Data files for: Whole-genome sequences of 183 infectious bronchitis viruses from Korean poultry surveillance, 1986-2022

Data files accompanying a Scientific Data descriptor of 183 complete infectious bronchitis virus(IBV) genomes from the national poultry disease surveillance collection of the Animal and PlantQuarantine Agency, Republic of Korea: 178 field isolates recovered from chickens between 1986 and2022, and 5 commercial vaccine strains. The genomes themselves are at NCBI under BioProject PRJNA1537317, with the raw reads in theSequence Read Archive as study SRP741337 and the assembled, annotated genomes in GenBank. Thesefiles are the per-genome records, the sample metadata, the S1 phylogeny behind the lineageassignment, and the values plotted in the figures. per_genome_records.tsv One row per genome: BioSample, SRA run and GenBank accession; assembly length, contig count, ambiguous bases, the route by which the assembly was finished and any declared gap; median read depth, positions without read support and the proportion of reads classified as IBV; the annotation reference and outcome; the S1 lineage with the support of the assigning node and the identity to the prototype of that lineage; the sub-lineage resolved by the tree and the sub-lineage assigned in earlier work; the within-sample population call; the sequencing batch; and the MD5 of the assembly. sample_metadata.tsv One row per genome, as deposited in BioSample: isolate name, collection date, collection site, coordinates, host, host disease, sampled tissue, collecting institution, and a note holding flock type, age and clinical signs where recorded, or the product details of the vaccine strains. Values that could not be established from the originating laboratory's records read "missing" rather than being left blank, so that a checked absence is distinguishable from an omission. S1_phylogeny_alignment_330taxa.fasta The trimmed S1 alignment the lineage assignment was made from: the first 1,700 nt of the spike coding sequence of each of the 183 genomes, added to a framework of 44 lineage prototypes and 103 labelled context sequences, 330 sequences over 1,591 columns. S1_phylogeny_tree.nwk The maximum-likelihood tree, with SH-aLRT and ultrafast bootstrap support at each node. S1_phylogeny_tree_consensus.nwk The consensus tree from the same run. S1_phylogeny_taxa.tsv Every sequence in the alignment with its source (lineage prototype, published context sequence, or this dataset) and its label. S1_phylogeny_lineage_assignment.tsv The lineage and sub-lineage assigned to each of the 183 genomes, with the support of the node each assignment was made at. figure_source_data.xlsx The values plotted in Figures 1 and 2 of the descriptor, one sheet per panel, with a README sheet. The analysis code that produced these files is archived separately athttps://doi.org/10.5281/zenodo.23179043.