RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy

Retrovirology

Volumn 6, Issue , 2009, Pages 101-

  Shao, Wei ^a   Kearney, Mary ^b   Maldarelli, Frank ^b   Mellors, John W ^c   Stephens, Robert M ^a   Lifson, Jeffrey D ^a   KewalRamani, Vineet N ^b   Ambrose, Zandrea ^c   Coffin, John M ^d   Palmer, Sarah E ^b,e  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^d TUFTS UNIVERSITY   (United States)

^e SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; EFAVIRENZ; EMTRICITABINE; RNA DIRECTED DNA POLYMERASE INHIBITOR; TENOFOVIR;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANTIBIOTIC RESISTANCE; ARTICLE; CONTROLLED STUDY; GENE MUTATION; GENETIC VARIABILITY; HOMOZYGOSITY; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MACACA; MONOTHERAPY; NONHUMAN; PERSISTENT INFECTION; POPULATION DYNAMICS; SHORT COURSE THERAPY; SIMIAN IMMUNODEFICIENCY VIRUS; VIREMIA; VIRUS GENOME; WILD TYPE;

ANIMALS; ANTI-HIV AGENTS; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; BENZOXAZINES; BIODIVERSITY; CLUSTER ANALYSIS; DRUG RESISTANCE, VIRAL; HIV-1; MACACA; MUTATION, MISSENSE; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; RNA, VIRAL; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS;

ANIMALIA; HUMAN IMMUNODEFICIENCY VIRUS 1; MACACA; MACACA NEMESTRINA; SIMIAN IMMUNODEFICIENCY VIRUS; SIMIAN-HUMAN IMMUNODEFICIENCY VIRUS;

EID: 70749107342     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-6-101     Document Type: Article

References (34)

1. Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 1995, 267(5197):483-489. 10.1126/science.7824947, 7824947.
2. Yang OO, Daar ES, Jamieson BD, Balamurugan A, Smith DM, Pitt JA, Petropoulos CJ, Richman DD, Little SJ, Brown AJ. Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. Journal of virology 2005, 79(2):860-868. 538553, 15613314, 10.1128/JVI.79.2.860-868.2005.
3. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(21):7552-7557. 2387184, 18490657, 10.1073/pnas.0802203105.
4. Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, Keele BF, Derdeyn CA, Farmer P, Hunter E, Allen S, Manigart O, Mulenga J, Anderson JA, Swanstrom R, Haynes BF, Athreya GS, Korber BT, Sharp PM, Shaw GM, Hahn BH. Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. Journal of virology 2008, 82(8):3952-3970. 2293010, 18256145, 10.1128/JVI.02660-07.
5. Poss M, Rodrigo AG, Gosink JJ, Learn GH, de Vange Panteleeff D, Martin HL, Bwayo J, Kreiss JK, Overbaugh J. Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. Journal of virology 1998, 72(10):8240-8251. 110179, 9733867.
6. Roquebert B, Malet I, Wirden M, Tubiana R, Valantin MA, Simon A, Katlama C, Peytavin G, Calvez V, Marcelin AG. Role of HIV-1 minority populations on resistance mutational pattern evolution and susceptibility to protease inhibitors. AIDS 2006, 20(2):287-289. 10.1097/01.aids.0000202650.03279.69, 16511425.
7. Goudsmit J, de Ronde A, de Rooij E, de Boer R. Broad spectrum of in vivo fitness of human immunodeficiency virus type 1 subpopulations differing at reverse transcriptase codons 41 and 215. Journal of virology 1997, 71(6):4479-4484. 191667, 9151839.
8. Lipsitch M, Nowak MA. The evolution of virulence in sexually transmitted HIV/AIDS. Journal of theoretical biology 1995, 174(4):427-440. 10.1006/jtbi.1995.0109, 7666673.
9. Kolber MA. Development of drug resistance mutations in patients on highly active antiretroviral therapy: does competitive advantage drive evolution. AIDS reviews 2007, 9(2):68-74.
10. Johnson VA, Brun-Vezinet F, Clotet B, Gunthard HF, Kuritzkes DR, Pillay D, Schapiro JM, Richman DD. Update of the drug resistance mutations in HIV-1: 2007. Top HIV Med 2007, 15(4):119-125.
11. Goulder PJ, Brander C, Tang Y, Tremblay C, Colbert RA, Addo MM, Rosenberg ES, Nguyen T, Allen R, Trocha A, Altfeld M, He S, Bunce M, Funkhouser R, Pelton SI, Burchett SK, McIntosh K, Korber BT, Walker BD. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 2001, 412(6844):334-338. 10.1038/35085576, 11460164.
12. Leslie AJ, Pfafferott KJ, Chetty P, Draenert R, Addo MM, Feeney M, Tang Y, Holmes EC, Allen T, Prado JG, Altfeld M, Brander C, Dixon C, Ramduth D, Jeena P, Thomas SA, St John A, Roach TA, Kupfer B, Luzzi G, Edwards A, Taylor G, Lyall H, Tudor-Williams G, Novelli V, Martinez-Picado J, Kiepiela P, Walker BD, Goulder PJ. HIV evolution: CTL escape mutation and reversion after transmission. Nature medicine 2004, 10(3):282-289. 10.1038/nm992, 14770175.
13. Charpentier C, Dwyer DE, Mammano F, Lecossier D, Clavel F, Hance AJ. Role of minority populations of human immunodeficiency virus type 1 in the evolution of viral resistance to protease inhibitors. Journal of virology 2004, 78(8):4234-4247. 374292, 15047838, 10.1128/JVI.78.8.4234-4247.2004.
14. Coombs D, Gilchrist MA, Ball CL. Evaluating the importance of within- and between-host selection pressures on the evolution of chronic pathogens. Theoretical population biology 2007, 72(4):576-591. 10.1016/j.tpb.2007.08.005, 17900643.
15. Ball CL, Gilchrist MA, Coombs D. Modeling within-host evolution of HIV: mutation, competition and strain replacement. Bulletin of mathematical biology 2007, 69(7):2361-2385. 10.1007/s11538-007-9223-z, 17554585.
16. Ambrose Z, Boltz V, Palmer S, Coffin JM, Hughes SH, Kewalramani VN. In vitro characterization of a simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques. Journal of virology 2004, 78(24):13553-13561. 533891, 15564466, 10.1128/JVI.78.24.13553-13561.2004.
17. Ambrose Z, Palmer S, Boltz VF, Kearney M, Larsen K, Polacino P, Flanary L, Oswald K, Piatak M, Smedley J, Shao W, Bischofberger N, Maldarelli F, Kimata JT, Mellors JW, Hu SL, Coffin JM, Lifson JD, KewalRamani VN. Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy. Journal of virology 2007, 81(22):12145-12155. 2169021, 17855539, 10.1128/JVI.01301-07.
18. Ayouba A, Tene G, Cunin P, Foupouapouognigni Y, Menu E, Kfutwah A, Thonnon J, Scarlatti G, Monny-Lobe M, Eteki N, Kouanfack C, Tardy M, Leke R, Nkam M, Nlend AE, Barré-Sinoussi F, Martin PM, Nerrienet E, . Yaoundé European Network for the Study of In Utero Transmission of HIV-1 Low rate of mother-to-child transmission of HIV-1 after nevirapine intervention in a pilot public health program in Yaounde, Cameroon. Journal of acquired immune deficiency syndromes 2003, 34(3):274-280. 10.1097/00126334-200311010-00003, 14600571.
19. Guay LA, Musoke P, Fleming T, Bagenda D, Allen M, Nakabiito C, Sherman J, Bakaki P, Ducar C, Deseyve M, Emel L, Mirochnick M, Fowler MG, Mofenson L, Miotti P, Dransfield K, Bray D, Mmiro F, Jackson JB. Intrapartum and neonatal single-dose nevirapine compared with zidovudine for prevention of mother-to-child transmission of HIV-1 in Kampala, Uganda: HIVNET 012 randomised trial. Lancet 1999, 354(9181):795-802. 10.1016/S0140-6736(99)80008-7, 10485720.
20. Jackson JB, Musoke P, Fleming T, Guay LA, Bagenda D, Allen M, Nakabiito C, Sherman J, Bakaki P, Owor M, Ducar C, Deseyve M, Mwatha A, Emel L, Duefield C, Mirochnick M, Fowler MG, Mofenson L, Miotti P, Gigliotti M, Bray D, Mmiro F. Intrapartum and neonatal single-dose nevirapine compared with zidovudine for prevention of mother-to-child transmission of HIV-1 in Kampala, Uganda: 18-month follow-up of the HIVNET 012 randomised trial. Lancet 2003, 362(9387):859-868. 10.1016/S0140-6736(03)14341-3, 13678973.
21. Taha TE, Kumwenda NI, Hoover DR, Fiscus SA, Kafulafula G, Nkhoma C, Nour S, Chen S, Liomba G, Miotti PG, Broadhead RL. Nevirapine and zidovudine at birth to reduce perinatal transmission of HIV in an African setting: a randomized controlled trial. Jama 2004, 292(2):202-209. 10.1001/jama.292.2.202, 15249569.
22. Frost SD, Dumaurier MJ, Wain-Hobson S, Brown AJ. Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(12):6975-6980. 34518, 11381143, 10.1073/pnas.131056998.
23. Lemey P, Rambaut A, Pybus OG. HIV evolutionary dynamics within and among hosts. AIDS reviews 2006, 8(3):125-140.
24. Nijhuis M, Deeks S, Boucher C. Implications of antiretroviral resistance on viral fitness. Current opinion in infectious diseases 2001, 14(1):23-28. 10.1097/00001432-200102000-00005, 11979111.
25. Matamoros T, Kim B, Menendez-Arias L. Mechanistic insights into the role of Val75 of HIV-1 reverse transcriptase in misinsertion and mispair extension fidelity of DNA synthesis. Journal of molecular biology 2008, 375(5):1234-1248. 10.1016/j.jmb.2007.11.021, 18155043.
26. Hofman MJ, Higgins J, Matthews TB, Pedersen NC, Tan C, Schinazi RF, North TW. Efavirenz therapy in rhesus macaques infected with a chimera of simian immunodeficiency virus containing reverse transcriptase from human immunodeficiency virus type 1. Antimicrobial agents and chemotherapy 2004, 48(9):3483-3490.
27. Van Rompay KK, Johnson JA, Blackwood EJ, Singh RP, Lipscomb J, Matthews TB, Marthas ML, Pedersen NC, Bischofberger N, Heneine W, North TW. Sequential emergence and clinical implications of viral mutants with K70E and K65R mutation in reverse transcriptase during prolonged tenofovir monotherapy in rhesus macaques with chronic RT-SHIV infection. Retrovirology 2007, 4:25. 1852805, 17417971, 10.1186/1742-4690-4-25.
28. Lacey SF, Larder BA. Novel mutation (V75T) in human immunodeficiency virus type 1 reverse transcriptase confers resistance to 2',3'-didehydro-2',3'-dideoxythymidine in cell culture. Antimicrobial agents and chemotherapy 1994, 38(6):1428-1432.
29. Kleim JP, Rosner M, Winkler I, Paessens A, Kirsch R, Hsiou Y, Arnold E, Riess G. Selective pressure of a quinoxaline nonnucleoside inhibitor of human immunodeficiency virus type 1(HIV-1) reverse transcriptase (RT) on HIV-1 replication results in the emergence of nucleoside RT-inhibitor-specific (RT Leu-74-->Val or Ile and Val-75-->Leu or Ile) HIV-1 mutants. Proceedings of the National Academy of Sciences of the United States of America 1996, 93(1):34-38. 40173, 8552634, 10.1073/pnas.93.1.34.
30. Svicher V, Sing T, Santoro MM, Forbici F, Rodriguez-Barrios F, Bertoli A, Beerenwinkel N, Bellocchi MC, Gago F, d'Arminio Monforte A, Antinori A, Lengauer T, Ceccherini-Silberstein F, Perno CF. Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. Journal of virology 2006, 80(14):7186-7198. 1489024, 16809324, 10.1128/JVI.02084-05.
31. Trignetti M, Sing T, Svicher V, Santoro MM, Forbici F, D'Arrigo R, Bellocchi MC, Santoro M, Marconi P, Zaccarelli M, Trotta MP, Bellagamba R, Narciso P, Antinori A, Lengauer T, Perno CF, Ceccherini-Silberstein F. Dynamics of NRTI resistance mutations during therapy interruption. AIDS research and human retroviruses 2009, 25(1):57-64.
32. Kearney M, Palmer S, Maldarelli F, Shao W, Polis MA, Mican J, Rock-Kress D, Margolick JB, Coffin JM, Mellors JW. Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase. AIDS (London, England) 2008, 22(4):497-501.
33. Palmer S, Kearney M, Maldarelli F, Halvas EK, Bixby CJ, Bazmi H, Rock D, Falloon J, Davey RT, Dewar RL, Metcalf JA, Hammer S, Mellors JW, Coffin JM. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. Journal of clinical microbiology 2005, 43(1):406-413. 540111, 15635002, 10.1128/JCM.43.1.406-413.2005.
34. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular biology and evolution 2007, 24(8):1596-1599.