Figure 2.

Allelic frequencies in B.1.160 in Quebec and in the patient’s infection. The top row displays the percentages for a total of 2627 B.1.160 consensus sequences from the LSPQ database. The four following rows show intra-host frequencies for the patient’s mutations for each time point. Only mutations with intra-host frequencies above 5% for Illumina sequences (D1 and D116) and 10% for Nanopore sequences (D111 and D172) for at least one time point are presented. Because of the respective error rates of both sequencing technologies, discrepancies of up to 5% for Illumina sequences (D1 and D116) and 10% for Nanopore sequences (D111 and D172) are likely to be sequencing artifacts. Non-synonymous mutations are written on top, and the color represents the nucleotide change. We observed a genome-wide total of 22 C to U substitutions on 55 intra-host mutations (40%). The additional mutations seen on D111 in Figure 1b but not in Figure 2 can be explained by the different filters used in the default Nextstrain settings and our in-house pipeline (detailed in the Section 3).