This dataset includes epidemiology, clinical signs, gross and microscopic pathology, and virology data from two red foxes (Vulpes vulpes) and one fisher (Pekania pennanti) submitted to the USGS-National Wildlife Health Center for cause-of-death determination and confirmed positive for highly pathogenic avian influenza (HPAI) H5N1 by USDA’s National Veterinary Services Laboratories. The foxes were juveniles from North Dakota and the fisher was an adult from Wisconsin. Clinical signs included neurological deficits such as ataxia, lethargy, or paralysis. Gross and microscopic lesions included myocardial pallor, pulmonary and hepatic congestion, meningoencephalitis, interstitial pneumonia, myocardial necrosis, and hepatic necrosis. Highly pathogenic avian influenza H5N1 2.3.4.4 was detected in swabs and/or organ tissues by PCR; genotype B3.1 was identified in the foxes and B3.2 was identified in the fisher. Death of all three animals was attributed to HPAI.

This data set describes genomic sequence information from 2022 used to infer spatiotemporal trends pertaining to the introductions of highly pathogenic H5N1 avian influenza viruses into Alaska and spread among wild birds, backyard poultry, and mammals.

This data set describes genomic sequence information from 2022 used to infer spatiotemporal trends pertaining to the introductions of highly pathogenic H5N1 avian influenza viruses into Alaska and spread among wild birds, backyard poultry, and mammals.

Clade 2.3.4.4b Eurasian-origin H5N1 entered North America in late 2021 and spread across the continent. While studies have characterized the antibody response mounted by dabbling ducks following exposure, little data is available for diving ducks. This study sought to identify influenza A virus (IAV) infection and antibodies in Lesser and Greater Scaup captured in Maryland, Illinois, and Rhode Island. In Maryland, IAV seroprevalence increased from the 2021/2022 to 2022/2023 sampling season, with IAV antibody prevalence increasing for juvenile (38% to 80%) and adult (82% to 90%) Lesser Scaup. While adult Lesser Scaup sampled in Illinois in 2021/2022 had IAV antibody prevalence comparable to those sampled in Maryland (76% and 82%, respectively), they had higher antibody prevalence to both H5 (48% and 18%) and N1 (68% and 35%), potentially due to being sampled in March versus December and January. Greater Scaup captured in Rhode Island had comparable IAV, H5, and N1 antibody seroprevalence to Lesser Scaup in Maryland during the same season. Our data suggest that Lesser Scaup had limited antibodies to highly pathogenic H5 IAV prior to the introduction of clade 2.3.4.4b H5N1 to North America, but relevant antibodies were widely observed in the months and year following.

,Treatment groups of ducks were exposed to different virus doses (2, 4, 6 log10 50% egg infectious doses) and by different routes (contact or intrachoanal). The experimental setting was a laboratory with animal care as approved by the institutional animal care and use committee as appropriate for the species and age of bird. Data are the virus titers shed by the oral and cloacal route for individual mallard ducks exposed to H5N1 highly pathogenic avian influenza virus by day post exposure. Samples were collected through 11 days post exposure. Virus titer equivalents were determined by quantitative real-time RT-PCR. Serological data are serum antibody titers to the challenge virus as determined by hemagglutination inhibition assay (reciprocal of the log2 dilution) determined with serum collected 10 or 11 days post exposure.,,

Dataset containing avian influenza screening results for waterfowl and gulls sampled during autumn in (or near) Izembek National Wildlife Refuge (NWR), Alaska, 2011-2024. These data contain information on species, age, and sex of birds sampled, collection dates, and laboratory testing information used to determine the presence and absence of influenza A viruses (IAVs).

Data set containing avian influenza sampling information for late summer and early autumn waterfowl and gulls within and around the Izembek National Wildlife Refuge (NWR), Alaska, 2011-2016. Data contains species, age, sex, collection data and location of sampled migratory birds. Laboratory specific data used to identify presence and absence of influenza A viruses (IAVs) from collected samples are included.

These data describe the prevalence of infection with and antibodies to clade 2.3.4.4b HP H5N1 in Snow Geese in the Central Valley of California, along with corresponding movement data. These data show differential outcomes of HPAI infection in this species.

,Data are the individual group values for oral and cloacal virus shedding and antibody titers for reach treatment group from: Mo et al., The pathogenicity and transmission of live bird market H2N2 avian influenza viruses in chickens, Pekin ducks, and guinea fowl. Vet Mic 260:109180, 2021. https://doi.org/10.1016/j.vetmic.2021.109180,Methods: Six H2N2 low pathogenic avian influenza viruses from US LBMs were selected based on recency and to represent the different genotypes present in the live birds markets during the time period (i.e., the presence or absence of a NA stalk deletion): A/duck/PA/14-030488-5/2014 (Dk/PA/14), A/chicken/NY/16-032621-2/2016 (Ck/NY/16), A/chicken/CT/17-008911-4/2017 (Ck/CT/17), A/chicken/NY/18-002471-4/2018 (CK/NY/02471/18), A/chicken/NY/18-042097-3/2018 (Ck/NY/042097/18) and A/chicken/NY/19-012787-1/2019 (Ck/NY/19). Isolates were evaluated in White Leghorn chickens (Gallus gallus), guinea fowl (Numida meleagris) and Pekin ducks (Anas platyrhynchos). Chickens and guinea fowl were challenged at 4 weeks of age and Pekin ducks were challenged at 2 weeks of age with 6log10 of virus by the intra-choanal route. “Contact” birds, which were hatch-mates of the inoculated birds, were co-housed with the inoculated birds 24hrs post inoculation to evaluate transmission. Viral loads in OP and CL swabs collected at 2, 4, 7, 10, and 14 days post inoculation were determined by quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR). RNA was extracted from swabs using the MagMAX96 Viral RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA) and the KingFisher Flex Magnetic Particle Processing System (Thermo Fisher Scientific), with an additional wash step to remove inhibitors (Das et al., 2009). The qRT‐PCR for AIV detection was conducted based on the standard USDA M gene AIV qRT‐PCR procedure (Spackman et al., 2002) using an Applied Biosystems® 7500 Fast Real‐Time PCR system (Thermo Fisher Scientific). Cycle threshold (Ct) values were determined by the 7500 Fast Software v2.3. For relative quantification, Ct values were converted to titer equivalents based on the standard curve method (Larionov et al., 2005). Values were established from ten-fold dilutions of the same titrated stock of the virus used to challenge the birds. The limit of detection was determined to be 0.8Log10 per reaction. Serological testing for antibodies to the virus utilized the hemagglutination inhibition (HI) assays using homologous antigens were performed to quantify antibody responses with serum collected from chickens, guinea fowl and Pekin ducks at 14 dpi based on the standard protocol (OIE, 2019). HI titers were reported as reciprocal log2 titers, and titers greater than 3 log2 (1:8) were considered positive.,,

This data set describes three independent viral introductions of Highly pathogenic H5N1 avian influenza viruses into Alaska.