Raw sequence reads of SARS-CoV-2 from hospitalized patients. Severe acute respiratory syndrome coronavirus 2

Low genetic diversity of SARS-CoV-2 presents a challenge for local transmission inference by whole genome sequencing. While detection of shared within-host variants to identify transmission pairs may be a solution, little is known about the structure of SARS-CoV-2 intrahost diversity. We used Illumina sequencing with 325 residual specimens to determine within-host genetic variation over the course of infection and the extent of parallel variation. Studies using intrahost diversity for transmission inference must account for several sources of error and confounding variables.