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WGS-representativity

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WGS representativity analysis of A/dairy_cattle/Texas/24-008749-002/2024

  1. We downloaded SRA assemblies of cattle H5N1 genes from BV-BRC on June 13, 2024. These strains were merged with the previously published B3.13 strains and the duplicates were removed. This resulted in n=367 whole genome B3.13 sequences, 334 of which were from cattle.

  2. We built a WGS phylogeny from the concatenated whole genome sequences using IQ-Tree 2 as follows

iqtree2 -s combined.aln -spp iqtree.partitions.nexus -B 1000 -bnni -redo
mv iqtree.partitions.nexus.treefile cattle.all.wgs.tre
  1. We built a consensus WGS of cattle strains using smof.
cat combined.aln | smof grep "cattle" | smof consensus > cattle.consensus.fasta

And compared the A/dairy_cattle/Texas/24-008749-002/2024 genome with the consensus genome in UGENE.

  1. We evaluated the representativity of A/dairy_cattle/Texas/24-008749-002/2024 using PARNAS.
parnas -t cattle.all.wgs.tre --prior ".*Texas/24-008749-002/2024.*" --evaluate --constrain-fully ".*cattle.*"