CD8 and CD4 epitope predictions in RV144: No strong evidence of a T-cell driven sieve effect in HIV-1 Breakthrough sequences from trial participants

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Dommaraju, Kalpana ^a,b   Kijak, Gustavo ^a,b   Carlson, Jonathan M ^c   Larsen, Brendan B ^d   Tovanabutra, Sodsai ^a,b   Geraghty, Dan E ^e   Deng, Wenjie ^d   Maust, Brandon S ^d   Edlefsen, Paul T ^e   Sanders Buell, Eric ^a,b   Ratto Kim, Silvia ^a,b   DeSouza, Mark S ^f   Rerks Ngarm, Supachai ^g   Nitayaphan, Sorachai ^f   Pitisuttihum, Punnee ^h   Kaewkungwal, Jaranit ^h   O'Connell, Robert J ^f   Robb, Merlin L ^a,b   Michael, Nelson L ^a   Mullins, James I ^d   Kim, Jerome H ^a   Rolland, Morgane ^a,b   more..

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^b Henry Jackson Foundation   (United States)

^c MICROSOFT RESEARCH   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e Fred Hutchinson Cancer Research Center   (United States)

^f ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^g MINISTRY OF PUBLIC HEALTH   (Thailand)

^h MAHIDOL UNIVERSITY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAG PROTEIN; GLYCOPROTEIN GP 120; HLA A11 ANTIGEN; HLA A2 ANTIGEN; HLA B ANTIGEN; HLA B46 ANTIGEN; HLA DRB1 ANTIGEN; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; NEF PROTEIN; PLACEBO; POL PROTEIN; PROTEOME; UNCLASSIFIED DRUG; VIRUS ENVELOPE PROTEIN; ERDOSTEINE; HLA ANTIGEN; THIOGLYCOLIC ACID DERIVATIVE; THIOPHENE DERIVATIVE;

AMINO ACID SEQUENCE; ANTIBODY RESPONSE; ARTICLE; BINDING AFFINITY; BREAKTHROUGH INFECTION; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELLULAR IMMUNITY; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; DRUG EFFICACY; EVOLUTION; EVOLUTIONARY DISTANCE; GENOTYPE; HLA TYPING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 CRF01 AE; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPE B; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; RANDOMIZED CONTROLLED TRIAL; RANDOMIZED CONTROLLED TRIAL (TOPIC); SIEVE EFFECT; UNINDEXED SEQUENCE; VIRUS GENOME; VIRUS LOAD; ADOLESCENT; ADULT; ALLELE; CHEMISTRY; CLINICAL TRIAL; CYTOLOGY; FEMALE; GENETICS; HIV INFECTIONS; MALE; PHASE 3 CLINICAL TRIAL; YOUNG ADULT;

HUMAN IMMUNODEFICIENCY VIRUS 1;

ADOLESCENT; ADULT; AIDS VACCINES; ALLELES; CD4-POSITIVE T-LYMPHOCYTES; CD8-POSITIVE T-LYMPHOCYTES; EPITOPES, T-LYMPHOCYTE; FEMALE; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENOTYPE; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HLA ANTIGENS; HUMANS; MALE; PROTEOME; THIOGLYCOLATES; THIOPHENES; YOUNG ADULT;

EID: 84908583720     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0111334     Document Type: Article

References (18)

1. Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Chiu J, et al. (2009) Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med 361: 2209-2220.
2. Rolland M, Edlefsen PT, Larsen BB, Tovanabutra S, Sanders-Buell E, et al. (2012) Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Nature.
3. Liao HX, Bonsignori M, Alam SM, McLellan JS, Tomaras GD, et al. (2013) Vaccine induction of antibodies against a structurally heterogeneous site of immune pressure within HIV-1 envelope protein variable regions 1 and 2. Immunity 38: 176-186.
4. Haynes BF, Gilbert PB, McElrath MJ, Zolla-Pazner S, Tomaras GD, et al. (2012) Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N Engl J Med 366: 1275-1286.
5. Rolland M, Heckerman D, Deng W, Rousseau C, Coovadia H, et al. (2008) Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PLoS ONE 3: e1424.
6. Rolland M, Tovanabutra S, deCamp AC, Frahm N, Gilbert PB, et al. (2011) Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nat Med 17: 366-371.
7. Hurley CK, Mack SJ, Mickelson E, Marsh S, Tilanus MGJ, et al. (2006) HLA typing and informatics. in immunobiology of the human MHC, in J A Hansen (ed), 13th International Histocompatibility Workshop protocols IHWG Press, Seattle, WA: 179-352.
8. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, et al. (2007) NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2: e796.
9. Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S (2010) NetMHCIIpan-2.0 -Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Res 6: 9.
10. Rolland M, Frahm N, Nickle DC, Jojic N, Deng W, et al. (2011) Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences. PLoS ONE 6: e17969.
11. Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, et al. (2007) HIVspecific probabilistic models of protein evolution. PLoS One 2: e503.
12. Carlson JM, Brumme ZL, Rousseau CM, Brumme CJ, Matthews P, et al. (2008) Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol 4: e1000225.
13. Karasavvas N, Billings E, Rao M, Williams C, Zolla-Pazner S, et al. (2012) The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120. AIDS Res Hum Retroviruses 28: 1444-1457.
14. de Souza MS, Ratto-Kim S, Chuenarom W, Schuetz A, Chantakulkij S, et al. (2012) The Thai phase III trial (RV144) vaccine regimen induces T cell responses that preferentially target epitopes within the V2 region of HIV-1 envelope. J Immunol 188: 5166-5176.
15. Douek DC, Betts MR, Hill BJ, Little SJ, Lempicki R, et al. (2001) Evidence for increased T cell turnover and decreased thymic output in HIV infection. J Immunol 167: 6663-6668.
16. de Souza MS, Ratto-Kim S, Chuenarom W, Schuetz A, Chantakulkij S, et al. (2012) The Thai phase III trial (RV144) vaccine regimen induces T cell responses that preferentially target epitopes within the V2 region of HIV-1 envelope. Journal of immunology 188: 5166-5176.
17. Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, et al. (2014) Analysis of HLA A∗02 Association with Vaccine Efficacy in the RV144 HIV-1 Vaccine Trial. Journal of virology 88: 8242-8255.
18. Edlefsen PT, Gilbert PB, Rolland M (2013) Sieve analysis in HIV-1 vaccine efficacy trials. Curr Opin HIV AIDS 8: 432-436.