Abstract
HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.
Highlights
IntroductionPublished: 26 August 2021HIV-1 is one of the deadliest pathogens known to mankind. Since the 19800 s, the virus has claimed >30 million lives and infected >75 millions worldwide [1]
Published: 26 August 2021HIV-1 is one of the deadliest pathogens known to mankind
The median substitution rate for pol across all subtypes/circulating recombinant forms (CRFs) and tree reconstructions was 1.36 × 10−3 substitutions site−1 year−1 (Figure 1A) compared to 3.10 × 10−3 ssy for env (Figure 2A), confirming faster evolution of env, which is well-known to be under diversifying selection in response to host immune surveillance
Summary
Published: 26 August 2021HIV-1 is one of the deadliest pathogens known to mankind. Since the 19800 s, the virus has claimed >30 million lives and infected >75 millions worldwide [1]. The HIV-1 reverse transcriptase enzyme lacks proof reading ability and generates significant genetic diversity due to mutations during essentially every round of replication [5]. These mutations are subjected to different evolutionary pressures exerted by the host immune system and clinical management, which select for immune and drug-escape variants [6,7]. Recombination can produce chimeric lineages from existing lineages that have evolved within a single infected person, and among different subtypes in co-infected persons These recombinants can cause their own outbreaks, and rise to high prevalence, as seen in several countries [8].
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