Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.

ABSTRACT: The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionat

SUBMITTER: Mushegian AA 

PROVIDER: S-EPMC9413716 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature