SARS-CoV-2 within-host diversity

The limited variation observed among SARS-CoV-2 consensus sequences makes it difficult to reconstruct transmission linkages and identify common sources of infection in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host SARS-CoV-2 variation for predicting transmission linkages. We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples from four prospective studies and combined sequence data with information on household membership, a proxy for transmission linkage. Although only a subset of within-host variation is consistently shared across likely transmission pairs, shared iSNVs may augment the information in consensus sequences for predicting transmission linkages.