Fig. 1: Overview of vaccination and SARS-CoV-2 whole-genome sequencing data from the San Francisco Bay Area.

a, Plot showing the percentage of eligible individuals in San Francisco County who had received an FDA-authorized vaccine from the beginning of mass vaccine rollout until 30 June 2021 (blue line) and the number of new SARS-CoV-2 positive cases per 100,000 people in San Francisco County (orange line). The peach-coloured area denotes the study timeframe for sample collection (1 February to 30 June 2021). b, Plot showing the proportion of sequenced genomes with identified lineages from all cases (black line) and from fully vaccinated breakthrough cases (dark red line). The dotted line shows the proportion of sequenced genomes from breakthrough cases, regardless of whether a lineage was identified. c, Plot showing the distribution of SARS-CoV-2 lineages identified using Pangolin algorithm³¹ from sequenced COVID-19 cases from San Francisco County, aggregated biweekly from 1 February to 30 June 2021. d, Plots showing the distribution of Pangolin-identified SARS-CoV-2 lineages from all sequenced (top), unvaccinated (middle) and fully vaccinated breakthrough (bottom) cases. e, Plots showing the proportion of sequenced genomes carrying mutations associated with antibody resistance (L452R/Q, E484K/Q and/or F490S) among all sequenced (top), unvaccinated (middle) and fully vaccinated breakthrough (bottom) cases. f. Plots showing the proportion of sequenced genomes carrying mutations associated with enhanced infectivity (L452R/Q, N501Y/T and/or F490S) among all sequenced (top), unvaccinated (middle) and fully vaccinated breakthrough (bottom) cases. Proportions were calculated relative to the total number of sequenced cases and aggregated biweekly from 1 February to 30 June 2021.