Fig. 3: SARS-CoV-2 within-host variation in lions and hyenas varies by species.

A Fourteen within-host variants throughout the SARS-CoV-2 genome were identified in lions and hyenas (N = 58 samples). Each row represents one nasal swab sample, and collection date and animal identifier are indicated on the y-axis. Each tile represents a mutation detected in that sample relative to the consensus sequence of SARS-CoV-2 genomes recovered from the two infected tigers and is colored by allele frequency. Black dots indicate nonsynonymous single nucleotide variants. SARS-CoV-2 genome indicates the genomic loci of the eleven coding region mutations. Code to prepare plot was adapted from the R package ‘outbreakinfo’. Number of (B) within-host variants (Wilcoxon two-sample two-sided test, W = 273, p = 0.000107), C transitions and transversions, and (D) predicted effects of mutation by species.