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. 2022 Dec 15;9(1):veac118. doi: 10.1093/ve/veac118

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© The Author(s) 2023. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Divergence from founder sequence over time in the pol gene. (A) Divergence from founder overall and split for sites initially in consensus and non-consensus states. The reference used to define consensus and non-consensus sites is the HIV-1 group M consensus. Colored percentages are the fraction of sites corresponding to the related curve. Non-consensus sites represent only 6 per cent of the gene but diverge faster over time. Overall, 87 per cent of this divergence are due to reversions, while only 13 per cent are mutations toward another non-consensus nucleotide. (B) The data set from Panel A further split among the first, second, and third codon positions. The difference in evolution speed is greatest for nucleotides in the second position. (C) Ratio of non-consensus to consensus evolution rates computed from the curves in Panel B (Supplementary Figs. S3 and S4 for env and gag). The ratio is highest for second positions (triangles), where mutations can not be synonymous, followed by first and third positions.