Format

Send to

Choose Destination
Retrovirology. 2016 Jun 1;13(1):38. doi: 10.1186/s12977-016-0269-6.

Molecular clock of HIV-1 envelope genes under early immune selection.

Author information

1
Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, 90089, USA.
2
Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, 14642, USA.
3
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
4
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
5
Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, 90089, USA. hayoun@usc.edu.

Abstract

BACKGROUND:

The molecular clock hypothesis that genes or proteins evolve at a constant rate is a key tool to reveal phylogenetic relationships among species. Using the molecular clock, we can trace an infection back to transmission using HIV-1 sequences from a single time point. Whether or not a strict molecular clock applies to HIV-1's early evolution in the presence of immune selection has not yet been fully examined.

RESULTS:

We identified molecular clock signatures from 1587 previously published HIV-1 full envelope gene sequences obtained since acute infection in 15 subjects. Each subject's sequence diversity linearly increased during the first 150 days post infection, with rates ranging from [Formula: see text] to [Formula: see text] with a mean of [Formula: see text] per base per day. The rate of diversification for 12 out of the 15 subjects was comparable to the neutral evolution rate. While temporal diversification was consistent with evolution patterns in the absence of selection, mutations from the founder virus were highly clustered on statistically identified selection sites, which diversified more than 65 times faster than non-selection sites. By mathematically quantifying deviations from the molecular clock under various selection scenarios, we demonstrate that the deviation from a constant clock becomes negligible as multiple escape lineages emerge. The most recent common ancestor of a virus pair from distinct escape lineages is most likely the transmitted founder virus, indicating that HIV-1 molecular dating is feasible even after the founder viruses are no longer detectable.

CONCLUSIONS:

The ability of HIV-1 to escape from immune surveillance in many different directions is the driving force of molecular clock persistence. This finding advances our understanding of the robustness of HIV-1's molecular clock under immune selection, implying the potential for molecular dating.

KEYWORDS:

Envelope gene; HIV-1; Mathematical model; Molecular clock

PMID:
27246201
PMCID:
PMC4888660
DOI:
10.1186/s12977-016-0269-6
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center