High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19
Fig 3
Variant haplotypes of the SARS-CoV-2 virion surface protein gene region detected in upper respiratory tract samples from 7 hospitalized study participants with COVID-19.
Each participant label indicates day of clinical illness and the number of SGS obtained for the sample in parentheses. Haplotype diagrams (left) depicting SARS-CoV-2 SGS are as in Fig 2. Non-synonymous or synonymous mutations in each haplotype relative to the WA-1 reference sequence are shown with pink or blue tick marks. Amino acid changes (middle) and percentages of all SGS in the sample attributable to indicated haplotypes (right) are as in Fig 2. The haplotype matching the consensus for each sample is represented in grey; variant haplotypes with at least 1 non-synonymous mismatch to sample consensus are in pink.