Fig. 2: Phylogenetic and temporal analyses of SARS-CoV-2 genomes.

a, Phylogenetic tree showing the patterns of divergence and clade assignments of 797 sequenced SARS-CoV-2 positive genomes from California in the study, along with reference genomes from a globally representative dataset obtained from Nextstrain⁴⁷ (grey branches). Study genomes from fully vaccinated (n = 103, red circles) or unvaccinated (n = 694, grey circles) cases are shown. Clades corresponding to the major SARS-CoV-2 variants identified in the study are named, including those that carry antibody-resistant mutations (dark red boldface text). The length of each branch is proportional to the number of mutations occurring on that branch. b, The same phylogenetic tree, except that the length of each branch is determined by inference of the molecular clock phylogeny using TreeTime⁵⁰, which positions terminal nodes according to the sampling times and internal nodes at the most likely time of divergence. c, Pie charts showing the proportions of SARS-CoV-2 genomes containing identified mutations associated with antibody resistance (L452R/Q, E484K/Q and/or F490S) among fully vaccinated (top row) and unvaccinated (bottom row) cases per month over a 5-month period (from February to June 2021). The charts are shaded according to genomes carrying ≥1 mutation associated with antibody resistance (L452R/Q, E484K/Q and/or F490S) (red), or lacking an antibody-resistant mutation (black). Fisher’s Exact test (two-tailed) was used to calculate P values. NS, non-significant; *P < 0.05, **P < 0.01.