Prolonged and Substantial Discordance in Prevalence of Raltegravir-Resistant HIV-1 in Plasma versus PBMC Samples Revealed by 454 "Deep" Sequencing

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Lee, Guinevere Q ^a,b   Swenson, Luke C ^a,b   Poon, Art F Y ^a,b   Martin, Jeffrey N ^c   Hatano, Hiroyu ^c   Deeks, Steven G ^c   Harrigan, P Richard ^a,b  

^a BRITISH COLUMBIA CENTRE FOR EXCELLENCE IN HIV AIDS   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABACAVIR; DARUNAVIR; EMTRICITABINE; ETRAVIRINE; HUMAN GROWTH HORMONE; LAMIVUDINE; MARAVIROC; RALTEGRAVIR; RITONAVIR; TENOFOVIR; TIPRANAVIR;

ADULT; ARTICLE; CASE REPORT; COHORT ANALYSIS; CONTROLLED STUDY; ETHNICITY; GENE MUTATION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MALE; NUCLEOTIDE SEQUENCE; PERIPHERAL BLOOD MONONUCLEAR CELL; PHYLOGENY; POLYMERASE CHAIN REACTION; PREVALENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VIRUS LOAD;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV-1; HUMANS; LEUKOCYTES, MONONUCLEAR; MALE; MIDDLE AGED; PLASMA; PROSPECTIVE STUDIES; PYRROLIDINONES;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84866869125     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046181     Document Type: Article

References (31)

1. Devereux HL, Loveday C, Youle M, Sabin CA, Burke A, et al. (2000) Substantial correlation between HIV type 1 drug-associated resistance mutations in plasma and peripheral blood mononuclear cells in treatment-experienced patients. AIDS Res Hum Retroviruses 16: 1025-1030.
2. Sarmati L, Nicastri E, Uccella I, D'Ettorre G, Parisi SG, et al. (2003) Drug-associated resistance mutations in plasma and peripheral blood mononuclear cells of human immunodeficiency virus type 1-infected patients for whom highly active antiretroviral therapy is failing. J Clin Microbiol 41: 1760-1762.
3. Soto-Ramirez LE, Rodriguez-Diaz R, Duran AS, Losso MH, Salomon H, et al. (2008) Antiretroviral resistance among HIV type 1-infected women first exposed to antiretrovirals during pregnancy: plasma versus PBMCs. AIDS Res Hum Retroviruses 24: 797-804.
4. Simmonds P, Zhang LQ, McOmish F, Balfe P, Ludlam CA, et al. (1991) Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis. J Virol 65: 6266-6276.
5. Paolucci S, Baldanti F, Campanini G, Zavattoni M, Cattaneo E, et al. (2001) Analysis of HIV drug-resistant quasispecies in plasma, peripheral blood mononuclear cells and viral isolates from treatment-naive and HAART patients. J Med Virol 65: 207-217.
6. Bi X, Gatanaga H, Ida S, Tsuchiya K, Matsuoka-Aizawa S, et al. (2003) Emergence of protease inhibitor resistance-associated mutations in plasma HIV-1 precedes that in proviruses of peripheral blood mononuclear cells by more than a year. J Acquir Immune Defic Syndr 34: 1-6.
7. Ghosn J, Pellegrin I, Goujard C, Deveau C, Viard JP, et al. (2006) HIV-1 resistant strains acquired at the time of primary infection massively fuel the cellular reservoir and persist for lengthy periods of time. Aids 20: 159-170.
8. Wang YM, Dyer WB, Workman C, Wang B, Peng NK, et al. (2007) Drug resistance and viral evolution in plasma and peripheral blood cells during structured treatment interruption (STI) and non-interrupted HAART. Curr HIV Res 5: 235-250.
9. Turriziani O, Bucci M, Stano A, Scagnolari C, Bellomi F, et al. (2007) Genotypic resistance of archived and circulating viral strains in the blood of treated HIV-infected individuals. J Acquir Immune Defic Syndr 44: 518-524.
10. Saracino A, Gianotti N, Marangi M, Cibelli DC, Galli A, et al. (2008) Antiretroviral genotypic resistance in plasma RNA and whole blood DNA in HIV-1 infected patients failing HAART. J Med Virol 80: 1695-1706.
11. Johnson V, Calvez V, Günthard HF, Paredes R, Pillay D, et al. (2011) 2011 update of the drug resistance mutations in HIV-1. Topics in antiviral medicine 19: 156-164.
12. Nakahara K, Wakasa-Morimoto C, Kobayashi M, Miki S, Noshi T, et al. (2009) Secondary mutations in viruses resistant to HIV-1 integrase inhibitors that restore viral infectivity and replication kinetics. Antiviral Res 81: 141-146.
13. Shafer RW, (2006) Rationale and uses of a public HIV drug-resistance database. J Infect Dis 194Suppl: S51-8.
14. Sichtig N, Sierra S, Kaiser R, Daumer M, Reuter S, et al. (2009) Evolution of raltegravir resistance during therapy. J Antimicrob Chemother 64: 25-32.
15. da Silva D, Van Wesenbeeck L, Breilh D, Reigadas S, Anies G, et al. (2010) HIV-1 resistance patterns to integrase inhibitors in antiretroviral-experienced patients with virological failure on raltegravir-containing regimens. J Antimicrob Chemother 65: 1262-1269 doi:dkq099 [pii] 10.1093/jac/dkq099.
16. Hatano H, Lampiris H, Fransen S, Gupta S, Huang W, et al. (2010) Evolution of integrase resistance during failure of integrase inhibitor-based antiretroviral therapy. J Acquir Immune Defic Syndr 54: 389-393.
17. Canducci F, Barda B, Ceresola E, Spagnuolo V, Sampaolo M, et al. (2010) Evolution patterns of raltegravir-resistant mutations after integrase inhibitor interruption. Clin Microbiol Infect 17: 928-934 doi:10.1111/j.1469-0691.2010.03375.x.
18. Charpentier C, Karmochkine M, Laureillard D, Tisserand P, Belec L, et al. (2008) Drug resistance profiles for the HIV integrase gene in patients failing raltegravir salvage therapy. HIV Med 9: 765-770 doi:HIV628 [pii] 10.1111/j.1468-1293.2008.00628.x.
19. Codoñer FM, Pou C, Thielen A, García F, Delgado R, et al. (2010) Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure. Antiviral research 88: 281-286 doi:10.1016/j.antiviral.2010.09.016.
20. Mukherjee R, Jensen ST, Male F, Bittinger K, Hodinka RL, et al. (2011) Switching between raltegravir resistance pathways analyzed by deep sequencing. AIDS (London, England) 25: 1951-1959 doi:10.1097/QAD.0b013e32834b34de.
21. Armenia D, Vandenbroucke I, Fabeni L, Van Marck H, Cento V, et al. (2012) Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing. The Journal of infectious diseases 205: 557-567 doi:10.1093/infdis/jir821.
22. Harrigan PR, Dong W, Wynhoven B, Mo T, Hall T, et al. (2002) Performance of RECall basecalling software for high-throughput HIV Drug resistance basecalling using "in-house" methods. XIV International AIDS Conference. Barcelona, Spain. p. Abstract TuPeB4598.
23. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R, (2011) Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. PNAS 108: 20166-20171.
24. Wirden M, Soulie C, Valantin MA, Fourati S, Simon A, et al. (2011) Historical HIV-RNA resistance test results are more informative than proviral DNA genotyping in cases of suppressed or residual viraemia. J Antimicrob Chemother 66: 709-712.
25. Abbate I, Rozera G, Tommasi C, Bruselles a, Bartolini B, et al. (2011) Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients who are candidates for CCR5 antagonist treatment. Clinical microbiology and infection?: the official publication of the European Society of Clinical Microbiology and Infectious Diseases 17: 725-731 doi:10.1111/j.1469-0691.2010.03350.x.
26. Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, et al. (2009) Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations. Retrovirology 6: 15 doi:10.1186/1742-4690-6-15.
27. Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G (2009) Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent. AIDS: 2541-2546.
28. Baatz F, Struck D, Lemaire M, De Landtsheer S, Servais J-Y, et al. (2011) Rescue of HIV-1 long-time archived X4 strains to escape maraviroc. Antiviral research 92: 488-492 doi:10.1016/j.antiviral.2011.10.003.
29. Bunnik EM, Swenson LC, Edo-Matas D, Huang W, Dong W, et al. (2011) Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing. PLoS pathogens 7: e1002106 doi:10.1371/journal.ppat.1002106.
30. Swenson LC, Moores A, Low AJ, Thielen A, Dong W, et al. (2010) Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA. J Acquir Immune Defic Syndr 54: 506-510.
31. Dalmau J, Codoñer FM, Erkizia I, Pino M, Pou C, et al. (2012) In-Depth Characterization of Viral Isolates from Plasma and Cells Compared with Plasma Circulating Quasispecies in Early HIV-1 Infection. PloS one 7: e32714 doi:10.1371/journal.pone.0032714.