Fig. 5: Strong signatures of positive selection were detected across species and SARS-CoV-2 genome segments. | Nature Communications

Fig. 5: Strong signatures of positive selection were detected across species and SARS-CoV-2 genome segments.

From: SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas

Fig. 5: Strong signatures of positive selection were detected across species and SARS-CoV-2 genome segments.The alternative text for this image may have been generated using AI.

 A Full SARS-CoV-2 genomes from hyenas were under positive selection (πN/πS ratio >1). B Positive selection was observed in the nucleocapsid (N) gene across all species. C Mixed signatures of positive and purifying selection were detected in ORF1ab, S and ORF3a, and (D) no or exclusively purifying signatures of selection were detected in the remaining gene segments. The ratio of nonsynonymous (πN) to synonymous (πS) nucleotide diversity was calculated as a measure of the type and strength of selection acting on SARS-CoV-2 populations. Each point represents the πN/πS ratio of (A) a SARS-CoV-2 virus population observed in the last nasal swab sample collected for each individual (N = 16 animals; N = 2 tigers, N = 11 lions, and N = 3 hyenas), or (B, C, D) a SARS-CoV-2 gene segment observed in one sample calculated as the mean of two technical sequencing replicates (N = 63 samples total; N = 54 samples from 11 lions, N = 3 samples from two tigers and N = 6 samples from three hyenas). Black dashed lines indicate πN/πS ratio of 1, and colored lines indicate the mean for each species. Points that are not fully visible represent samples for which πS = 0, which results in infinite πN/πS. These points are indicated with half points along plot borders and were not used in mean calculations. The abbreviated gene segment is indicated at the top of each plot (nucleocapsid (N), open reading frame (ORF), spike (S), envelope (E), membrane (M)).

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