H5N1 viruses are well adapted to domestic ducks and geese, and ducks appear to be a major reservoir ( 31 ); however, terns have also emerged as an important source of virus spread ( 32 ). The mode of transmission among infected cattle is also unknown; however, horizontal transmission has been suggested because disease developed in resident cattle herds in Michigan, Idaho, and Ohio farms that received infected cattle from the affected regions, and those cattle tested positive for HPAI H5N1 ( 33 ). Experimental studies are needed to decipher the transmission routes and pathogenesis (e.g., replication sites and movement) of the virus within infected cattle.

In conclusion, we showed that dairy cattle are susceptible to infection with HPAI H5N1 virus and can shed virus in milk and, therefore, might potentially transmit infection to other mammals via unpasteurized milk. A reduction in milk production and vague systemic illness were the most commonly reported clinical signs in affected cows, but neurologic signs and death rapidly developed in affected domestic cats. HPAI virus infection should be considered in dairy cattle when an unexpected and unexplained abrupt drop in feed intake and milk production occurs and for cats when rapid onset of neurologic signs and blindness develop. The recurring nature of global HPAI H5N1 virus outbreaks and detection of spillover events in a broad host range is concerning and suggests increasing virus adaptation in mammals. Surveillance of HPAI viruses in domestic production animals, including cattle, is needed to elucidate influenza virus evolution and ecology and prevent cross-species transmission.

Dr. Burrough is a professor and diagnostic pathologist at the Iowa State University College of Veterinary Medicine and Veterinary Diagnostic Laboratory. His research focuses on infectious diseases of livestock with an emphasis on swine.

Acknowledgment

We thank the faculty and staff at the ISUVDL who contributed to the processing and analysis of clinical samples in this investigation, the veterinarians involved with clinical assessments at affected dairies and various conference calls in the days before diagnostic submissions that ultimately led to the detection of HPAI virus in the cattle, and the US Department of Agriculture National Veterinary Services Laboratory and NAHLN for their roles and assistance in providing their expertise, confirmatory diagnostic support, and communications surrounding the HPAI virus cases impacting lactating dairy cattle.

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• Figure 1 . Mammary gland lesions in cattle in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. A, B) Mammary...
• Figure 2 . Lesions in cat tissues in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Tissue sections were stained...
• Figure 3 . Phylogenetic analysis of hemagglutinin gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate...
• Figure 4 . Phylogenetic analysis of neuraminidase gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate...
• Table 1 . Microscopic lesions observed in cattle in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024
• Table 2 . Microscopic lesions observed in cats in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024
• Table 3 . PCR results from various specimens in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024

Suggested citation for this article : Burrough ER, Magstadt DR, Petersen B, Timmermans SJ, Gauger PC, Zhang J, et al. Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Emerg Infect Dis. 2024 Jul [ date cited ]. https://doi.org/10.3201/eid3007.240508

DOI: 10.3201/eid3007.240508

Original Publication Date: April 29, 2024

Table of Contents – Volume 30, Number 7—July 2024

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Eric R. Burrough, Iowa State University Veterinary Diagnostic Laboratory, 1937 Christensen Dr, Ames, IA 50011, USA

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Technology Development Initiative – Paper of the Month – May 2024

Image copyright: Nature

FARESHARE: An open-source apparatus for assessing drinking microstructure in socially housed rats

Published in Digital Psychiatry and Neuroscience (2023)

Jude A. Frie and Jibran Y. Khokhar

Paper presented by Dr. Renata Marchette and selected by the NIDA TDI Paper of the Month Committee

Publication Brief Description

Monitoring drinking behavior in grouped housed animals can provide a more naturalistic setting that can facilitate the investigation of intrinsic and extrinsic factors influencing drinking behavior (e.g.  circadian rhythms and social hierarchy). The authors describe an open-source and cost-effective alternative to the limited commercial options. The system can measure both the volume consumed and drinking bouts microstructure in socially housed animals by employing short-range radio frequency identification. It is fully customizable and is compatible with standard housing cages; the Arduino system allows the integration of time-locked, closed-loop interventions, manipulations, and measurements (e.g., fiber photometry recordings, optogenetic stimulation/inhibition). Overall, the authors use step-by-step instructions to a describe a system for monitoring drinking behavior in rodents.

Frie, Jude A.; Khokhar, Jibran Y.

FARESHARE: An open-source apparatus for assessing drinking microstructure in socially housed rats Journal Article

In: NPP—Digital Psychiatry and Neuroscience, vol. 2, no. 1, pp. 1, 0000 , ISBN: 2948-1570 .

Abstract | Links

• https://doi.org/10.1038/s44277-024-00002-z
• doi:10.1038/s44277-024-00002-z

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