Genomic diversity of respiratory pathogens in clinical versus community surveillance: a comparative analysis of SARS-CoV-2, RSV, and influenza viruses in Washington State

Background Genomic surveillance of respiratory viruses typically relies on sequences from individuals seeking health care, and whether these sequences represent the viruses circulating in the community is not well-characterized. We aimed to compare the diversity, proportion, and dynamics of influenza, respiratory syncytial virus (RSV), and SARS-CoV-2 between clinical and community samples. Methods In this retrospective comparative genomic analysis, we used whole-genome sequences from community-based surveillance studies in the Seattle area, and clinical sequences from the Washington State Depa

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