Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.

ABSTRACT: Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within

SUBMITTER: Ortiz AT 

PROVIDER: S-EPMC9196117 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature