Increasingly successful highly active antiretroviral therapy delays the emergence of new HLA class I-associated escape mutations in HIV-1

Clinical Infectious Diseases

Volumn 54, Issue 11, 2012, Pages 1652-1659

  Knapp, David J H F ^a   Brumme, Zabrina L ^a,b   Huang, Sheng Yuan ^a   Wynhoven, Brian ^a   Dong, Winnie W Y ^a   Mo, Theresa ^a   Harrigan, P Richard ^a,c   Brumme, Chanson J ^a  

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

^b SIMON FRASER UNIVERSITY   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; HLA ANTIGEN CLASS 1; NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; PROTEINASE INHIBITOR; VIRUS RNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ARTICLE; CD4+ T LYMPHOCYTE; COHORT ANALYSIS; CYTOTOXIC T LYMPHOCYTE; FOLLOW UP; GENOTYPE; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HLA SYSTEM; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; IMMUNE RESPONSE; MULTIVARIATE ANALYSIS; NUCLEOTIDE SEQUENCE; OBSERVATIONAL STUDY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TREATMENT RESPONSE; UNIVARIATE ANALYSIS; VIRUS LOAD; VIRUS MUTATION;

ADULT; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; BRITISH COLUMBIA; EPITOPES, T-LYMPHOCYTE; FEMALE; HISTOCOMPATIBILITY ANTIGENS CLASS I; HIV INFECTIONS; HIV-1; HUMANS; IMMUNE EVASION; MALE; MUTATION; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; POLYMORPHISM, GENETIC; SELECTION, GENETIC; T-LYMPHOCYTES, CYTOTOXIC; VIRAL LOAD;

EID: 84861082186     PISSN: 10584838     EISSN: 15376591     Source Type: Journal    
DOI: 10.1093/cid/cis253     Document Type: Article

References (31)

1. Goulder PJ, Phillips RE, Colbert RA, et al. Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat Med 1997; 3:212-7.
2. Borrow P, Lewicki H, Wei X, et al. Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat Med 1997; 3:205-11.
3. Larder BA, Kemp SD. Multiple mutations in HIV-1 reverse tran-scriptase confer high-level resistance to zidovudine (AZT). Science 1989; 246:1155-8.
4. Richman DD. Clinical significance of drug resistance in human immunodeficiency virus. Clin Infect Dis 1995; 21(Suppl 2):S166-9.
5. 1 T cells in peripheral blood after initiation of highly active antiretroviral therapy. J Virol 2001; 75:6508-16.
6. Weekes MP, Wills MR, Sissons JG, Carmichael AJ. Large HIV-specific CD8 cytotoxic T-lymphocyte (CTL) clones reduce their overall size but maintain high frequencies of memory CTL following highly active antiretroviral therapy. Immunology 2006; 118:25-38.
7. Casazza JP, Betts MR, Hill BJ, et al. Immunologic pressure within class I-restricted cognate human immunodeficiency virus epitopes during highly active antiretroviral therapy. J Virol 2005; 79:3653-63.
8. Karlsson AC, Deeks SG, Barbour JD, et al. Dual pressure from anti-retroviral therapy and cell-mediated immune response on the human immunodeficiency virus type 1 protease gene. J Virol 2003; 77:6743-52.
9. Mueller SM, Schaetz B, Eismann K, et al. Dual selection pressure by drugs and HLA class I-restricted immune responses on human immunodeficiency virus type 1 protease. J Virol 2007; 81:2887-98.
10. Moore CB, John M, James IR, Christiansen FT, Witt CS, Mallal SA. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 2002; 296:1439-43.
11. Bhattacharya T, Daniels M, Heckerman D, et al. Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science 2007; 315:1583-6.
12. Brumme ZL, Brumme CJ, Heckerman D, et al. Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog 2007; 3:e94.
13. Brumme ZL, John M, Carlson JM, et al. HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One 2009; 4:e6687.
14. Rousseau CM, Daniels MG, Carlson JM, et al. HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c pro-teome: immune escape and viral load. J Virol 2008; 82:6434-46.
15. Matthews PC, Prendergast A, Leslie A, et al. Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J Virol 2008; 82:8548-59.
16. Poon AF, Kosakovsky Pond SL, Bennett P, Richman DD, Leigh Brown AJ, Frost SD. Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathog 2007; 3:e45.
17. Hogg RS, Heath KV, Yip B, et al. Improved survival among HIV-infected individuals following initiation of antiretroviral therapy. JAMA 1998; 279:450-4.
18. Harrigan PR, Hogg RS, Dong WW, et al. Predictors of HIV drug-resistance mutations in a large antiretroviral-naive cohort initiating triple antiretroviral therapy. J Infect Dis 2005; 191:339-47.
19. Huang X, Zhang J. Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci 1996; 12:497-506.
20. Carlson JM, Brumme ZL, Rousseau CM, et al. Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol 2008; 4:e1000225.
21. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003; 100:9440-5.
22. Johnson VA, Brun-Vezinet F, Clotet B, et al. Update of the drug resistance mutations in HIV-1: December 2010. Top HIV Med 2010; 18:156-63.
23. Kawashima Y, Pfafferott K, Frater J, et al. Adaptation of HIV-1 to human leukocyte antigen class I. Nature 2009; 458:641-5.
24. John M, Moore CB, James IR, Mallal SA. Interactive selective pressures of HLA-restricted immune responses and antiretroviral drugs on HIV-1. Antivir Ther 2005; 10:551-5.
25. Huang KH, Goedhals D, Carlson JM, et al. Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS One 2011; 6:e19018.
26. Williamson S, Perry SM, Bustamante CD, Orive ME, Stearns MN, Kelly JK. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol Biol Evol 2005; 22:456-68.
27. Brumme ZL, Brumme CJ, Carlson J, et al. Marked epitope-and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol 2008; 82:9216-27.
28. Feeney ME, Tang Y, Roosevelt KA, et al. Immune escape precedes breakthrough human immunodeficiency virus type 1 viremia and broadening of the cytotoxic T-lymphocyte response in an HLA-B27-positive long-term-nonprogressing child. J Virol 2004; 78:8927-30.
29. Brumme Z, John M, Carlson J, et al. HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol, and Nef genes. PLoS One 2009; 4:e6687.
30. Leitner T, Halapi E, Scarlatti G, et al. Analysis of heterogeneous viral populations by direct DNA sequencing. Biotechniques 1993; 15: 120-7.
31. Palmer S, Kearney M, Maldarelli F, et al. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol 2005; 43:406-13.