Genetic Consequences of Antiviral Therapy on HIV-1

Overview

Journal Comput Math Methods Med

Publisher Hindawi

Specialty Medical Informatics

Date 2015 Jul 15

PMID 26170895

Citations 6

Authors

Miguel Arenas

Affiliations

Soon will be listed here.

Abstract

A variety of enzyme inhibitors have been developed in combating HIV-1, however the fast evolutionary rate of this virus commonly leads to the emergence of resistance mutations that finally allows the mutant virus to survive. This review explores the main genetic consequences of HIV-1 molecular evolution during antiviral therapies, including the viral genetic diversity and molecular adaptation. The role of recombination in the generation of drug resistance is also analyzed. Besides the investigation and discussion of published works, an evolutionary analysis of protease-coding genes collected from patients before and after treatment with different protease inhibitors was included to validate previous studies. Finally, the review discusses the importance of considering genetic consequences of antiviral therapies in models of HIV-1 evolution that could improve current genotypic resistance testing and treatments design.

Citing Articles

Substitution Models of Protein Evolution with Selection on Enzymatic Activity.

Ferreiro D, Khalil R, Sousa S, Arenas M Mol Biol Evol. 2024; 41(2).

PMID: 38314876 PMC: 10873502. DOI: 10.1093/molbev/msae026.

The evolution of the HIV-1 protease folding stability.

Ferreiro D, Khalil R, Gallego M, Osorio N, Arenas M Virus Evol. 2023; 8(2):veac115.

PMID: 36601299 PMC: 9802575. DOI: 10.1093/ve/veac115.

HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models.

Del Amparo R, Arenas M Genes (Basel). 2022; 13(1).

PMID: 35052404 PMC: 8774313. DOI: 10.3390/genes13010061.

Analysis of evolutionary rate of HIV-1 subtype B using blood donor samples in Japan.

Shinohara N, Matsumoto C, Matsubayashi K, Nagai T, Satake M Virus Genes. 2018; 54(3):457-460.

PMID: 29511955 DOI: 10.1007/s11262-018-1548-1.

HIV-1 drug-resistant mutations and related risk factors among HIV-1-positive individuals experiencing treatment failure in Hebei Province, China.

Lu X, Zhao H, Zhang Y, Wang W, Zhao C, Li Y AIDS Res Ther. 2017; 14(1):4.

PMID: 28114955 PMC: 5260017. DOI: 10.1186/s12981-017-0133-3.

References

Ibanez A, Clotet B, Martinez M . Human immunodeficiency virus type 1 population bottleneck during indinavir therapy causes a genetic drift in the env quasispecies. J Gen Virol. 2000; 81(Pt 1):85-95. DOI: 10.1099/0022-1317-81-1-85. View

Najera R, Delgado E, Perez-Alvarez L, Thomson M . Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS. 2003; 16 Suppl 4:S3-16. DOI: 10.1097/00002030-200216004-00002. View

Bretscher M, Althaus C, Muller V, Bonhoeffer S . Recombination in HIV and the evolution of drug resistance: for better or for worse?. Bioessays. 2004; 26(2):180-8. DOI: 10.1002/bies.10386. View

Nickle D, Heath L, Jensen M, B Gilbert P, Mullins J, Kosakovsky Pond S . HIV-specific probabilistic models of protein evolution. PLoS One. 2007; 2(6):e503. PMC: 1876811. DOI: 10.1371/journal.pone.0000503. View

Batorsky R, Kearney M, Palmer S, Maldarelli F, Rouzine I, Coffin J . Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc Natl Acad Sci U S A. 2011; 108(14):5661-6. PMC: 3078368. DOI: 10.1073/pnas.1102036108. View

Wu T, Schiffer C, Gonzales M, Taylor J, Kantor R, Chou S . Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol. 2003; 77(8):4836-47. PMC: 152121. DOI: 10.1128/jvi.77.8.4836-4847.2003. View

Nijhuis M, Boucher C, Schipper P, Leitner T, Schuurman R, Albert J . Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy. Proc Natl Acad Sci U S A. 1998; 95(24):14441-6. PMC: 24392. DOI: 10.1073/pnas.95.24.14441. View

Rhee S, Gonzales M, Kantor R, Betts B, Ravela J, Shafer R . Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 2003; 31(1):298-303. PMC: 165547. DOI: 10.1093/nar/gkg100. View

Gotte M . The distinct contributions of fitness and genetic barrier to the development of antiviral drug resistance. Curr Opin Virol. 2012; 2(5):644-50. DOI: 10.1016/j.coviro.2012.08.004. View

10.

Castro-Nallar E, Perez-Losada M, Burton G, Crandall K . The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol. 2011; 62(2):777-92. PMC: 3258026. DOI: 10.1016/j.ympev.2011.11.019. View

11.

Mona S, Ray N, Arenas M, Excoffier L . Genetic consequences of habitat fragmentation during a range expansion. Heredity (Edinb). 2013; 112(3):291-9. PMC: 3931167. DOI: 10.1038/hdy.2013.105. View

12.

Zollner B, Feucht H, Weitner L, Adam A, Schroter M, Schafer P . Application of HIV-1 genotypic-resistance testing prevents the evolution of further resistance mutations in heavily pretreated patients. J Clin Virol. 2001; 21(1):37-45. DOI: 10.1016/s1386-6532(00)00183-9. View

13.

Quinones-Mateu M, Gao Y, Ball S, Marozsan A, Abraha A, Arts E . In vitro intersubtype recombinants of human immunodeficiency virus type 1: comparison to recent and circulating in vivo recombinant forms. J Virol. 2002; 76(19):9600-13. PMC: 136488. DOI: 10.1128/jvi.76.19.9600-9613.2002. View

14.

Branham M, Ross E, Govender T . Predictive models for maximum recommended therapeutic dose of antiretroviral drugs. Comput Math Methods Med. 2012; 2012:469769. PMC: 3299291. DOI: 10.1155/2012/469769. View

15.

Wensing A, Calvez V, Gunthard H, Johnson V, Paredes R, Pillay D . 2014 Update of the drug resistance mutations in HIV-1. Top Antivir Med. 2014; 22(3):642-50. PMC: 4392881. View

16.

Fraser C . HIV recombination: what is the impact on antiretroviral therapy?. J R Soc Interface. 2006; 2(5):489-503. PMC: 1618498. DOI: 10.1098/rsif.2005.0064. View

17.

Kitrinos K, Nelson J, Resch W, Swanstrom R . Effect of a protease inhibitor-induced genetic bottleneck on human immunodeficiency virus type 1 env gene populations. J Virol. 2005; 79(16):10627-37. PMC: 1182671. DOI: 10.1128/JVI.79.16.10627-10637.2005. View

18.

Wensing A, van Maarseveen N, Nijhuis M . Fifteen years of HIV Protease Inhibitors: raising the barrier to resistance. Antiviral Res. 2009; 85(1):59-74. DOI: 10.1016/j.antiviral.2009.10.003. View

19.

Harada S, Yoshimura K, Yamaguchi A, Boonchawalit S, Yusa K, Matsushita S . Impact of antiretroviral pressure on selection of primary human immunodeficiency virus type 1 envelope sequences in vitro. J Gen Virol. 2013; 94(Pt 5):933-943. PMC: 4093781. DOI: 10.1099/vir.0.047167-0. View

20.

Perez-Losada M, Arenas M, Galan J, Palero F, Gonzalez-Candelas F . Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. Infect Genet Evol. 2014; 30:296-307. PMC: 7106159. DOI: 10.1016/j.meegid.2014.12.022. View