Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts.

ABSTRACT: Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and doe

SUBMITTER: Valesano AL 

PROVIDER: S-EPMC7836113 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature