<figure class="image image-style-align-right"><a href="https://ceirr-public-website-static-prod.s3.amazonaws.com/CEIRR_Avian-Infobyte_08262024.pdf" target="_blank" rel="noopener noreferrer"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/CEIRR_Avian_Infobyte_Final_Draft_750x971_3794527f51.png?updated_at=2024-09-11T14:53:18.132Z"></a><figcaption>“Wild Bird Surveillance: Influenza Movement on Flyways” Infobyte. To view a full-size PDF version, click the image above.</figcaption></figure>Conducting influenza surveillance in wild and domestic animal hosts is part of the CEIRR Network’s core mission to study respiratory viruses with pandemic potential. Wild birds, especially shorebirds and waterfowl, represent a significant reservoir of influenza viruses in part due to their migration patterns allowing viruses to spread over large geographic regions quite quickly. Researchers from St. Jude Children’s Research Hospital CEIRR (<a href="https://www.ceirr-network.org/centers/sjceirr" target="_blank" rel="noopener noreferrer">SJCEIRR</a>), <a href="https://vet.uga.edu/person/david_e-_stallknecht/" target="_blank" rel="noopener noreferrer">David Stallknecht, Ph.D.</a> and <a href="https://vet.uga.edu/person/poulson-rebecca/" target="_blank" rel="noopener noreferrer">Rebecca Poulson, Ph.D.</a>, lead avian influenza surveillance in wild bird populations at the University of Georgia (UGA). The main goals of these efforts aim to understand the 1. ecology and epidemiology of avian influenza viruses in a wide range of avian hosts, 2. viral persistence in wild bird populations, 3. how these viruses move with wild animal hosts, and 4. the significance of highly pathogenic (HP) H5N1 in wild bird populations.Since 2014, the CEIRR Network (and previous iteration called <a href="https://www.ceirr-network.org/about/the-legacy-of-ceirs" target="_blank" rel="noopener noreferrer">CEIRS</a>) has sampled nearly 260,000 wild birds for avian influenza viruses. Surveillance efforts cover much of North America with sampling in all four major migratory patterns, called flyways: the Pacific, Central, Mississippi, and Atlantic. These loosely defined and overlapping migratory zones extend well-beyond North America, as well. All four flyways stretch into South America (not shown) where many waterfowl migrate during the North American winters; notably the Atlantic flyway overlaps with flyways in Europe (not shown). The vast geographic area that migratory birds cover highlights the importance of researching the pandemic potential of avian influenza A viruses (IAVs) in spurring the next outbreak. Multiple types of IAVs could be present in a migrating bird population at the same time. Some gene segments of these viruses can mix, often termed viral reassortment, leading to new strains of influenza. Birds traveling with these IAVs can spread the virus to other bird species, or even to land animals and mammals. To understand the impact of avian influenza on wild bird populations, Drs. Stallknecht, Poulson, and others in the field surveilled IAVs in <a href="https://www.ceirr-network.org/resources/publications?keyword=36105667" target="_blank" rel="noopener noreferrer">bald eagles</a>, <a href="https://www.ceirr-network.org/resources/publications?keyword=27309076" target="_blank" rel="noopener noreferrer">snow geese</a>, <a href="https://www.ceirr-network.org/resources/publications?keyword=31131568" target="_blank" rel="noopener noreferrer">mallards</a>, and <a href="https://www.ceirr-network.org/resources/publications?keyword=33105913" target="_blank" rel="noopener noreferrer">ruddy turnstones</a>, among other species. In an interview with the iDPCC, Drs. Stallknecht and Poulson shared more about how they got involved in studying avian influenza in wild birds, the importance and impact of their research, and how their work challenges paradigms to expand our understanding of avian influenza dynamics in wild birds.&nbsp;How Did They Start Studying Influenza in Wild Birds?Both Dr. Stallknecht and Dr. Poulson are faculty at the Southeastern Cooperative Wildlife Disease Study at the College of Veterinary Medicine at UGA, and both had serendipitous entries into the field of avian influenza in wild birds. Dr. Stallknecht, Professor Emeritus at UGA, started working with flu in the 1980's as a wildlife biologist working on a USDA task force assigned to an outbreak of HP H5N2 in poultry in Pennsylvania. There he met and worked with a renowned avian flu expert from St. Jude Children’s Research Hospital, <a href="https://www.stjude.org/directory/w/robert-webster.html" target="_blank" rel="noopener noreferrer">Robert Webster, Ph.D.</a> This was followed by graduate work on influenza in wild blue-winged teal at Louisiana State University, and he’s been studying influenza ever since, including his involvement in the CEIRR and CEIRS Networks from the beginning.Dr. Poulson, who’s now an Assistant Professor, began studying influenza after she moved to Georgia. She applied for a research technician role in Dr. Stallknecht’s lab and quickly fell in love with the field, eventually completing her Ph.D. with Dr. Stallknecht. Dr. Poulson loves that the avian influenza field is “so constantly changing and there are so many underexplored and unanswered questions.” Giving a personal reason why she’s stayed in the field, “Ruddy turnstones also, separately, are very charismatic.”&nbsp;Importance of Wild Avian Surveillance and ResearchDrs. Stallknecht and Poulson focus on the future to inform present conservation efforts in wild birds. They value wildlife and aim to keep these natural resources “front and foremost” in their research. Dr. Poulson always advocates for wildlife to be an “equal member at the table” when discussing health: “The health and well-being of these animals and their populations is critically important to entire ecosystems. And sometimes I feel like that gets lost in conversations.” Their group views their research from the wild bird perspective: working to understand the wildlife reservoir, how viruses persist, and when and where they’re capable of entering into that reservoir.When Drs. Stallknecht and Poulson started detecting infections of a new strain of influenza (HP H5N1) in North American wild birds, they also saw increases in mortality in many wild bird species: eagles, condors, ducks, and more. The fieldwork became emotionally taxing. However, when they began investigating snow geese, and applying antibody tests not normally applied to wild bird surveillance, they found that many infected birds including black vultures, condors, eagles, and even mammals, actually survive infection. This was encouraging to learn and provided much need information to understand possible impacts on wildlife populations.The iDPCC dove deeper into the health and safety of animal populations to better grasp the risk of influenza transmission from wild birds to mammals. Dr. Stallknecht notes that the risk is nearly impossible to quantify in the wild, but described three major scenarios where avian influenza transmits to another species:<ol><li>Most wild bird infections are caused by low pathogenic avian influenza (LPAI), which can but rarely pass to wild or domestic mammals. These viruses do “spill over” to domestic poultry on occasion and can cause severe problems.&nbsp;</li><li>In contrast, highly pathogenic avian influenza (HPAI) infections have a higher risk to “spill over” into wild mammals because they often kill their bird host. Wild mammals and predatory birds may come across weak or deceased birds and eat the carrion. Direct contact with HPAI is the main factor in determining whether a wild animal will acquire an infection.</li><li>With HPAI, infections also have been detected in domestic mammals (cats, dairy cows) but direct transmission from wild birds is rare, and these problems are usually associated with human error, such as not providing an adequate barrier between wild birds and these animals.</li></ol>Because of the potential death toll and transmission to other species, detecting positive cases of HPAI rings the alarm bells. Their group quickly studies the characteristics of the virus and assesses the risk to wildlife. Unfortunately, this presents a series of challenges. “Basically, we're dealing with a problem right now that we don’t know where it’s going, and we don’t know how bad it will be, and this type of event will happen again, even if we get beyond this one,” explains Dr. Stallknecht. While these viruses of concern present complex issues, Drs. Stallknecht and Poulson focus on understanding the trajectory of the virus and what may be possible, so they can devise strategies to keep wildlife safe and impacts low.&nbsp;Challenging Paradigms in Shorebird MigrationThe paradigm in North America holds that shorebirds migrate from South America in early spring towards their Arctic breeding grounds and stop in Delaware Bay via the Atlantic flyway. The birds fuel up on horseshoe crabs before continuing their journey to the Arctic. This sparked an intuitive site for influenza sampling efforts that are still <a href="https://www.ceirr-network.org/news/influenza-surveillance-efforts-in-north-american-shorebirds-is-the-start-to-understanding-and-anticipating-threats-posed-by-a-h5-n1" target="_blank" rel="noopener noreferrer">ongoing by SJCEIRR</a> researchers. The Network has learned a lot about the wildlife and virus dynamics within Delaware Bay over the years. A major problem lies in what happens outside of the bay. Dr. Poulson notes, “It’s hard to pinpoint where the viruses detected at Delaware Bay come from.”To start teasing apart the inputs of influenza into the Delaware Bay ecosystem, Drs. Stallknecht and Poulson leveraged their proximity to the southeastern US coastlines. They increased sampling on South Carolina, Georgia, and Florida coasts over several years to interrogate shorebird species in different times of year to understand how these viruses are maintained, and then subsequently moved to new locations. Using nano-tag telemetry on ruddy turnstones in the southeast, they tracked virus and bird movement over time and space. They found that many birds stop in the southeast US and can bypass Delaware Bay on their way to the Arctic. They’re starting to tie together movement and maintenance of viruses at different times of year based on genetic similarity. They found genetic similarity of IAV in the southeast during winter and detected similar genetic signatures in IAV at Delaware Bay months later. Dr. Poulson highlights the utility of this “multi-pronged approach [of] linking telemetry, viral movement, and genetic data to better understand the role of shore birds in disseminating viruses to different locations.”To wrap up our discussion, Dr. Poulson recalls a common phrase in the field: “The more we learn about flu, the less we know.” There are many open questions and challenges when studying wild populations, but Drs. Stallknecht and Poulson’s passion for the health of these ecosystems drives them to maintain their effort. However, they’re not alone in this effort. Dr. Poulson noted, “Lots of dots on that map, right? And lots of collection efforts. But in fact, that is representative of just a handful of dedicated groups historically having collected all those data. That’s a small but mighty and critically important effort.” Drs. Stallknecht and Poulson are proud to belong in the CEIRR Network community for so many years and look forward to researching influenza’s role in these dynamic, wild bird ecosystems.<hr>To read more about this topic, check out:<ul><li><a href="https://www.ceirr-network.org/resources/publications?keyword=36105667" target="_blank" rel="noopener noreferrer">Alkie TN, et al. (2022) A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways. Virus evolution. 8(2): veac077.</a></li><li><a href="https://www.ceirr-network.org/resources/publications?keyword=27309076" target="_blank" rel="noopener noreferrer">Wong JK, et al. (2016) Antibodies to Influenza A Viruses in Wintering Snow Geese (Chen caerulescens) in Texas. Avian diseases. 60(1 Suppl): 337–340.</a></li><li><a href="https://www.ceirr-network.org/resources/publications?keyword=31131568" target="_blank" rel="noopener noreferrer">Hollander LP, et al. (2019) Prevalence of Influenza A Viruses in Ducks Sampled in Northwestern Minnesota and Evidence for Predominance of H3N8 and H4N6 Subtypes in Mallards, 2007-2016. Avian diseases. 63(sp1): 126–130.</a></li><li><a href="https://www.ceirr-network.org/resources/publications?keyword=33105913" target="_blank" rel="noopener noreferrer">Poulson R, et al. (2020) Influenza A Viruses in Ruddy Turnstones (Arenaria interpres); Connecting Wintering and Migratory Sites with an Ecological Hotspot at Delaware Bay. Viruses. 12(11): 1205.</a></li><li>Additional CEIRR publications on <a href="https://www.ceirr-network.org/resources/publications?keyword=wild%20bird" target="_blank" rel="noopener noreferrer">influenza in wild birds</a> or <a href="https://www.ceirr-network.org/resources/publications?keyword=flyway" target="_blank" rel="noopener noreferrer">influenza in flyways</a>.</li></ul>

In The News

SJCEIRR

iDPCC

Influenza

Surveillance

Infobyte

SJCEIRR researchers study the movement of avian influenza in wild bird populations for pandemic preparedness and research response.

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Wild Bird Surveillance: Influenza Movement on Flyways

<figure class="image image-style-align-right"><img src="https://ceirr-public-website-static-stag.s3.amazonaws.com/figure_H5_in_ferrets_cropped_675x616_da700c1fe1.png?updated_at=2024-08-27T15:42:12.548Z"><figcaption>Figure 1. Role of prior H1N1 immunity on mortality and replication of cattle H5N1 in ferrets. Two groups of ferrets were infected with A/dairy cattle/Texas/24008749001/2024; group 1 had been infected with A/CA/07/09 H1N1pdm09 98 days priors (n=5) and group 2 were immunologically naïve (n=5). A) Study schematic B) Mortality of ferrets in each group (n=2 per group) C) Clinical signs on various days, n=5 on days 1-3 and n=2 on days 4 until end of the study D) Nasal wash titers in both groups E) Viral load in the ferret tissues within the animals.</figcaption></figure>University of Pennsylvania CEIRR (<a href="https://www.ceirr-network.org/centers/penn-ceirr" target="_blank" rel="noopener noreferrer">Penn-CEIRR</a>) researchers at the Center for Vaccine Research at the University of Pittsburgh <a href="https://mmg.secure.pitt.edu/person/valerie-le-sage" target="_blank" rel="noopener noreferrer">Valerie Le Sage, Ph.D.</a> and <a href="https://med.emory.edu/directory/profile/?u=SLAKDAW" target="_blank" rel="noopener noreferrer">Seema Lakdawala, Ph.D</a>., along with collaborators studying the lethal bovine H5N1 outbreak found that prior immunity to the virus protected against the disease in ferrets.Goal: Human infections of the cattle H5N1 virus occur in the presence of prior human seasonal immunity. However, the replication and pathogenesis of the virus in animal models is done in the absence of prior influenza immunity.Approach: To address this gap, ferrets with or without prior H1N1pdm09 immunity were intranasally inoculated with the dairy cattle H5N1 virus (clade 2.3.4.4b) at a dose of 104 TCID50/mL and sacrificed on day 3 (n=3) for assessment of viral load (Figure 1a). Two additional animals were followed out to day 14 to examine mortality.Results: All animals with prior H1N1 immunity survived challenge with the lethal H5N1 virus (Figure 1b). Assessment of clinical signs such as weight loss and playfulness revealed very modest clinical signs in all five animals with prior immunity compared to those that were immunologically naive (Figure 1c). Viral load in the nasal washes for all animals (n=5 days 1-3; n=2 days 4-8) was significantly lower in H1N1-immune ferrets compared to animals without prior immunity (Figure 1d). Infection with cattle H5N1 produced a systemic infection in ferrets without prior immunity as observed with virus detection in the liver, heart, spleen, and intestine (Figure 1e). However, only respiratory infection was observed in ferrets with prior H1N1 immunity (Figure 1e).Conclusion: Taken together, these data suggest that immunity with prior human seasonal viruses can reduce the severity of disease from the highly pathogenic avian influenza (HPAI) cattle H5N1 virus and may explain why the human cases have been less severe during the current outbreak.<hr>This article is part of a manuscript that was submitted for publication but has not been certified by peer review. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

Bovine H5N1 Outbreak

Penn-CEIRR

Outbreaks

Researchers in Penn-CEIRR aimed to better understand how prior immunity to influenza affects the severity of bovine H5N1 infection.

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Prior Immunity to the 2009 H1N1 Pandemic Virus Protects Against Lethal Cattle H5N1 Virus Infection in Ferrets 

<figure class="image image-style-align-right"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/ANM_2024_i_DPCC_team_600x480_bc4dc20ea0.png?updated_at=2024-08-23T16:01:37.429Z"><figcaption>iDPCC team at the Tech and Training Bar. Left to right: Holly May, Janine Clay, Andrew Taylor, and Dylan McClung</figcaption></figure>The CEIRR Network took over New York City for the 3rd CEIRR Annual Network Meeting from July 21st-24th. Over 350 members attended the meeting at the New York Academy of Medicine, hosted by the Center for Research on Influenza Pathogenesis and Transmission (<a href="https://www.ceirr-network.org/centers/cript" target="_blank" rel="noopener noreferrer">CRIPT</a>), to share their research on influenza, SARS-CoV-2, and other emerging viruses with pandemic potential. On the first day, attendees participated in a variety of breakout sessions about data management (led by the <a href="https://www.ceirr-network.org/centers/idpcc/" target="_blank" rel="noopener noreferrer">iDPCC</a>), scientific communications and outreach (<a href="https://www.ceirr-network.org/centers/idpcc/" target="_blank" rel="noopener noreferrer">iDPCC</a>), clinical research (<a href="https://www.niaid.nih.gov/" target="_blank" rel="noopener noreferrer">NIAID</a>), risk assessment (<a href="https://www.ceirr-network.org/centers/emory-ceirr" target="_blank" rel="noopener noreferrer">Emory-CEIRR</a>), and the SAVE Program (<a href="https://www.ceirr-network.org/centers/sjceirr" target="_blank" rel="noopener noreferrer">SJCEIRR</a> and <a href="https://www.ceirr-network.org/centers/cript" target="_blank" rel="noopener noreferrer">CRIPT</a>). The first day ended with a Network-wide social and networking session.Over the next three days of the Annual Network Meeting, more than 50 session speakers shared their research updates based on each of the seven CEIRR Centers’ themes:<ul><li>“Infection and immunity in at-risk populations and severe disease” – <a href="https://www.ceirr-network.org/centers/cider/" target="_blank" rel="noopener noreferrer">CIDER</a></li><li>“Influenza: The virus, the host, and the disease” – <a href="https://www.ceirr-network.org/centers/cript" target="_blank" rel="noopener noreferrer">CRIPT</a></li><li>“Influenza virus dynamics, host interactions, and immunity” – <a href="https://www.ceirr-network.org/centers/emory-ceirr" target="_blank" rel="noopener noreferrer">Emory-CEIRR</a></li><li>“Utilizing AI tools to support the CEIRR Network” – <a href="https://www.ceirr-network.org/centers/idpcc" target="_blank" rel="noopener noreferrer">iDPCC</a></li><li>“Respiratory virus infections: linking human surveillance to clinical outcomes” – <a href="https://www.ceirr-network.org/centers/jh-ceirr" target="_blank" rel="noopener noreferrer">JH-CEIRR</a></li><li>“Viral evolution, human immunity, and protection against seasonal and pandemic viral strains” – <a href="https://www.ceirr-network.org/centers/penn-ceirr" target="_blank" rel="noopener noreferrer">Penn-CEIRR</a></li><li>“Emerging pathogens” – <a href="https://www.ceirr-network.org/centers/sjceirr" target="_blank" rel="noopener noreferrer">SJCEIRR</a></li></ul>In addition, trainees and early-career investigators presented over 200 posters and 40 flash talks, split evenly across two sessions. Attendees voted on three categories for poster awards, and the first-place earners were:<ul><li>James Ferguson, <a href="https://ward.scripps.edu/members/" target="_blank" rel="noopener noreferrer">Andrew Ward lab</a>, Penn-CEIRR – Outstanding Poster (Session A)</li><li>Ivan Tomic, <a href="https://atomic-lab.org/team/" target="_blank" rel="noopener noreferrer">Adriana Tomic lab</a>, JH-CEIRR – Outstanding Poster (Session B)</li><li>Cosette Schneider, <a href="https://www.medschool.umaryland.edu/profiles/coughlan-lynda/" target="_blank" rel="noopener noreferrer">Lynda Coughlan lab</a>, CRIPT – Innovation in Research</li><li>Alesandra Rodriguez, <a href="https://ward.scripps.edu/members/" target="_blank" rel="noopener noreferrer">Andrew Ward lab</a>, Penn-CEIRR – Best Poster Design</li></ul>In a long-standing tradition, the scientific research sessions were accompanied by multiple social and networking activities throughout the meeting, including CEIRR trivia, a scavenger hunt, and a networking trading card game. Each attendee earns points for their CEIRR Center by participating in each activity with the goal of winning the Teambuilding Prize. Graduate student Nahara Vargas-Maldonado (<a href="https://www.ceirr-network.org/centers/emory-ceirr" target="_blank" rel="noopener noreferrer">Emory-CEIRR</a>) collected the most trading cards, professor and data manager Jessica Kissinger, Ph.D. (<a href="https://www.ceirr-network.org/centers/cider/" target="_blank" rel="noopener noreferrer">CIDER</a>) won the scavenger hunt, and <a href="https://www.ceirr-network.org/centers/penn-ceirr" target="_blank" rel="noopener noreferrer">Penn-CEIRR</a> took home the gold in the Center Teambuilding competition.For additional coverage of the meeting, check out CEIRR Network posts using #ANM2024 on <a href="https://x.com/search?q=(%23ANM2024)%20(from%3ACEIRRNetwork)&amp;src=typed_query&amp;f=live" target="_blank" rel="noopener noreferrer">Twitter/X</a> and <a href="https://www.linkedin.com/search/results/content/?fromOrganization=%5B%2292725191%22%5D&amp;keywords=%23ANM2024&amp;origin=FACETED_SEARCH&amp;sid=K*q&amp;sortBy=%22relevance%22" target="_blank" rel="noopener noreferrer">LinkedIn</a>. We can’t wait for the next successful meeting in 2025 hosted by <a href="https://www.ceirr-network.org/centers/cider/" target="_blank" rel="noopener noreferrer">CIDER</a>!

Meetings

CRIPT

Emory-CEIRR

CIDER

JH-CEIRR

Conferences

The third CEIRR Annual Network Meeting featured over 50 session speakers, 40 flash talks, over 200 posters, and ample networking activities among researchers and staff.

iDPCC team at the Tech and Training Bar. Left to right: Holly May, Janine Clay, Andrew Taylor, and Dylan McClung

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CEIRR Annual Network Meeting 2024

Refer to the NIAID Guidelines below or in <a href="https://ceirr-public-website-static-prod.s3.amazonaws.com/CEIRR+Bovine+H5+Milk+Sequencing+Best+Practices+Guidelines_Draft_081224.pdf" target="_blank" rel="noopener noreferrer">PDF format</a> (updated August 12, 2024). All reference materials and metadata templates are available on the <a href="https://www.ceirr-network.org/resources/data-standards" target="_blank" rel="noopener noreferrer">CEIRR Data Standards webpage</a>.<hr><h2>Background and Justification</h2>In March 2024, the first cases of highly pathogenic avian influenza (HPAI) H5N1 virus were reported in dairy cattle in the United States, with virus being detected in the milk of affected animals. To address potential concerns around metadata sensitivity as well as the complexity of characterizing the source of milk samples, <a href="https://www.ceirr-network.org/" target="_blank" rel="noopener noreferrer">NIAID’s Centers of Excellence for Influenza Research and Response</a>, in coordination with US government partners and academic influenza researchers, have prepared a set of best practice guidelines for the appropriate collection and sharing of data from viral isolate samples related to the outbreak.&nbsp;<h2>Application of Guidelines</h2><ul><li>These guidelines will apply to all research conducted using CEIRR Network funding from NIH/NIAID.</li><li>We recommend that all influenza researchers utilize the following guidelines where possible for community dissemination of data pertaining to the characterization of retail milk and other associated HPAI H5 samples.</li></ul>&nbsp;<figure class="image image-style-align-center"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/Bovine_h5n1_updated_080624_1250x961_428886a4f4.png?updated_at=2024-08-06T22:23:25.116Z"><figcaption>Guidelines for Reporting Data - Bovine H5N1 Outbreak Naming Convention Schematic</figcaption></figure><hr><h2>Guideline 1: Use of a Centralized Data Repository</h2><ul style="list-style-type:disc;"><li>Recommend sharing sampling data within a centralized data repository.<ul style="list-style-type:circle;"><li>Recommended repository-&nbsp;<a href="https://www.bv-brc.org/view/Taxonomy/11320#view_tab=surveillance" target="_blank" rel="noopener noreferrer">BV-BRC Surveillance Data</a></li><li>While data may also be shared elsewhere, the intention is for the repository to become a ‘standard’ resource for retail milk results.</li><li>The advantage and incentive of the shared data repository is the ability to quickly compare data with that submitted by other researchers.</li></ul></li><li>In addition to a centralized data repository, it is recommended that a shared data reporting template, format, and minimum metadata standards are utilized so that data can be easily aggregated, compared, and analyzed.<ul style="list-style-type:disc;"><li>Suggested templates are available on the&nbsp;<a href="https://www.ceirr-network.org/resources/data-standards" target="_blank" rel="noopener noreferrer">CEIRR Network Data Standards webpage</a> and outlined in the provided Naming Conventions Schematic.</li></ul></li></ul>&nbsp;<h2>Guideline 2: Data Reporting Practices</h2>There are separate best practices for single animal or single farm samples, and for commingled or retail milk samples. Refer to the appropriate section for your sample type.&nbsp;<ul style="list-style-type:disc;"><li>Single Animal or Single Farm Sampling<ul style="list-style-type:circle;"><li>Metadata Template:&nbsp;Use the schematic to determine the appropriate CEIRR iDPCC template to use for SRA data or metadata collection and reporting.<ul style="list-style-type:square;"><li>For animal swabs or farm samples including milk tank and environmental samples (such as surface or milking equipment swabs), metadata should indicate source of sample (exp. animal or environmental swab vs milk).</li></ul></li><li>CEIRR Investigator Data Submission:&nbsp;Data generated using CEIRR funding (genomic, transcriptomic, immunologic, serology, etc.) should be submitted to the CEIRR iDPCC before submission to the relevant repository.<ul style="list-style-type:square;"><li>CEIRR investigators will submit data via the appropriate template to the CEIRR iDPCC.&nbsp;</li><li>iDPCC will conduct QA/QC processing and standardization of metadata, and then will submit to NCBI, GenBank, and/or NIAID’s BV-BRC according to data type.</li><li>Raw sequence read data:&nbsp;all raw sequence reads should be submitted directly to <a href="https://www.ceirr-network.org/resources/data-standards#derived-analysis" target="_blank" rel="noopener noreferrer">SRA</a>.</li></ul></li><li>Sequence nomenclature:&nbsp;Refer to the schematic above.<ul style="list-style-type:disc;"><li>Single animal or single farm samples will be treated as standard host-associated sampling with the associated strain designation (ex: A/host/state/isolate/year).</li></ul></li></ul></li></ul>&nbsp;<ul style="list-style-type:disc;"><li>Multiple-Farm Pooled, Commingled, Commercial, or Retail Milk Samples<ul style="list-style-type:circle;"><li>Metadata Template: <a href="https://www.ceirr-network.org/resources/data-standards" target="_blank" rel="noopener noreferrer">iDPCC Milk Sequence Submission Metadata Template v1.0</a><ul style="list-style-type:square;"><li>For environmental samples (such as surface or processing equipment swabs), metadata should indicate source of sample (exp. animal or environmental swab vs milk).</li><li>For commingled or commercial milk, clearly identify if sequence generated is from lab virus isolation or bulk sequencing.</li></ul></li><li>CEIRR Investigator Data Submission:&nbsp;Data generated using CEIRR funding (genomic, transcriptomic, immunologic, serology, etc.) should be submitted to the CEIRR iDPCC before submission to the relevant repository.<ul style="list-style-type:square;"><li>CEIRR investigators will submit data via the appropriate template to the CEIRR iDPCC.</li><li>iDPCC will conduct QA/QC processing and standardization of metadata, and then will submit to NCBI, GenBank, and/or NIAID’s BV-BRC according to data type.&nbsp;</li><li>Raw sequence read data:&nbsp;all raw sequence reads should be submitted directly to <a href="https://www.ceirr-network.org/resources/data-standards#derived-analysis" target="_blank" rel="noopener noreferrer">SRA</a>.</li></ul></li><li>PCR positive retail milk samples:&nbsp;confirm and report location of milk processing plant, not the dairy farm or original producer.<ul style="list-style-type:square;"><li>Retail milk is defined here as purchased from grocery store or similar outlet following distribution from a processing plant.</li><li>For commingled samples obtained from processing plants or similar operations, prior to commercial distribution, report the state where the operation is located.</li><li>To determine where retail milk was processed, the National Uniform Coding System for Packaging Identification of Milk and Milk Product Processing Plants can be found <a href="https://www.fda.gov/media/180018/download?attachment" target="_blank" rel="noopener noreferrer">here</a>.</li></ul></li><li>Sequence nomenclature:&nbsp;Refer to the schematic above.<ul style="list-style-type:square;"><li>For commingled or commercial milk, strain identifier should begin ‘MILK-’.&nbsp;</li><li>For commingled milk from multiple farms or commercial milk, strain_location should default to ‘USA’ in the metadata table and subsequently the strain name.&nbsp;</li><li>More specific location data (two-letter state abbreviation), related to the location of the processing plant or commingled source, will be captured in the metadata table; however, this information will not contribute to the strain name.&nbsp;<ul style="list-style-type:disc;"><li>Due to the sensitive nature surrounding the release of the metadata, the location data will be access controlled by BV-BRC and the iDPCC and will only be available upon request. Please email <a href="mailto:support@ceirr-network.org" target="_blank" rel="noopener noreferrer">support@ceirr-network.org</a> for more information.</li></ul></li></ul></li></ul></li></ul>&nbsp;<h2>Guideline 3: Reporting of Sensitive Results</h2><ul style="list-style-type:disc;"><li>CEIRR Investigators are required to inform NIAID and the CEIRR Program Officers PRIOR to the preprint, publication, or otherwise release of any research findings.</li><li>It is recommended that all researchers, whether CEIRR affiliated or not, notify CEIRR, NIH/NIAID, and other USG partners of the presence of mammalian adaptations or other mutations of concern detected in variants 10 days prior to posting the data, so that the information may be verified, and a unified public health response can be organized.</li></ul><hr><h2>Points of Contact</h2><ul><li>Please reach out to the NIAID CEIRR Program Team at <a href="mailto:NIAID_CEIRR@nih.gov" target="_blank" rel="noopener noreferrer">NIAID_CEIRR@nih.gov</a> with any questions regarding these guidelines or if you have any results you would like to report.</li><li>If you have any specific questions about the implementation of the metadata templates, please reach out directly to the CEIRR Influenza Data Processing and Communication Center (iDPCC)’s support team at <a href="mailto:support@ceirr-network.org" target="_blank" rel="noopener noreferrer">support@ceirr-network.org</a>.</li></ul>

NIAID, CEIRR, and collaborators prepared a set of best practices to guide the appropriate collection and sharing of data regarding the source of milk samples from the bovine H5N1 outbreak.

Guidelines for Reporting Data - Bovine H5N1 Outbreak Naming Convention Schematic

CEIRR

Epidemics10: 10th International Conference on Infectious Disease Dynamics

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