Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference.

ABSTRACT:

Background

The limited variation observed among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference.

Methods

We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage.

Results

Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymor

SUBMITTER: Walter KS 

PROVIDER: S-EPMC9898879 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature