Fig 1.
(A) The number of specimens per person successfully sequenced. (B) intra-host single nucleotide variants (iSNV) frequency is consistent across replicates for iSNV that pass quality control filtering. The insert shows iSNV frequency up to 0.1.
Fig 2.
Intrahost single nucleotide variant dynamics.
(A) iSNV frequency. (B) The number of iSNV per specimen. The number of iSNV per specimen by (C) vaccination status, (D) age with child <18 and adult 18 + , (E) clade, (F) and days post symptom onset. The red lines are the mean. Vaccinated individuals and BA.1 infections had fewer iSNV per specimen than unvaccinated individuals and Delta or BA.2 infections.
Fig 3.
Divergence rates using a per specimen estimate.
(A) Divergence rate (divergence/site/day) for all specimens by days post infection. Divergence rate (divergence/site/day) using the specimen with the highest viral titer by (B) vaccination status, (C) age, (D) clade, and (E) gene. (F) is a zoomed in version of (E), note y-axis. For nonsynonymous mutations children had higher rates than adults, and spike had a higher rate than ORF1a. Black lines are the mean divergence rate. Green is synonymous, and purple is nonsynonymous.
Table 1.
iSNV that are in the same position as lineage defining mutations in spike for the subsequent variant wave.
Table 2.
iSNV with a positive selection coefficient. Selection coefficient values are from the 8hr generation time results.
Fig 4.
iSNV under positive selection and their corresponding allele trajectories.
(A) WFABC selection coefficients for iSNV under positive selection for the whole genome and (B) for spike. (C) The allele trajectories of the iSNV with positive selection coefficients by individual. (D) The allele trajectories separated by locus for iSNV in individual 103403, denoted with an asterisk in (C). Green is synonymous, and purple is nonsynonymous. WFABC = Wright Fisher Approximate Bayesian Computation; iSNV = intra-host single nucleotide variants.