,The dataset contains measurements from a swine research study evaluating influenza A immune responses and protection for replicon particle and live attenuated influenza virus vaccines. The research study was conducted by United States Department of Agriculture, Agricultural Research Service (USDA-ARS) scientists and postdoctoral scientists at the National Animal Disease Center, USDA-ARS to characterize heterologous virus immunity from live attenuated influenza A virus vaccines and IAV replicon particle vaccines. A better understanding of vaccine immune responses to heterologous viruses will aid in development of improved swine IAV vaccination strategies. The dataset contains lesion scores, virus shedding in nasal swabs and bronchoalveolar lavage fluid, serum and bronchoalveolar lavage fluid antibody responses, and isolated blood and lung T cell responses.,

,Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to PRRSV infection. However, the genetic control of T3 and T4 during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with PRRSV. Sera from 5-week-old pigs (N=1792) at 11 days post inoculation (DPI) with PRRSV were assayed for T3 levels (piglet_T3). Sera from fetuses (N=1267) at 12 or 21 days post maternal inoculation (DPMI) with PRRSV of sows (N=145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60K Illumina or 650K Affymetrix SNP panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using JWAS. All three traits were low to moderately heritable (10 to 16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26±0.03 and 0.67±0.14, respectively. Nine significant QTL were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest QTL identified on SSC5, explaining 15% of the GV. Three significant QTL were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the GV. Five significant QTL were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the GV. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Thyroid hormone levels following PRRSV infection were heritable and had positive genetic correlations with growth rate. Multiple QTL with moderate effects were identified for T3 and T4 levels during challenge with PRRSV and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to PRRSV infection, revealing factors associated with genomic control of host resilience.,Funded/supported by: US National Pork Board (NPB) (#07-233, #09-208, #10-033, #09-244, and #10-033); swine breeding companies Genus PIC plc, Newsham/Choice Genetics, FAST Genetics, Genetiporc, Genesus, Topigs Norsvin and PigGen Canada, Inc.; PRRS Coordinated Agricultural Project (PRRS-CAP); USDA-NIFA Award #2008-55620-19132; Genome Canada project #2209_F; USDA-NIFA Translational Genomics ( # 2013-68004-20362), USDA sponsored National Research Support Project 8 (NRSP-8) Swine Genome and Bioinformatics research programs; Kansas State University and USDA ARS (1245-32000-098 and 8042-32000-117); USDA ARS (# 8042–32000-102); SCINet project of the USDA ARS (0500-00093-001-00-D); USDA ARS Headquarters Postdoctoral Fellowship; Genome Canada (2014LSARP_8202); Genome Prairie (Project 346143); Genome Alberta.,,

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.

,The dataset includes clinical data from an experimental swine and ferret challenge and transmission study with 3 strains of swine H1 influenza A virus. Data are presented in two spreadsheets, one for pigs and one for ferrets.,,

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/. Click the Download button to access the Sample and data relationship dataset file.

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/.

,An investigation of antigenic relationships between North American swine H3N2 influenza A viruses (IAV) and human seasonal vaccine strains was conducted to assess the zoonotic risk to humans. Human seasonal H3N2 vaccine strains isolated from 1973 to 2014 (n=20) were obtained from the World Health Organization Global Influenza Surveillance and Response Network through St. Jude Children’s Research Hospital to use for serological assays, such as hemagglutination inhibition (HI) assays. Human seasonal vaccine strains were cultured on MDCK cells or eggs and the HA gene was verified by sequencing on a Sanger method at National Animal Disease Center (NADC). A consensus HA sequence was generated using Geneious Software.,

,Interspecies human-to-swine IAV transmission occurs globally and contributes to increased IAV diversity in pig populations. We present data that a swine isolate from a 2018-2019 human-to-swine transmission event was shed for multiple days in challenged and contact pigs. By characterizing this introduction through bioinformatic, molecular, and animal experimental approaches, these findings better inform animal health practices and in vaccine decision-making. Since wholly human seasonal H3N2 viruses in the U.S. were not previously identified as being transmissible in pigs (i.e. reverse zoonosis), these findings reveal the interspecies barriers for transmission to pigs may not require significant changes to all human seasonal H3N2.,

,Influenza A virus in swine hemagglutinin (HA) gene sequence data for 9 virus strains.,,