Fig. 4: SARS-CoV-2 minor variants across tissues.

A Number of variants and viral population diversity (Shannon entropy) for each sample with >500x depth of coverage, arranged by subject (ordered by time between symptom onset and death). In the boxplot, boxes delineate quartiles and whiskers show the range, excluding outliers (as determined by the interquartile range). S01 and S02 had only two samples for comparison and were not analyzed further for circulation or compartmentalization; the remainder of the subjects had 4–11 samples. The ‘*’ designates uncertainty around the time between symptom onset and death. B On the left, all variants are displayed as genome position vs frequency for each of subjects S03-S06. The size of the points reflects the number of tissues the variant was observed in; the standard deviation of the frequency at which the variant occurred across tissues is depicted by error bars. Red points reflect nonsynonymous changes whereas grey points reflect synonymous or noncoding variants. Dashed lines are present at 10 and 90% frequency; variants falling between dashed lines were considered high-frequency. On the right, high-frequency variants were quantified and diagrams were constructed to demonstrate genetic distance. Dashed line represents the number of SNPs differentiating the consensus genome from SARS-CoV-2 Wuhan reference strain (NC_045512.2).