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

Abstract

Here, 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.

Authors:
; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; Work for Others (WFO)
OSTI Identifier:
1618902
Alternate Identifier(s):
OSTI ID: 1321764
Report Number(s):
LA-UR-15-25156
Journal ID: ISSN 1742-4690; 38; PII: 269
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Published Article
Journal Name:
Retrovirology
Additional Journal Information:
Journal Name: Retrovirology Journal Volume: 13 Journal Issue: 1; Journal ID: ISSN 1742-4690
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; biological science; HIV-1; envelope gene; molecular clock; mathematical model

Citation Formats

Park, Sung Yong, Love, Tanzy M. T., Perelson, Alan S., Mack, Wendy J., and Lee, Ha Youn. Molecular clock of HIV-1 envelope genes under early immune selection. United Kingdom: N. p., 2016. Web. doi:10.1186/s12977-016-0269-6.
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Park, Sung Yong, Love, Tanzy M. T., Perelson, Alan S., Mack, Wendy J., & Lee, Ha Youn. Molecular clock of HIV-1 envelope genes under early immune selection. United Kingdom. https://doi.org/10.1186/s12977-016-0269-6
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Park, Sung Yong, Love, Tanzy M. T., Perelson, Alan S., Mack, Wendy J., and Lee, Ha Youn. Wed . "Molecular clock of HIV-1 envelope genes under early immune selection". United Kingdom. https://doi.org/10.1186/s12977-016-0269-6.
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@article{osti_1618902,
title = {Molecular clock of HIV-1 envelope genes under early immune selection},
author = {Park, Sung Yong and Love, Tanzy M. T. and Perelson, Alan S. and Mack, Wendy J. and Lee, Ha Youn},
abstractNote = {Here, 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.},
doi = {10.1186/s12977-016-0269-6},
journal = {Retrovirology},
number = 1,
volume = 13,
place = {United Kingdom},
year = {Wed Jun 01 00:00:00 EDT 2016},
month = {Wed Jun 01 00:00:00 EDT 2016}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s12977-016-0269-6
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Cited by: 6 works
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Figures / Tables:

Fig. 1 Fig. 1: HIV-1 diversity dynamics of 15 subjects. a Diversity increase as a function of time for the first 150 days since the first sample for 15 HIV-1 infected individuals, CAP045, CH040, CH042, CH058, CH077, CH131, CH159, CH162, CH164, CH185, CH198, CH256, CH505, SUMA0874 and WEAU0578. A total of 1587more » HIV-1 full envelope gene sequences were obtained from references. The population dynamics showed a statistically significant linear diversification rate of 2.69 (±0.29) × 10−5 per site per day (p < 0.0001). The solid line represents the fit of the mixed effects model and the dotted line represents the neutral diversification rate, 2.16 × 10−5 per site per day. b Diversity dynamics over 2 years since the first sample of the 15 subjects. The solid curve denotes the best-fit of the mixed effects model to these overall dynamics. Over the 2 year time frame, the envelope gene sequence population diversifies linearly at a rate of 2.30 × 10−5 per site per day (p < 0.0001) and quadratically at a rate of −0.00122 × 10−5 per site per day2 (p = 0.028). The dotted line again represents the neutral diversification rate, 2.16 × 10−5 per site per day« less
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    Recent advances in understanding HIV evolution
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