Data from: Dairy cows inoculated with highly pathogenic avian influenza virus H5N1

Raw read data from: Baker AL, Arruda B, Palmer MV, Boggiatto P, Davila KS, Buckley A, Zanella GC, Snyder CA, Anderson TK, Hutter CR, Nguyen TQ. Markin, A., Lantz, K., Posey, E.A., Torchetti, M.K., Robbe-Austerman, S., magstadt, D.R., Gorden, P.J. Dairy cows inoculated with highly pathogenic avian influenza virus H5N1. Nature. 2024 Oct 15:1-3.
Additional details on data processing and computational pipelines are provided at: GitHub - flu-crew/dairy-cattle-hpai-experiment: data and code to support Baker et al. HPAI H5N1 in dairy cattle
The Highly Pathogenic Avian Influenza (HPAI) H5N1 genotype B3.13 virus used this study was collated (A/dairy cattle/Texas/24- 531 008749-002/2024: TX/24: NCBI PP755581- PP755588) with other B3.13 strains generated within Nguyen et al. and newly sequenced data collected between April 16 and May 8, 2024. Influenza A virus Ribonucleic acid (RNA) from samples was amplified, then we generated complementary DNA (cDNA) libraries by using the Illumina DNA Sample Preparation Kit, (M) Tagmentation (Illumina, 535 https://www.illumina.com) and either the iSeq or NextSeq Reagent Kit v2 (Illumina) according to manufacturer instructions. We performed reference-guided assembly of genome sequences using IRMA v1.1.5. To analyze the Illumina short read data for 82 samples collected during the experimental challenge, we used the “Flumina” pipeline (https://github.com/flu-crew/Flumina) for processing and analyzing influenza data. The pipeline uses Python v3.10, R v4.4 (R Development Core Team 2024), and SnakeMake to organize programs and script execution. The reads are preprocessed using FASTP, removing adapter contamination, low complexity sequences, and other artifacts. Consensus contigs for phylogenetics were assembled using IRMA v1.1.5. The pipeline maps cleaned reads to the reference cattle strain derived from sequencing the stock inoculum of A/dairy cattle/Texas/24-008749-002/2024 using BWA (bwa index –a bwtsw). High frequency single nucleotide variants (SNV) were called with GATK v.4.4 41 and low frequency SNVs were called with LoFreq. To assess potential SNV phenotypic changes, a database was generated using the Sequence Feature Variant Types tool from the Influenza Research Database for all eight genes. To estimate genome-wide natural selection, we used the program SNPGenie on the VCF files.