Fig. 4: Evolution of the B.1.641 Ontario white-tailed deer lineage.
From: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission
Evolution of the B.1.641 lineage is presented relative to other animal-derived genomes, the ancestral B.1 lineage and the global SARS-CoV-2 diversity. a, Spike mutations present within the Ontario white-tailed deer (WTD) lineage. Amino acid changes present in all five Ontario WTD sequences and associated human case (orange); only in the human sample (yellow); and only in a single WTD genome (purple). Animal symbols indicate mutations in bat-, deer-, pangolin- and hamster-derived SARS-CoV-2 sequences. ‘+’ indicates presence of the mutation in additional non-human animal species, and green indicates those in Michigan mink samples. ‘*’ indicates spike mutations that were inferred to have originated subsequent to the divergence of B.1.641 from their MRCA with the Michigan-derived human samples. Spike annotations were derived from UniProt P0DTC2 (DEL, deletion; FS, frameshift; TM, transmembrane; RBD, receptor binding domain; NTD, N-terminal domain) and are not shown to scale. A complete list of mutations from across the entire genome can be found in Supplementary Table 2. b, Root-to-tip regression analysis based on the representative SARS-CoV-2 diversity in the global ML phylogeny (Fig. 2). Substitutions per site per year trends (and 95% confidence intervals) from ordinary least squares regression analyses are shown for all human samples (0.9 × 10−3 to 1.0 × 10−3), animal-derived samples (1.0 × 10−3 to 1.1 × 10−3), the B.1 lineage (0.4 × 10−3 to 0.6 × 10−3) and the Ontario WTD clade (0 to 8 × 10−3). c, Consensus substitutions (%) corresponding to a change from a reference C allele to an alternative U allele. Boxes represents the 25% quartile, median and 75% quartile, with error bars capturing the minimum and maximum values within 1.5× interquartile range. This was calculated from consensus sequences across a subsample of global human SARS-CoV-2 diversity (earliest and most recent genomes from each PANGO lineage, n = 3,127), global animal diversity (all animal genomes in GISAID at time of sampling, n = 1,522), B.1 lineage (all genomes assigned to this lineage in GISAID as of January 2022, n = 206) and B.1.641.
