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Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
Author to whom correspondence should be addressed.
Academic Editor: Miguel A. Martínez
Viruses 2020, 12(11), 1312;
Received: 21 October 2020 / Revised: 12 November 2020 / Accepted: 13 November 2020 / Published: 16 November 2020
(This article belongs to the Special Issue Diversity and Evolution of HIV and HCV)
Site-specific evolutionary rate shifts are defined as protein sites, where the rate of substitution has changed dramatically across the phylogeny. With respect to a given clade, sites may either undergo a rate acceleration or a rate deceleration, reflecting a site that was conserved and became variable, or vice-versa, respectively. Sites displaying such a dramatic evolutionary change may point to a loss or gain of function at the protein site, reflecting adaptation, or they may indicate epistatic interactions among sites. Here, we analyzed full genomes of HIV and SIV-1 and identified 271 rate-shifting sites along the HIV-1/SIV phylogeny. The majority of rate shifts occurred at long branches, often corresponding to cross-species transmission branches. We noted that in most proteins, the number of rate accelerations and decelerations was equal, and we suggest that this reflects epistatic interactions among sites. However, several accessory proteins were enriched for either accelerations or decelerations, and we suggest that this may be a signature of adaptation to new hosts. Interestingly, the non-pandemic HIV-1 group O clade exhibited a substantially higher number of rate-shift events than the pandemic group M clade. We propose that this may be a reflection of the height of the species barrier between gorillas and humans versus chimpanzees and humans. Our results provide a genome-wide view of the constraints operating on proteins of HIV-1 and SIV. View Full-Text
Keywords: phylogenetics; rate shifts; cross-species transmission; HIV phylogenetics; rate shifts; cross-species transmission; HIV
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MDPI and ACS Style

Gelbart, M.; Stern, A. Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV. Viruses 2020, 12, 1312.

AMA Style

Gelbart M, Stern A. Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV. Viruses. 2020; 12(11):1312.

Chicago/Turabian Style

Gelbart, Maoz, and Adi Stern. 2020. "Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV" Viruses 12, no. 11: 1312.

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