Genomics
INFLUENZA A, INFLUENZA B, INFLUENZA
All seven full genome sequences generated for the influenza A‐positive samples from three different shelters were identified as A(H1N1)pdm09 viruses. We generated a maximum likelihood phylogenetic tree containing these seven samples along with all A(H1N1)pdm09 genomes deposited in GISAID that were collected in WA from 10/2019 to 3/2020 (N = 158) (Figure Maximum likelihood phylogenetic trees for (A) influenza A and (B) influenza B. Trees include all sequenced study samples and all genomes for samples collected in Washington (WA) during the study timeframe that have been deposited in GISAID.All 16 full genome sequences generated for the influenza B‐positive samples from five different shelters were identified as Victoria lineage viruses. A phylogenetic tree containing these samples along with all Victoria genomes deposited in WA GISAID collected from 10/2019 to 3/2020 (N = 189) was generated (Figure A total of 86% (6 of 7) of sequenced A(H1N1)pdm09 and 81% (13 of 16) of B/Victoria lineage viruses were most closely related to another sequence from the same shelter when analyzed with WA GISAID sequences. There were cases where inter‐shelter transmission was a possibility, most notably the close relationship between the influenza B shelter D sample and two shelter E samples (pairwise distance of two). The average pairwise distances between influenza A genomes and influenza B genomes from the same shelter were 2.0 and 7.0, respectively, versus average pairwise distances of 53.4 and 16.8 for genomes from different shelters.The NA and PA genic regions of the 23 shelter genomes were reviewed at the consensus level for known mutations associated with reduced susceptibility to oseltamivir or baloxavir, respectively, and no evidence of reduced antiviral susceptibility was identified.