Research Project: Control Strategies to Prevent and Respond to Diseases Outbreaks Caused by Avian Influenza Viruses

Location: Exotic & Emerging Avian Viral Diseases Research

2025 Annual Report

Objectives
1. Characterize the ecology, epidemiology, and pathogenesis of emerging avian influenza viruses with a focus on the One-Health concept. 1.A. Characterize the pathogenesis of new and variant avian influenza virus (AIV) isolates and determine quantifiable species-specific transmission parameters of AIVs for modeling and outbreak preparedness. 1.B. Conduct the molecular characterization of new and variant AIVs including phylogenetics, and network analysis. 1.C. Examine novel or emerging viruses that may have an impact on poultry health or where poultry pathogens affect public health. 1.D. Assess the inter- and intra-species transmission dynamics of LPAI viruses, which will also contribute to investigating mechanisms and pathways of intra-host virus evolution. 1.E. Investigate determinants of virulence and mechanism behind increased pathology seen with some LPAI virus subtypes. 2. Elucidate the host-pathogen interactions of avian influenza virus infections. 2.A. Investigate virus-specific factors and viral molecular markers associated with infectivity, pathogenicity, and transmissibility of influenza viruses in avian species including virus tissue tropism and replication. 2.B. Investigate host-specific factors associated with the infectivity, pathogenicity, and transmissibility in different avian species of current and emerging influenza viruses including species, breed, age, and physiological state of the bird, and concomitant infections. 2.C. Characterize the innate and adaptive immune response to avian influenza virus infection in different avian models that are either susceptible, tolerant, or resistant to infection. 3. Develop intervention strategies to effectively control avian influenza viruses and contain disease outbreaks. 3.A. Improve virus control and recovery strategies by producing data on the environmental ecology of AIV. 3.B. Evaluate and improve existing and new diagnostic tests and testing strategies for avian influenza virus surveillance, detection, and recovery from disease outbreaks. 3.C.1. Evaluate existing or develop new vaccine platforms and strategies designed to rapidly control and prevent avian influenza virus outbreaks in the various components of poultry production. 3.C.2 Investigate the impact of immunosuppressive viruses on the efficacy of AIV vaccines in chickens. 3.D. Characterize the effect of vaccine induced immunity on virus evolution. 3.E. Utilize precision engineering of the chicken genome to develop genome edited poultry with increased resistance to avian influenza virus. 3.F. Identify correlates of vaccine protection in avian species, including different breeds and ages. 3.G. Determine mechanisms and immune-system-wide effects of vaccines with rapid onset of broadly protective immunity. 3.H. Determine the role of vaccines in driving escape mutations and how to prevent them.

Approach
These objectives include a combination of basic and applied research that will generate knowledge and help develop tools to improve our ability to prevent and control avian influenza virus (AIV). These research goals are highly interrelated and will be accomplished with similar tools and approaches (Figure 1); thus, experiments will often contribute to more than one objective. The first objective includes the characterization of new strains of AIV and other viruses, which constantly emerge in nature. The second objective complements the first with a more in-depth focus on the specific viral and host factors that contribute to host adaptation, transmission, and virulence. The third objective will improve current practical intervention strategies including diagnostics, vaccines, development of AIV resistant poultry, and will enhance our understanding of the ecology of AIV in poultry. For objectives 1 and 3: Utilizing sequencing in vitro and in vivo models, low pathogenic avian influenza virus (LPAIV) will be tested to identify how host range is determined and markers for virus pathogenicity identified. Multiple types of immune system models and reagents with in vitro models and in vivo models will be used to characterize the immune response to LPAIV viral infection and vaccines.

Progress Report
During FY2025 progress was made on most objectives with an emphasis on responding to the H5 highly pathogenic avian influenza virus (HPAIV) outbreak that has affected over 174 million poultry and dairy cows on more than 1,070 farms in the last 3 years. Additionally, avian metapneumovirus subtype A and B was introduced for the first time into the United States and has resulted in widespread outbreaks in both turkeys and chickens; unit scientists responded to this emerging virus to help mitigate the impact on U.S. farmers. Objective 1 is aimed at responding to outbreaks of novel viruses that affect the U.S. poultry industry. The most impactful achievement of the research unit was work related to the highly pathogenic avian influenza (HPAI) outbreak in dairy cattle that was first diagnosed in March 2024. This was the first time HPAI was documented to infect dairy cattle. The virus caused a severe mastitis and there were high levels of virus in milk from infected cows. Spread of the virus from dairy cows to humans, cats, peridomestic birds and mammals were reported. Because of the novelty of the outbreak and the requirement to do the research in a Biosafety level 3 (BSL-3) laboratory, the research unit was encouraged to support the response effort because of staff qualifications and experience working with HPAI and BSL-3 facility capabilities. The project team concentrated on the food safety aspects of the outbreak including determining whether virus in the milk was a concern for public health. Initial studies confirmed that high levels of live virus could be found in bulk milk samples coming from infected farms. Although, it is well known that influenza can be inactivated by heat, it was unclear whether the current pasteurization processing of milk would inactivate the virus considering the protective properties of the milk proteins and fats. Additionally, the predominant method of commercial pasteurization is with a continuous flow pasteurizer that heats the milk to 72C for 15 secs (high temperature short time pasteurization) before it is quickly cooled for storage. In collaboration with the U.S. Food and Drug Administration (FDA) a continuous flow pasteurizer was installed in our laboratory’s BSL-3 space to conduct pasteurization studies that simulated standard industrial conditions and showed conclusively that pasteurization was effective at inactivating HPAI in milk. This research was of high importance to the dairy industry because it demonstrated that current methods of pasteurization were effective to maintain a safe milk supply. In two different studies, additional high priority projects with the FDA surveyed retail milk and dairy products to see if HPAI could be detected in samples purchased from grocery stores across the U.S. Although viral RNA was detected in 17-20% of the samples, no infectious virus was found. This further showed that the virus was inactivated during standard commercial dairy processing and therefore safe for consumers. Viral genetic material in the milk samples were also sequenced which showed the same variant of the virus was found in all the samples, which helped confirm a single initial introduction of virus was spreading through cows nationwide. Finally, additional studies were conducted that showed spiked virus in raw hamburger meat was efficiently inactivated with USDA Food Safety Inspection Service (FSIS) recommended cooking temperatures. This year, two subtypes of avian metapneumovirus (AMPV) were introduced into the U.S. for the first time. This outbreak spread widely among turkey and chicken flocks which resulted in respiratory disease, drops in egg production, and secondary viral and bacterial infections that caused substantial economic losses in affected flocks. Because of the impact of the virus on commercial poultry, scientists in the unit were allowed to redirect an APHIS agreement from egg drop syndrome to allow for a more vigorous response to AMPV. Key research accomplishments included: 1) sequencing the first AMPV A subtype virus; 2) isolation of both AMPV subtype A and B in cell culture and subsequently transferring these viruses to the APHIS Center for Veterinary Biologics; 3) updating and validating real-time RT-PCR based molecular diagnostics to allow for rapid and sensitive testing of poultry flocks; and 4) completion of several studies evaluating how the virus was spreading between flocks. This research was conducted in close collaboration with field veterinarians and the information developed was rapidly disseminated to the poultry industry. Additional disease concerns were also identified in the course of the AMPV studies including resurgence of reticuloendotheliosis virus which causes tumors in turkeys. Research on SARS COV-2 was concluded this fiscal year including research on a cell culture system to predict species susceptibility to infection. Early studies had identified the ACE2 gene as being important in species susceptibility, and project scientists extended these studies to show that several bat ACE2 genes allowed some virus replication for the early SARS COV-2 virus strains, but the later human-origin viruses were less likely to infect bat ACE2 cell lines. This supports the clinical observation of fewer detections of SARS COV-2 in animals as the virus has become more adapted to humans. Under Objective 2 studies on the immune response of birds to avian influenza virus (AIV) were conducted to look at how immune dendritic cells (DCs) respond in cell culture to infection from high and low pathogenic AIV. It was demonstrated that AIV can replicate inside of DCs and cause enhanced cytokine expression that ultimately resulted in cell death. In addition, the DCs underwent morphological changes that resulted in immune dysregulation and the presence of scattered cellular debris. This research demonstrates targeted killing of dendritic cells, which are important for antigen presentation in the immune response and enhances virus replication, likely contributes to disease pathogenesis. Mitigation methods for the control of avian influenza continues as a high priority. Under Objective 3 multiple vaccine studies were conducted for H5 HPAI including studies with herpesvirus of turkey (HVT) vectored vaccines. Two commercial HVT vaccines were effective at protecting chickens against HPAI. These vaccines are given in the hatchery either in ovo or at day of age and are likely to be used if vaccination is authorized in the U.S. One of the biggest gaps for poultry vaccination is the lack of vaccines that can be administered through spray or water (mass administration) to avoid having to catch and vaccinate birds individually. Additional studies evaluated a live attenuated avian influenza vaccine that can potentially be used as a mass administered vaccine in the field. These studies provide proof-of-concept that a mass administered vaccine can be developed. A deadly outbreak of HPAI in condors, an endangered species, raised concerns that further outbreaks could lead to extinction. The decision was made to vaccinate the birds with a killed vaccine. A field study was conducted in California condors to vaccinate them for HPAI using an inactivated product. Using black vultures (for safety) and then in condors, ARS scientists conducted successful safety studies and documented that the birds developed an immune response that is likely to be protective against HPAI. Several studies were conducted to improve the utility of whole genome sequencing for AIV. It has become standard practice to sequence the entire genome of outbreak viruses to help determine the origin of the virus and to predict pathogenicity. In a series of studies using next generation sequencing technology, comparisons were made among commercial reagents to determine an optimal combination providing the best speed and sensitivity to complete full genome sequencing on AIVs. In addition, different primers were compared to improve full genome sequencing and to allow multiple samples to be tested at the same time. This has provided key advances at improving the cost and efficiency of these methods while provide improved data quality. Finally, studies were conducted to improve serological (antibody-based) monitoring of poultry vaccinated for HPAI to ensure detection of infection in birds that were vaccinated then infected from birds which were only vaccinated (DIVA). The major drawback to vaccination for HPAI is the negative impacts on the export of poultry and poultry products due to concern of unintentional spread of the virus through these products. A DIVA vaccine and companion antibody test that allows for the serologic differentiation of animals that are only vaccinated from animals that were vaccinated and subsequently infected may help export partners accept poultry products if vaccination is used. Project scientists developed a new test to measure antibodies to the neuraminidase protein, which is not in most vaccines, and compared that to current testing methods that target antibodies to other proteins. It was found that the new neuraminidase test provided greater sensitivity and could be used with more types of vaccines that the other tests. This research supports the DIVA principle and the techniques have been transferred to APHIS for further field testing.

Accomplishments
1. Pasteurization inactivates avian influenza in milk. In March of 2024 there was the first detection of highly pathogenic avian influenza (HPAI) in dairy cows in Texas and high levels of virus were found in raw milk early after infection. Because HPAI is a potential zoonotic pathogen, there was a risk for human infections from virus in milk and other dairy products. ARS (Athens, Georgia) and FDA scientists tested whether the most commonly used commercial method of milk pasteurization, high temperature short time (HTST) continuous flow pasteurization which heats milk to 72C for 15 seconds, was effective at inactivating the virus. The data showed conclusive evidence of complete inactivation of virus using HTST pasteurization, thus demonstrating the safety of pasteurized milk and dairy products.

2. Evaluation of U.S. licensed vaccines for protection from highly pathogenic avian influenza. Vaccination can be an effective control strategy for avian influenza viruses in poultry and several vaccines have previously been licensed in the U.S. Vaccination for highly pathogenic avian influenza (HPAI) is currently not used in the U.S. because of trade implications. ARS scientists in Athens, Georgia compared two licensed herpesvirus of turkeys (HVT) vectored vaccines with a recent HPAI challenge virus and found that both vaccines were effective at protecting chickens from clinical disease but not from infection. After challenge, the chickens had a measurable antibody response that could differentiate the vaccinated and the vaccinated and then infected chickens. These studies provide evidence that the tested vaccines are effective against HPAI and would likely be protective if vaccination was used in chickens.

3. Initial characterization of highly pathogenic avian influenza in dairy cattle. In March of 2024 there was an unprecedented detection of highly pathogenic avian influenza (HPAI) in dairy cows in Texas that caused mastitis with abnormal milk and some mortality. ARS scientists in Ames, Iowa and Athens, Georgia participated with university and government scientists to characterize the virus in dairy cows. The virus was isolated and genetically sequenced which showed it to be similar to avian influenza viruses carried by wild birds. High levels of virus were found in the raw milk and different tissues of the infected cows. The virus was widely spread among dairy farms and represents a serious concern for zoonotic spread of HPAI virus to humans, particularly by raw milk products.

4. Characterization of the immune response to avian influenza virus. The immune response of birds to avian influenza virus (AIV) is still largely unknown, especially the contributions of immune cell populations necessary for protection. A better understanding of how the virus evades the immune system will aid in the discovery of disease resistance pathways. ARS scientists in Athens, Georgia analyzed the specific interaction between immune dendritic cells (DCs) with infection from high and low pathogenic AIV. It was demonstrated that AIV can replicate inside of DCs and cause enhanced cytokine expression that ultimately resulted in cell death. In addition, the DCs underwent morphological changes that resulted in immune dysregulation and the presence of scattered cellular debris. This research demonstrates targeted killing of host immune cells enhances virus replication and likely contributes to disease pathogenesis.

5. Survey of retail milk products for detection of avian influenza virus. The recently described outbreak of highly pathogenic avian influenza in dairy cattle and the determination that infectious virus could be found in raw milk creates a concern for human health. ARS (Athens, Georgia) and FDA scientists collaborated to conduct a survey of retail milk confirming that influenza virus could be detected in a percentage of some retail dairy products. Representative dairy product samples from 17 U.S. states were collected and tested for viral RNA using rRT-PCR. More than 20% of the samples contained viral RNA. These samples were further tested to determine if live virus was present and all the samples were negative for live virus. The study demonstrated how widespread the outbreak in dairy cattle was and confirmed pasteurization was effective at killing the virus in raw milk.

6. Development of efficacious modified live vaccines for avian influenza virus.. Vaccination is an effective strategy for control of avian influenza virus (AIV) in poultry. Modified live attenuated AIV vaccines (MLV) were developed by ARS researchers in Athens, Georgia. These vaccines offer a distinct advantage over existing options as they can be applied by mass vaccination methods, including drinking water, which is highly desired in commercial settings. The MLV vaccines provided protection against morbidity and mortality, as well as reduced virus shedding which can reduce transmission potential to other birds. The MLV vaccines have built in safety features required for live virus vaccines. These novel vaccines provide new opportunities for field vaccination to protect birds against AIV.

7. Testing of commercial dairy products for avian influenza virus. In March of 2024 highly pathogenic avian influenza (HPAI) was detected in dairy cows in Texas and infectious virus was found in raw milk. Because HPAI is a potential zoonotic pathogen, there was concern about virus in milk and other dairy products posing a risk for human infections. ARS (Athens, Georgia) and FDA scientists developed methods to test for avian influenza virus (AIV) in cheese and used these methods to test a variety of commercial dairy products. Samples were initially screened by rRT-PCR which can detect viral RNA, but it doesn’t confirm if the samples have live virus. Of the 17% of samples that were rRT-PCR positive, all were negative for live virus which confirms that commercial pasteurization methods are effective at inactivating AIV.

8. Genetic characterization of highly pathogenic avian influenza viruses in dairy cows. In March 2024 an unprecedented outbreak of highly pathogenic avian influenza was diagnosed in dairy cattle. ARS (Ames, Iowa and Athens, Georgia), APHIS and university scientists collaborated to genetically sequence and characterize viruses from numerous dairy farms and compared the virus genes to viruses in wild bird, poultry, and other mammal samples. The sequence analysis showed that all the viruses from dairy cows were highly similar, and the sequence matched a wild bird virus isolated in 2023. The data supports that a single introduction of a wild bird avian influenza virus to dairy cattle occurred, and the virus was spread to other farms through the movement of infected dairy cows. It is likely that other animals including domestic cats, mice, poultry, and wild birds became infected from the dairy cattle, due in part because of the large amount of virus found in milk from infected animals. This study helps the understanding of the outbreak origin and helps explain the spread of the virus, which offers better understanding on how to prevent further spread of the virus.

9. Genetic characterization and optimized testing protocol for the emerging avian Metapneumovirus in the United States. In early 2024 the U.S. chicken and turkey industry was severely affected by a new poultry pathogen, avian metapneumovirus types A and B, that had not previously been found in this country. Diagnostic testing and confirmation were delayed because of the lack of available validated PCR tests for these viruses. In an effort to improve diagnostic testing, field samples were collected and the whole genome sequence for a representative avian metapneumovirus A virus was sequenced. Using this sequence information, available PCR tests were updated and validated to show high sensitivity and specificity. The updated tests were compared to imported commercial tests and all three tests performed similarly which allows veterinary diagnostic laboratories options for virus testing.

10. Characterization of wild bird hosts for highly pathogenic avian influenza virus (HPAIV). Although ducks are the most common host, numerous wild bird species can serve as carriers of HPAIV that can disseminate the virus globally and serve as a source of infection for poultry and other domestic animals. ARS scientists (Athens, GA) were part of the team that compiled and curated data from all available published studies on the pathogenesis of HPAIV in wild birds and elucidated the potential roles of different species for virus transmission to domestic animals due to mild disease and/or high levels of virus excretion. Specific wild bird species that are most likely to serve as major reservoirs (e.g., mallards, and other dabbling ducks), as well as species that may have a lesser role (e.g., song- birds and gulls), were identified. This allows for more targeted approaches to wild bird testing and control of wild birds on farms and development of detection, control, and mitigation strategies for poultry farmers, producers, and ranchers.

11. Confirmation that proper cooking kills avian influenza virus in hamburger. In March of 2024 highly pathogenic avian influenza (HPAI) was detected in dairy cows in Texas. Ground beef can be sourced from dairy cows and HPAI virus is a potential zoonotic pathogen. There was concern of virus contamination in meat from dairy cows with unrecognized infections. ARS scientists in Athens, Georgia and Wyndmoor, Pennsylvania evaluated whether avian influenza virus (AIV) would be inactivated at normal cooking temperatures in grilled hamburger meat that had been spiked with the virus. The data confirmed earlier results in chicken meat that proper cooking of hamburger (to USDA FSIS recommended standards) completely inactivated all the virus in the samples and even a rare hamburger virus levels would be substantially reduced. Although AIV in hamburger or other beef products is unlikely to occur, this work shows that proper cooking is an effective mitigation strategy.

12. Improved methods for testing vaccinated birds for infection with highly pathogenic avian influenza. An unprecedented outbreak of H5N1 highly pathogenic avian influenza was first detected in North America in 2021 and has since spread throughout the Americas. Because of the continued threat from wild birds, there is increased interest in the use of vaccination for the control of the disease in poultry. However an impediment to vaccination is the concern about how export of poultry and poultry products could be affected because current tests don’t easily determine if vaccinated birds have been infected. Therefore, ARS scientists in Athens, Georgia developed and evaluated different tests to identify whether vaccinated birds had been infected after vaccination (known as a DIVA test). The test identified a specific antibody and was shown to be very sensitive. This test could facilitate trade of vaccinated poultry by demonstrating freedom from active infection.

13. A cell culture model system to predict species susceptibility to SAR COV-2 infection. The SARS COV-2 virus caused a pandemic in humans in 2020, but the virus also infected, and in some cases, caused disease in other animals including farm raised mink. Many challenge studies in animal species were conducted to identify which animals were susceptible to the virus and could potentially act as hosts to infect humans. However, it is impractical to test every animal species. ARS scientists in Athens, Georgia developed a cell culture model system where the ACE2 gene, the gene required for SARS COV-2 to infect the host, was added from different animal species. This most recent work tested different bat species and showed the early SARS COV-2 viruses could infect these cells, but later human SARS COV-2 viruses could not. This supports the idea that as the virus becomes adapted to humans it becomes less able to infect other animal species.

14. Vaccination of California condors with highly pathogenic avian influenza to protect an endangered species. An unprecedented outbreak of H5N1 highly pathogenic avian influenza was first detected in North America in 2021, and it has since spread throughout the Americas causing a devastating disease in poultry, wild birds, and marine mammals. One of the species affected was California condors that resulted in high mortality in the infected birds, which raised concern because there are less than 600 condors in the world. ARS (Athens, Georgia), APHIS, US Fish and Wildlife Services, and field veterinarians developed a plan to vaccinate condors using a commercial vaccine product. After first doing safety tests in black vultures, a related species, California condors were vaccinated and it was demonstrated most had an antibody response to the vaccine that is likely protective. This is the first time vaccination has been used for highly pathogenic avian influenza in an endangered species, and vaccination is likely to continue as long as the threat persists.

15. Improved procedures for Next Generation Sequencing. The importance of full genome sequencing of viruses has become critically important in diagnostic testing to track viruses and to predict virulence. Incremental improvements in next generation sequencing technology allows for better sensitivity and lower costs, but there has been considerable variation in sequencing procedures. ARS scientists in Athen, Georgia and scientists at Iowa State University evaluated one critical step in the sequencing procedure for avian influenza viruses: the RNA extraction step. By comparing different RNA extraction methods, several methods were found to provide good results and studies confirmed the commonly used magnetic bead extraction method, which is already available in many labs for other tests, could be used successfully for AIV sequencing.

16. Successful development of procedures to work with highly pathogenic avian influenza virus with large scale food processing equipment. Since highly pathogenic avian influenza virus (HPAIV) was discovered in dairy cows it has been necessary to validate dairy product processing for virus inactivation. A complication is that food processing equipment is not designed to contain HPAIV. ARS scientists in Athens, Georgia designed and implemented procedures for containment devices to ensure that the validation processes could be conducted safely by creating a work-flow that would keep the virus in sealed containers at all times. The procedures and containment devices developed can be utilized with further work with HPAIV validation studies in food processing.

17. Avian influenza viruses were isolated from marine seal colonies. Avian influenza viruses (AIVs) are maintained in wild aquatic birds with frequent spillover into mammals. ARS scientists in Athens, Georgia, detailed the isolation of AIV from marine mammals reported over the last 45 years. Prior to 2016, all reports of AIV in seals specifically, were low pathogenicity viruses but the majority of reported AIV outbreaks caused fatal respiratory diseases in harbor seals. The current H5 clade 2.3.4.4 highly pathogenic AIV was detected in seals for the first time in 2016 resulting in mass mortality and was attributed to spillover from wild bird species based on genetic analysis. Marine mammals, especially seals, are susceptible to infection and disease from AIV and appear to carry wild bird related AIVs.

18. Improved sequencing protocols for avian influenza virus. As standard practice, viruses from outbreaks of avian influenza are genetically sequenced to provide information on the source of the outbreak and to predict the virulence of the outbreak virus, which informs control measures. In recent years sequencing technology has greatly improved and new methods are often referred to as “next generation sequencing (NGS)”. NGS has allowed faster and cheaper sequence data. ARS scientists in Athens, Georgia helped provide innovative approaches to improve this sequence technology to provide faster and more reliable results which included testing of alternative PCR enzymes and primer combinations. The result was improved performance with more reliable methods to get full genome sequencing specifically using a rapid sequencer device that is being increasingly used in veterinary diagnostic laboratories.

19. Enhanced diagnostics sequencing for avian pathogen detection. Diagnostic testing of clinical samples is critical to providing client care for food animals. Current submission procedures rely on culturing samples to identify pathogens contained within them. Newer molecular technologies, such as whole genome sequencing (WGS), offer a faster and more precise mechanism for pathogen identification in a sample. ARS scientists in Athens, Georgia, identified bacterial and viral pathogens directly by WGS of clinical samples from chickens with respiratory diseases. Results demonstrated reduced time to detection of the causative agent following sample submission compared to pathogen culture. WGS can be a favorable method for pathogen identification in clinical field cases.

Review Publications
Gonnerman, M., Leyson, C., Sullivan, J., Pantin Jackwood, M.J., Spackman, E., Mullinax, J., Prosser, D. 2024. A systematic review of laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America. Proceedings of the Royal Society. B. Biological Sciences. 291(2033):2024. https://doi.org/10.1098/rspb.2024.1845.
Suarez, D.L., Goraichuk, I.V., Killmaster, L.F., Spackman, E., Clausen, N.J., Colonius, T.J., Leonard, C.L., Metz, M.L. 2024. Testing of retail cheese, butter, ice cream and other dairy products for highly pathogenic avian influenza in the United States. Journal of Food Protection. 88(2025:e100431. https://doi.org/10.1016/j.jfp.2024.100431.
Goraichuk, I.V., Risalvato, J., Pantin Jackwood, M.J., Suarez, D.L. 2024. Improved Nanopore Influenza A whole genome sequencing protocol. Frontiers in Cellular and Infection Microbiology. Front. Cell. Infect. Microbiol. 14:1497278.. https://doi.org/10.3389/fcimb.2024.1497278.
Bakre, A.A., Sweeney, R.P., Espinoza, E., Suarez, D.L., Blehert, D.J., Kapczynski, D.R. 2025. The ACE2 receptor from common vampire bat (Desmodus rotundus) and pallid bat (Antrozous pallidus) support attachment and limited infection of SARS CoV-2 viruses in cell culture. Virology. 17(4), 507. https://doi.org/10.3390/v17040507.
Tewari, D., Sekhwal, M.K., Killian, M.L., Zellers, C., Nicholson, C., Schroder, B., Spackman, E., Hamberg, A. 2024. The attribution of human seasonal influenza H3N2 virus detection to the collector, not avian sources, during the 2022 highly pathogenic avian influenza outbreak in Pennsylvania, USA-implications for biosafety and biosecurity. Vector-Borne and Zoonotic Diseases. 2024(4):315-319. https://doi.org/10.3390/zoonoticdis4040027.
Chrzastek, K., Kapczynski, D.R. 2024. In silico genomic analysis of avian influenza viruses isolated from marine seal colonies. Pathogens. 13(11):1009. https://doi.org/10.3390/pathogens13111009.
Ibrahim, S., Spackman, E., Suarez, D.L., Goraichuk, I., Lee, C.W. 2025. Evaluation of an N1 NA antibody-specific enzyme-linked lectin assay for detection of H5N1 highly pathogenic avian influenza virus infection in vaccinated birds. Journal of Virological Methods. Journal of Virological Methods 334:115127. 2025. https://doi.org/10.1016/j.jviromet.2025.115127.
Faccin, F., Caceres, J., Gay, C., Seibert, B., Bentem, N., Rodriguez, L., Fraiha, A., Cardenas, M., Geiger, G., Ortiz, L., Carnaccini, S., Kapczynski, D.R., Rajao, D., Perez, D. 2024. Mass vaccination against H9N2 avian influenza A virus with a non-transmissible, reassortment-impaired modified live attenuated influenza virus vaccine. Nature. npj Vaccines 9, 136. https://doi.org/10.1038/s41541-024-00923-y.
Mo, J., Segovia, K., Chrzastek, K., Briggs, K., Kapczynski, D.R. 2024. Morphologic characterization and cytokine response of chicken bone-marrow derived dendritic cells to infection with high and low pathogenic avian influenza virus. Frontiers in Immunology. 15:1374838. https://doi.org/10.3389/fimmu.2024.1374838.
Lee, J., Lee, C.W., Suarez, D.L., Lee, S.A., Kim, T.N., Spackman, E. 2024. Efficacy of commercial recombinant HVT vaccines against a North American clade 2.3.4.4b H5N1 Highly Pathogenic Avian Influenza Virus in chickens. PLOS ONE. 19(7):e307100. https://doi.org/10.1371/journal.pone.0307100.
Chaves, M., Hashish, A., Osemeke, O., Sato, Y., Suarez, D.L., El-Gazzar, M. 2024. Evaluation of commercial RNA extraction protocols for Avian Influenza virus using Nanopore metagenomic sequencing. Pathogens. Viruses 2024, 16, 1429. https://doi.org/10.3390/v16091429.
Nguyen, T., Hutter, C., Markin, A., Thomas, M., Lantz, K., Killian, M., Janzen, G.M., Vijendran, S., Wagle, S., Inderski, B.T., Magstadt, D.R., Li, G., Diel, D.G., Frye, E., Dimitrov, K.M., Swinford, A.K., Thompson, A.C., Snevik, K., Suarez, D.L., Larkin, S.M., Schwabenlander, S., Ahola, S.C., Johnson, K.R., Baker, A.L., Austermann, S.R., Torchetti, M.K., Anderson, T.K. 2025. Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle in the United States. Science. 388(3745). https://doi.org/10.1126/science.adq0900.
Spackman, E., Goraichuk, I., Jones, D.R., Colonius, T., Mccoig, A., Suarez, D.L. 2024. Characterization of highly pathogenic avian influenza virus in retail dairy products in the United States. Journal of Virology. 98(7). https://doi.org/10.1128/jvi.00881-24.
Caserta, L.C., Frye, E.A., Butt, S.L., Laverack, M., Nooruzzaman, M., Covaleda, L.M., Suarez, D.L., Kapczynski, D.R., Dimitrov, K.M., Diel, D.G., Thompson, A.C., Koscielny, M.P., Cronk, B., Johnson, A., Kleinhenz, K., Edwards, E.E., Gomez, G., Hitchener, G., Martins, M., Morris, E.A., Hensley, T., Beeby, J.S., Lejeune, M., Swinford, A.K., Elvinger, F. 2024. Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle. Nature. 634:669–676. https://doi.org/10.1038/s41586-024-07849-4.
Luchansky, J.B., Porto Fett, A.C., Suarez, D.L., Spackman, E. 2024. Inactivation of avian influenza virus inoculated into ground beef patties cooked on a commercial open-flame gas grill. Journal of Food Protection. 87. https://doi.org/10.1016/j.jfp.2024.100325.
Spackman, E., Anderson, N., Walker, S., Suarez, D.L., Jones, D.R., Mccoig, A., Colonius, T., Roddy, T., Chaplinski, N.J. 2024. Inactivation of highly pathogenic avian influenza virus with high temperature short time continuous flow pasteurization and virus detection in bulk milk tanks. Journal of Food Protection. 87(10):2024. https://doi.org/10.1016/j.jfp.2024.100349.
Goraichuk, I., Davis, J.F., Afonso, C., Suarez, D.L. 2024. Sequencing of historic samples provide complete coding sequences of chicken calicivirus from the United States. Microbiology Resource Announcements. 0:e00777-24. https://doi.org/10.1128/mra.00777-24.
Katzner, T., Blackford, A.V., Donahue, M., Gibbs, S.E., Lenoch, J., Martin, M., Rocke, T., Root, J.J., Styles, D., Cooper, S., Dean, K., Dvornicky-Raymond, Z., Keller, D., Sanchez, C., Dunlap, B., Grier, T., Jones, M.P., Nitzel, G., Patrick, E., Purcell, M., Specht, A.J., Suarez, D.L. 2025. Safety and Immunogenicity of Poultry Vaccine for Protecting Critically Endangered Avian Species against Highly Pathogenic Avian Influenza Virus, United States. Emerging Infectious Diseases. 31:(6). https://doi.org/10.3201/eid3106.241558.
Goraichuk, I., Suarez, D.L. 2025. Custom barcoded primers for influenza A nanopore sequencing: enhanced performance with reduced preparation time. Frontiers in Cellular and Infection Microbiology. https://doi.org/10.3389/fcimb.2025.1545032.
Goraichuk, I.V., Torchetti, M., Killian, M., Kapczynski, D.R., Kulkarni, A., Sary, K., Suarez, D.L. 2024. Introduction of avian metapneumovirus subtype A to the United States: molecular insights and implications. Frontiers in Microbiology. 15. https://doi.org/10.3389/fmicb.2024.1428248.
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