Medicine and Health Sciences Commons^™

An Evaluation Of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology, Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia K. Torchetti

USDA Wildlife Services: Staff Publications

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing …

Investigation Of Risk Factors For Introduction Of Highly Pathogenic Avian Influenza H5n1 Infection Among Commercial Turkey Operations In The United States, 2022: A Case-Control Study, Kelly A. Patyk, Victoria L. Fields, Andrea L. Beam, Matthew A. Branan, Rachel E. Mcguigan, Alice Green, Mia K. Torchetti, Kristina Lantz, Alexis Freifeld, Katherine Marshall, Amy H. Delgado

USDA Wildlife Services: Staff Publications

Introduction: The 2022–2023 highly pathogenic avian influenza (HPAI) H5N1 outbreak in the United States (U.S.) is the largest and most costly animal health event in U.S. history. Approximately 70% of commercial farms affected during this outbreak have been turkey farms. Methods: We conducted a case-control study to identify potential risk factors for introduction of HPAI virus onto commercial meat turkey operations. Data were collected from 66 case farms and 59 control farms in 12 states. Univariate and multivariable analyses were conducted to compare management and biosecurity factors on case and control farms. Results: Factors associated with increased risk of infection …

Investigation Of Risk Factors For Introduction Of Highly Pathogenic Avian Influenza H5n1 Virus Onto Table Egg Farms In The United States, 2022: A Case–Control Study, Alice L. Green, Matthew Branan, Victoria L. Fields, Kelly Patyk, Stephanie K. Kolar, Andrea Beam, Katherine Marshall, Rachel Mcguigan, Matthew Vuolo, Alexis Freifeld, Mia Kim Torchetti, Kristina Lantz, Amy H. Delgado

USDA Wildlife Services: Staff Publications

Introduction: The 2022–2023 highly pathogenic avian influenza (HPAI) H5N1 outbreak in the United States (U.S.) is the most geographically extensive and costly animal health event in U.S. history. In 2022 alone, over 57 million commercial and backyard poultry in 47 U.S. states were affected. Over 75% of affected poultry were part of the commercial table egg production sector. Methods: We conducted a case–control study to identify potential risk factors for introduction of HPAI virus onto commercial table egg operations. Univariate and multivariable analyses were conducted to compare farm characteristics, management, and biosecurity factors on case and control farms. Results: Factors …

Environmental Transmission Of Influenza A Virus In Mallards, Kim M. Pepin, Clinton B. Leach, Nicole L. Barrett, Jeremy W. Ellis, Kaci K. Vandalen, Colleen T. Webb, Susan A. Shriner

USDA Wildlife Services: Staff Publications

Abstract

Influenza A viruses present a major challenge for animal and human health. They circulate widely in wild waterfowl and frequently spillover into poultry, emphasizing the need for risk-based surveillance in wild birds and an understanding of the relative importance of different transmission mechanisms. We addressed this objective with a replicated (N = 6) experimental infection study in which we serially exposed eight cohorts of four naïve contact mallards to an experimentally infected mallard and a shared water pool. Viral concentration in the water was a better predictor of transmission than several direct measures of viral shedding in the …

Avian Influenza A Viruses Reassort And Diversify Differently In Mallards And Mammals, Ketaki Ganti, Anish Bagga, Juliana Dasilva, Samuel S. Shepard, John R. Barnes, Susan A. Shriner, Katia Koelle, Anice C. Lowen

USDA Wildlife Services: Staff Publications

Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian …

Avian Influenza A Viruses Reassort And Diversify Differently In Mallards And Mammals, Ketaki Ganti, Anish Bagga, Juliana Dasilva, Samuel S. Shepard, John R. Barnes, Susan A. Shriner, Katia Koelle, Anice C. Lowen

USDA Wildlife Services: Staff Publications

Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian …

Continental-Scale Dynamics Of Avian Influenza In U.S. Waterfowl Are Driven By Demography, Migration, And Temperature, Erin E. Gorsich, Colleen T. Webb, Andrew A. Merton, Jennifer A. Hoeting, Ryan S. Miller, Matthew Farnsworth, Seth R. Swafford, Thomas J. Deliberto, Kerri Pedersen, Alan B. Franklin, Robert G. Mclean, Kenneth R. Wilson, Paul Doherty

USDA Wildlife Services: Staff Publications

Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlife has been conducted at local scales, yet fully understanding their spread and distribution requires assessing the mechanisms acting at both local, (e.g., intrinsic epidemic dynamics), and continental scales, (e.g., long-distance migration). Here, we combined a large, continental-scale data set on low pathogenic, Type A AIV in the United States with a novel network-based …

Effects Of Freshwater Crayfish On Influenza A Virus Persistence In Water, J. Jeffrey Root, Jeremy W. Ellis, Susan A. Shriner

USDA Wildlife Services: Staff Publications

Several investigations have recently assessed the ability of some aquatic invertebrates to act as tools for avian influenza A virus (IAV) surveillance as well as their potential role(s) in IAV ecology. Because of this, as well as the high IAV seroprevalence rates noted in select mesocarnivores that commonly inhabit aquatic and semi-aquatic habitats, we evaluated the effects that freshwater crayfish have on IAV in water at three dose levels and monitored for the presence of IAV in crayfish tissues (gill and green gland) and haemolymph at multiple time points. At relatively high, medium 432 and low (approximately 10 , 10 …