Combined antiretroviral therapy and immune pressure lead to in vivo HIV-1 recombination with ancestral viral genomes

Journal of Acquired Immune Deficiency Syndromes

Volumn 57, Issue 2, 2011, Pages 109-117

  Buzón, Maria José ^a   Wrin, Terri ^b   Codoñer, Francisco M ^a   Dalmau, Judith ^a   Phung, Pham ^b   Bonjoch, Anna ^c   Coakley, Eoin ^b   Clotet, Bonaventura ^a,c   Martinez Picado, Javier ^a,d  

^a HOSPITAL UNIVERSITARI GERMANS TRIAS I PUJOL   (Spain)

^b MONOGRAM BIOSCIENCES   (United States)

^c Fundació de Lluita Contral la SIDA   (Spain)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

drug interruption; drug resistance; PR inhibitors; recombination; replication capacity

Indexed keywords

ABACAVIR; AMPRENAVIR; ANTIRETROVIRUS AGENT; LAMIVUDINE; LOPINAVIR; NEUTRALIZING ANTIBODY; PROTEINASE; PROTEINASE INHIBITOR; RITONAVIR; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; SAQUINAVIR; TENOFOVIR; ZIDOVUDINE;

ANTIBODY TITER; ANTIVIRAL SUSCEPTIBILITY; ARTICLE; CASE REPORT; DRUG WITHDRAWAL; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; IN VIVO STUDY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; VIRUS ENVELOPE; VIRUS GENOME; VIRUS RECOMBINATION; VIRUS REPLICATION;

ADAPTATION, PHYSIOLOGICAL; ANTI-HIV AGENTS; BIOLOGICAL EVOLUTION; DRUG RESISTANCE, MULTIPLE, VIRAL; DRUG THERAPY, COMBINATION; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; NEUTRALIZATION TESTS; PHYLOGENY; REASSORTANT VIRUSES; RECOMBINATION, GENETIC; RETROSPECTIVE STUDIES; RNA, VIRAL; VIRUS REPLICATION;

EID: 79957957867     PISSN: 15254135     EISSN: 10779450     Source Type: Journal    
DOI: 10.1097/QAI.0b013e318215ab0a     Document Type: Article

References (48)

1. Kaufmann DE, Lichterfeld M, Altfeld M, et al. Limited durability of viral control following treated acute HIV infection. PLoS Med. 2004;1:e36.
2. Abadi J, Sprecher E, Rosenberg MG, et al. Partial treatment interruption of protease inhibitor-based highly active antiretroviral therapy regimens in HIV-infected children. J Acquir Immune Defic Syndr. 2006;41:298-303.
3. Bonjoch A, Buzon MJ, Llibre JM, et al. Transient treatment exclusively containing nucleoside analogue reverse transcriptase inhibitors in highly antiretroviral-experienced patients preserves viral benefit when a fully active therapy was initiated. HIV Clin Trials. 2008;9:387-398.
4. Deeks SG, Hoh R, Neilands TB, et al. Interruption of treatment with individual therapeutic drug classes in adults with multidrug-resistant HIV-1 infection. J Infect Dis. 2005;192:1537-1544. (Pubitemid 41504689)
5. García F, Plana M, Vidal C, et al. Dynamics of viral load rebound and immunological changes after stopping effective antiretroviral therapy. AIDS. 1999;13:F79-F86. (Pubitemid 29408440)
6. Harrigan PR, Whaley M, Montaner JS. Rate of HIV-1 RNA rebound upon stopping antiretroviral therapy. AIDS. 1999;13:F59-F62. (Pubitemid 29240180)
7. Ruiz L, Martinez-Picado J, Romeu J, et al. Structured treatment interruption in chronically HIV-1 infected patients after long-term viral suppression. AIDS. 2000;14:397-403. (Pubitemid 30182436)
8. Devereux HL, Emery VC, Johnson MA, et al. Replicative fitness in vivo of HIV-1 variants with multiple drug resistance-associated mutations. J Med Virol. 2001;65:218-224. (Pubitemid 32816690)
9. Kijak GH, Simon V, Balfe P, et al. Origin of human immunodeficiency virus type 1 quasispecies emerging after antiretroviral treatment interruption in patients with therapeutic failure. J Virol. 2002;76: 7000-7009. (Pubitemid 41246214)
10. Briones C, de Vicente A, Molina-París C, et al. Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo. Gene. 2006;384:129-138. (Pubitemid 44767961)
11. Bello G, Casado C, García S, et al. Co-existence of recent and ancestral nucleotide sequences in viral quasispecies of human immunodeficiency virus type 1 patients. J Gen Virol. 2004;85:399-407. (Pubitemid 38262574)
12. Kitchen CM, Lu J, Suchard MA, et al. Continued evolution in gp41 after interruption of enfuvirtide in subjects with advanced HIV type 1 disease. AIDS Res Hum Retroviruses. 2006;22:1260-1266. (Pubitemid 46095244)
13. Verhofstede C, Wanzeele FV, Van Der Gucht B, et al. Interruption of reverse transcriptase inhibitors or a switch from reverse transcriptase to protease inhibitors resulted in a fast reappearance of virus strains with a reverse transcriptase inhibitor-sensitive genotype. AIDS. 1999;13:2541-2546. (Pubitemid 30038032)
14. Yerly S, Rakik A, De Loes SK, et al. Switch to unusual amino acids at codon 215 of the human immunodeficiency virus type 1 reverse transcriptase gene in seroconvertors infected with zidovudine-resistant variants. J Virol. 1998;72:3520-3523. (Pubitemid 28188646)
15. Richman DD, Wrin T, Little SJ, et al. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci USA. 2003;100:4144-4149. (Pubitemid 36418171)
16. Wei X, Decker JM, Wang S, et al. Antibody neutralization and escape by HIV-1. Nature. 2003;422:307-312. (Pubitemid 36378357)
17. Trkola A, Kuster H, Leemann C, et al. Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point. Blood. 2004;104: 1784-1792. (Pubitemid 39202288)
18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-1797. (Pubitemid 38832724)
19. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008;25:1253-1256.
20. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52: 696-704. (Pubitemid 37365050)
21. Lewis F, Hughes GJ, Rambaut A, et al. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 2008;5:e50.
22. Martin D, Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics. 2000;16:562-563.
23. Martin DP, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics. 2005;21:260-262. (Pubitemid 40202028)
24. Kosakovsky Pond SL, Posada D, Gravenor MB, et al. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 2006;23:1891-1901. (Pubitemid 44412875)
25. Pond SL, Frost SD. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005;21: 2531-2533. (Pubitemid 40731616)
26. Lole KS, Bollinger RC, Paranjape RS, et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1999;73:152-160. (Pubitemid 28565356)
27. Kosakovsky Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005;22:1208-1222. (Pubitemid 40577758)
28. Petropoulos CJ, Parkin NT, Limoli KL, et al. A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob Agents Chemother. 2000;44:920-928. (Pubitemid 30165271)
29. Campbell TB, Schneider K, Wrin T, et al. Relationship between in vitro human immunodeficiency virus type 1 replication rate and virus load in plasma. J Virol. 2003;77:12105-12112. (Pubitemid 37339863)
30. Charpentier C, Dwyer DE, Mammano F, et al. Role of minority populations of human immunodeficiency virus type 1 in the evolution of viral resistance to protease inhibitors. J Virol. 2004;78:4234-4247. (Pubitemid 38437228)
31. Chun TW, Davey RT, Ostrowski M, et al. Relationship between preexisting viral reservoirs and the re-emergence of plasma viremia after discontinuation of highly active anti-retroviral therapy. Nat Med. 2000;6: 757-761. (Pubitemid 30469423)
32. Imamichi H, Crandall KA, Natarajan V, et al. Human immunodeficiency virus type 1 quasi species that rebound after discontinuation of highly active antiretroviral therapy are similar to the viral quasi species present before initiation of therapy. J Infect Dis. 2001;183:36-50. (Pubitemid 32043039)
33. Joos B, Fischer M, Kuster H, et al. HIV rebounds from latently infected cells, rather than from continuing low-level replication. Proc Natl Acad Sci USA. 2008;105:16725-16730.
34. Martinez-Picado J, Frost SD, Izquierdo N, et al. Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individuals. J Virol. 2002;76:12344-12348. (Pubitemid 35304333)
35. Noë A, Plum J, Verhofstede C. The latent HIV-1 reservoir in patients undergoing HAART: an archive of pre-HAART drug resistance. J Antimicrob Chemother. 2005;55:410-412. (Pubitemid 40542575)
36. Verhofstede C, Noë A, Demecheleer E, et al. Drug-resistant variants that evolve during nonsuppressive therapy persist in HIV-1-infected peripheral blood mononuclear cells after long-term highly active antiretroviral therapy. J Acquir Immune Defic Syndr. 2004;35: 473-483. (Pubitemid 38420656)
37. Judo MS, Wedel AB, Wilson C. Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res. 1998;26:1819-1825. (Pubitemid 28291822)
38. Meyerhans A, Vartanian JP, Wain-Hobson S. DNA recombination during PCR. Nucleic Acids Res. 1990;18:1687-1691.
39. Fang G, Zhu G, Burger H, Keithly JS, Weiser B. Minimizing DNA recombination during long RT-PCR. J Virol Methods. 1998;76:139-148. (Pubitemid 28537849)
40. Brown AJ, Cleland A. Independent evolution of the env and pol genes of HIV-1 during zidovudine therapy. AIDS. 1996;10:1067-1073. (Pubitemid 26283343)
41. Shi B, Kitchen C, Weiser B, et al. Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy. Virology. 2010;404:5-20.
42. Mild M, Esbjö rnsson J, Fenyö EM, et al. Frequent intrapatient recombination between human immunodeficiency virus type 1 R5 and X4 envelopes: implications for coreceptor switch. J Virol. 2007;81: 3369-3376. (Pubitemid 46456646)
43. van Rij RP, Worobey M, Visser JA, et al. Evolution of R5 and X4 human immunodeficiency virus type 1 gag sequences in vivo: evidence for recombination. Virology. 2003;314:451-459. (Pubitemid 37153329)
44. Leitner T, Escanilla D, Marquina S, et al. Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology. 1995;209:136-146.
45. Sabino EC, Shpaer EG, Morgado MG, et al. Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil. J Virol. 1994;68:6340-6346. (Pubitemid 24294885)
46. Charpentier C, Nora T, Tenaillon O, et al. Extensive recombination among human immunodeficiency virus type 1 quasispecies makes an important contribution to viral diversity in individual patients.JVirol. 2006;80:2472-2482. (Pubitemid 43271553)
47. Buzón MJ, Dalmau J, Puertas MC, et al. The HIV-1 integrase genotype strongly predicts raltegravir susceptibility but not viral fitness of primary virus isolates. AIDS. 2010;24:17-25.
48. Martinez-Picado J, Martínez MA. HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res. 2008;134:104-123.