Quantifying Differences in the Tempo of Human Immunodeficiency Virus Type 1 Subtype Evolution

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 2009 Oct 2

PMID 19793809

Citations 61

Authors

Ana B Abecasis

Anne-Mieke Vandamme

Philippe Lemey

Affiliations

Soon will be listed here.

Abstract

Human immunodeficiency virus type 1 (HIV-1) genetic diversity, due to its high evolutionary rate, has long been identified as a main cause of problems in the development of an efficient HIV-1 vaccine. However, little is known about differences in evolutionary rate between different subtypes. In this study, we collected representative samples of the main epidemic subtypes and circulating recombinant forms (CRFs), namely, sub-subtype A1, subtypes B, C, D, and G, and CRFs 01_AE and 02_AG. We analyzed separate data sets for pol and env. We performed a Bayesian Markov chain Monte Carlo relaxed-clock phylogenetic analysis and applied a codon model to the resulting phylogenetic trees to estimate nonsynonymous (dN) and synonymous (dS) rates along each and every branch. We found important differences in the evolutionary rates of the different subtypes. These are due to differences not only in the dN rate but also in the dS rate, varying in roughly similar ways, indicating that these differences are caused by both different selective pressures (for dN rate) and the replication dynamics (for dS rate) (i.e., mutation rate or generation time) of the strains. CRF02_AG and subtype G had higher rates, while subtype D had lower dN and dS rates than the other subtypes. The dN/dS ratio estimates were also different, especially for the env gene, with subtype G showing the lowest dN/dS ratio of all subtypes.

Citing Articles

Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.

Mai U, Charvel E, Mirarab S Syst Biol. 2024; 73(5):823-838.

PMID: 38970346 PMC: 11524793. DOI: 10.1093/sysbio/syae034.

Genetic Diversity and Low Therapeutic Impact of Variant-Specific Markers in HIV-1 Pol Proteins.

Troyano-Hernaez P, Reinosa R, Holguin A Front Microbiol. 2022; 13:866705.

PMID: 35910645 PMC: 9330395. DOI: 10.3389/fmicb.2022.866705.

Phylodynamics of HIV in the Mexico City Metropolitan Region.

Avila-Rios S, Garcia-Morales C, Reyes-Teran G, Gonzalez-Rodriguez A, Matias-Florentino M, Mehta S J Virol. 2022; 96(14):e0070822.

PMID: 35762759 PMC: 9327710. DOI: 10.1128/jvi.00708-22.

HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir.

Troyano-Hernaez P, Reinosa R, Holguin A Front Microbiol. 2022; 13:854974.

PMID: 35495642 PMC: 9039614. DOI: 10.3389/fmicb.2022.854974.

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

Nasir A, Dimitrijevic M, Romero-Severson E, Leitner T Viruses. 2021; 13(9).

PMID: 34578270 PMC: 8473000. DOI: 10.3390/v13091689.

References

Robbins K, Lemey P, Pybus O, Jaffe H, Youngpairoj A, Brown T . U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol. 2003; 77(11):6359-66. PMC: 155028. DOI: 10.1128/jvi.77.11.6359-6366.2003. View

Kosakovsky Pond S, Frost S . A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol. 2004; 22(2):223-34. DOI: 10.1093/molbev/msi009. View

Schmidt H, Strimmer K, Vingron M, von Haeseler A . TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002; 18(3):502-4. DOI: 10.1093/bioinformatics/18.3.502. View

Drummond A, Rambaut A . BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007; 7:214. PMC: 2247476. DOI: 10.1186/1471-2148-7-214. View

Keele B, Van Heuverswyn F, Li Y, Bailes E, Takehisa J, Santiago M . Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science. 2006; 313(5786):523-6. PMC: 2442710. DOI: 10.1126/science.1126531. View

Salminen M, Carr J, Burke D, McCutchan F . Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses. 1995; 11(11):1423-5. DOI: 10.1089/aid.1995.11.1423. View

Korber B, Muldoon M, Theiler J, Gao F, Gupta R, Lapedes A . Timing the ancestor of the HIV-1 pandemic strains. Science. 2000; 288(5472):1789-96. DOI: 10.1126/science.288.5472.1789. View

Zhu T, Korber B, Nahmias A, Hooper E, Sharp P, Ho D . An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature. 1998; 391(6667):594-7. DOI: 10.1038/35400. View

Kiwanuka N, Laeyendecker O, Robb M, Kigozi G, Arroyo M, McCutchan F . Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. J Infect Dis. 2008; 197(5):707-13. DOI: 10.1086/527416. View

10.

Lemey P, Kosakovsky Pond S, Drummond A, Pybus O, Shapiro B, Barroso H . Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol. 2007; 3(2):e29. PMC: 1797821. DOI: 10.1371/journal.pcbi.0030029. View

11.

Kosakovsky Pond S, Frost S, Muse S . HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2004; 21(5):676-9. DOI: 10.1093/bioinformatics/bti079. View

12.

Rambaut A, Posada D, Crandall K, Holmes E . The causes and consequences of HIV evolution. Nat Rev Genet. 2004; 5(1):52-61. DOI: 10.1038/nrg1246. View

13.

Rhodes T, Wargo H, Hu W . High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication. J Virol. 2003; 77(20):11193-200. PMC: 224990. DOI: 10.1128/jvi.77.20.11193-11200.2003. View

14.

Hemelaar J, Gouws E, Ghys P, Osmanov S . Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS. 2006; 20(16):W13-23. DOI: 10.1097/01.aids.0000247564.73009.bc. View

15.

Worobey M, Gemmel M, Teuwen D, Haselkorn T, Kunstman K, Bunce M . Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature. 2008; 455(7213):661-4. PMC: 3682493. DOI: 10.1038/nature07390. View

16.

Shapiro B, Rambaut A, Drummond A . Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 2005; 23(1):7-9. DOI: 10.1093/molbev/msj021. View

17.

Walker P, Pybus O, Rambaut A, Holmes E . Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. Infect Genet Evol. 2005; 5(3):199-208. DOI: 10.1016/j.meegid.2004.06.011. View

18.

Abecasis A, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R . Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol. 2007; 81(16):8543-51. PMC: 1951349. DOI: 10.1128/JVI.00463-07. View

19.

Choisy M, Woelk C, Guegan J, Robertson D . Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol. 2004; 78(4):1962-70. PMC: 369455. DOI: 10.1128/jvi.78.4.1962-1970.2004. View

20.

Seo T, Thorne J, Hasegawa M, Kishino H . A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics. 2002; 18(1):115-23. DOI: 10.1093/bioinformatics/18.1.115. View