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Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Author to whom correspondence should be addressed.
Academic Editors: William M. M. Switzer and Dimitrios Paraskevis
Viruses 2021, 13(9), 1689;
Received: 6 August 2021 / Revised: 19 August 2021 / Accepted: 23 August 2021 / Published: 26 August 2021
(This article belongs to the Special Issue HIV Molecular Epidemiology for Prevention 2020)
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. View Full-Text
Keywords: HIV-1; phylogenetics; evolutionary rate; subtypes HIV-1; phylogenetics; evolutionary rate; subtypes
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MDPI and ACS Style

Nasir, A.; Dimitrijevic, M.; Romero-Severson, E.; Leitner, T. Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs. Viruses 2021, 13, 1689.

AMA Style

Nasir A, Dimitrijevic M, Romero-Severson E, Leitner T. Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs. Viruses. 2021; 13(9):1689.

Chicago/Turabian Style

Nasir, Arshan, Mira Dimitrijevic, Ethan Romero-Severson, and Thomas Leitner. 2021. "Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs" Viruses 13, no. 9: 1689.

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