To determine the gender impact on the immune response of chickens, the mRNA was isolated and sequenced from the lungs of 48 chickens of 2 lines as three time-points post-infection (2,6, and 10 days post-infection), and in two treatment groups. The data can be retrieved by navigating to https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5859/.

Males and females from resistant Fayoumi and susceptible Leghorn chicken lines were either challenged with a lentogenic strain of Newcastle Disease virus or given a mock infection at 3 weeks of age. The lung transcriptomes generated by RNA-sequencing were studied using contrasts across the challenged and non-challenged birds, the two lines, and three time points (2,6, and 10 days post-infection) using Weighted Gene Co-expression Network Analysis (WGNCA). The data can be retrieved by navigating to https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5859/. Click the Download button to access the Sample and data relationship dataset file.

,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.,,

At 21 days of age, chickens were infected with Newcastle Disease virus (or a mock injection as controls), and spleens were harvested at 2 and 6 days post infection. mRNA was sequenced.

,Tabulated individual data points for data reported in the associated publication: Spackman E, Suarez DL, Lee CW, Pantin-Jackwood MJ, Lee SA, Youk S, Ibrahim S. Efficacy of inactivated and RNA particle vaccines against a North American Clade 2.3.4.4b H5 highly pathogenic avian influenza virus in chickens. Vaccine. 2023 Nov 30;41(49):7369-7376. doi: 10.1016/j.vaccine.2023.10.070. Epub 2023 Nov 4. PMID: 37932132.,The highly pathogenic avian influenza virus (HPAIV) isolate A/turkey/Indiana/22-003707-003/2022 H5N1 (TK/IN/22) and A/Gyrfalcon/Washington/41088/2014 H5N8 (GF/WA/14) isolate were each propagated and titrated in embryonating specific pathogen free (SPF) chicken eggs using standard procedures and titers were determined using the Reed-Muench method.,An in-house vaccine was produced by de novo synthesizing the HA gene of TK/IN/22 that was modified to be low pathogenic (LP) and placing it in a PR8 backbone using rg methods as described . The vaccine (SEP-22-N9) contained 6 genes from PR8 and a de novo synthesized N9 NA from A/blue winged teal/Wyoming/AH0099021/2016 (H7N9). The rg virus was inactivated by treatment with 0.1% beta-propiolactone. Vaccines were produced with Montanide ISA 71 VG (Seppic Inc., Fairfield, NJ) adjuvant at ambient temperature in a L5M-A high shear mixer (Silverson Machines, Inc., East Longmeadow, MA) for 30sec at 1,000rpm, then for 3min at 4,000rpm using an emulsifying screen in accordance with the adjuvant manufacturer’s instructions.,Sham vaccine was prepared in-house using sterile phosphate buffered saline as described above.,Commercial vaccines were supplied by the manufacturers. The commercial inactivated vaccine (1057.R1 serial 590088) (rgH5N1) (Zoetis Inc., Parsippany, NJ) was produced with the GF/WA/14 (clade 2.3.4.4c HA gene) and the remaining 7 gene segments including the NA from PR8 (1). The Sequivity vaccine (serial V040122NCF) (RP) (Merck and Co. Inc., Rahway, NJ) is an updated version of their replication restricted alphavirus vector vaccine that expresses the TK/IN/22 H5 HA (modified to be low pathogenic LP).,Three-week-old, mixed sex, SPF white leghorn chickens (Gallus gallus domesticus) were obtained from in-house flocks and were randomly assigned to vaccine groups.,All vaccines were administered by the subcutaneous route at the nape of the neck. Commercial vaccines were given at the volumes instructed by the manufacturer (0.5ml each). In-house vaccine was given at a dose of 512 hemagglutination units per bird in 0.5ml. Three weeks post vaccination chickens were challenged with 6.7 log10 50% egg infectious doses (EID50) of TK/IN/22 in 0.1ml by the intrachoanal route.,Oropharyngeal (OP) and cloacal (CL) swabs were collected from all birds at 2-, 4-, and 7-days post challenge (DPC). Swabs were also collected from dead and euthanized sham vaccinates at 1DPC.,To evaluate antibody-based DIVA-VI tests, blood for serum was collected from the RP and SEP-22-N9 vaccinated groups at 7, 10 and 14DPC because the SEP-22-N9 vaccine does not elicit antibodies to N1 and the RP vaccine does not elicit antibodies to the N1 or NP proteins.,Mortality and morbidity were recorded for 14DPC after which time the remaining birds were euthanized. If birds were severely lethargic or had neurological signs they were euthanized and were counted as mortality at the next observation time for mean death time calculations.,To determine if there was a difference in antibody levels based on the order of vaccination with the RP vaccine and an inactivated vaccine, groups of 20 chickens (hatch-mates of the chickens in the challenge study) were given one dose of each vaccine three weeks apart (Supplementary Table 1). The first dose was administered at three weeks of age using the RP or SEP-22-N9 vaccine as described above. Then a second dose of either the same vaccine or the other vaccine was administered three weeks later (six weeks of age). All birds were bled for serum three weeks after the second vaccination (nine

,An experimental challenge of Influenza A virus in genetically modified TMPRSS2 knockout pigs.,Resources in this dataset:,,

Data sets containing: (1) sample collection and influenza A virus (IAV) screening information for wild ducks, (2) water temperature data for six North American wetlands, (3) water quality measurement from those wetlands, (4) laboratory-based study of viral viability using Minnesota wetland water, (5) naive mallards challenged experimentally with IAVs identified from the field experiment, and (6) genetic sequence data for IAVs recovered from the challenge study.

Data sets containing: (1) sample collection and influenza A virus (IAV) screening information for wild ducks, (2) water temperature data for six North American wetlands, (3) water quality measurement from those wetlands, (4) laboratory-based study of viral viability using Minnesota wetland water, (5) naive mallards challenged experimentally with IAVs identified from the field experiment, and (6) genetic sequence data for IAVs recovered from the challenge study.

Data set containing avian influenza A virus (IAV) sampling information for Emperor Geese in Alaska, 2015-2017. The data are in three tables: 1) collection data and IAV screening results from fecal samples at several sites in southwestern Alaska, 2) results of blocking enzyme-linked immunosorbent assay (bELISA) tests for IAV antibodies in blood serum collected from nesting female Emperor geese near the Manokinak River on the Yukon-Kuskokwim River Delta, and 3) results of influenza virus microneutralization assays to test for the specific IAV subtypes in the Manokinak samples.

Data set containing avian influenza A virus (IAV) sampling information for Emperor Geese in Alaska, 2015-2017. The data are in three tables: 1) collection data and IAV screening results from fecal samples at several sites in southwestern Alaska, 2) results of blocking enzyme-linked immunosorbent assay (bELISA) tests for IAV antibodies in blood serum collected from nesting female Emperor geese near the Manokinak River on the Yukon-Kuskokwim River Delta, and 3) results of influenza virus microneutralization assays to test for the specific IAV subtypes in the Manokinak samples.