Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02-AG

Medicine (United States)

Volumn 95, Issue 32, 2016, Pages

  Heipertz, Richard A ^a   Ayemoba, Ojor ^b   Sanders Buell, Eric ^a,c   Poltavee, Kultida ^a,c   Pham, Phuc ^a,c   Kijak, Gustavo H ^a,c   Lei, Esther ^a,c   Bose, Meera ^a,c   Howell, Shana ^a,c   O'Sullivan, Anne Marie ^a,c   Bates, Adam ^a,c   Cervenka, Taylor ^a,c   Kuroiwa, Janelle ^a,c   Akintunde, Akindiran ^d   Ibezim, Onyekachukwu ^b   Alabi, Abraham ^d,e   Okoye, Obumneke ^b   Manak, Mark ^a,c   Malia, Jennifer ^a,f   Peel, Sheila ^a   Maisaka, Mohammed ^g   Singer, Darrell ^f,h   O'Connell, Robert J ^a   Robb, Merlin L ^a,c   Kim, Jerome H ^a   Michael, Nelson L ^a   Njoku, Ogbonnaya ^d   Tovanabutra, Sodsai ^a,c   more..

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

^b Health Implementation Programme   (Nigeria)

^c HENRY M JACKSON FOUNDATION FOR THE ADVANCEMENT OF MILITARY MEDICINE   (United States)

^d US Military HIV Research Program (HJF MRI)   (Nigeria)

^e Centre de Recherches Medicales de Lambarene (CERMEL)   (Central African Republic)

^f U S PUBLIC HEALTH SERVICE   (United States)

^g Department of Defense HIV Program ^*  (Nigeria)

^h NONE   (Nigeria)

Author keywords

Genetic complexity; HIV 1; Nigeria; Recombinant; Subtypes

Indexed keywords

ADULT; ARTICLE; CITY; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; GENE SEQUENCE; GRF02 AG; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS PREVALENCE; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPE G; IMMUNOASSAY; MALE; MULTI REGION HYBRIDIZATION ASSAY; NIGERIA; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RISK FACTOR; SENSITIVITY AND SPECIFICITY; VIRUS CHARACTERIZATION; VIRUS FORMS; VIRUS GENOME; VIRUS RECOMBINANT; VIRUS STRAIN; COHORT ANALYSIS; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETICS; HIV INFECTIONS; HUMAN IMMUNODEFICIENCY VIRUS 1; PHYLOGENY; PROCEDURES; RETROSPECTIVE STUDY;

COHORT STUDIES; FEMALE; GENE EXPRESSION REGULATION, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; MALE; NIGERIA; PHYLOGENY; POLYMORPHISM, GENETIC; REAL-TIME POLYMERASE CHAIN REACTION; RECOMBINATION, GENETIC; RETROSPECTIVE STUDIES; SEQUENCE ANALYSIS, DNA;

EID: 84983454158     PISSN: 00257974     EISSN: 15365964     Source Type: Journal    
DOI: 10.1097/MD.0000000000004346     Document Type: Article

References (39)

1. United Nations AIDS. Fact Sheet 2015. http://www.unaids.org/sites/ default/files/media-asset/20150901-FactSheet-2015-en.pdf. Accessed December 28, 2015
2. National Agency for the Control of AIDS. Nigeria Global AIDS Response Country Progress Report, 2015. http://www.unaids.org/sites/ default/files/country/documents/NGA-narrative-report-2015.pdf. Accessed December 28, 2015
3. Malik, K. The Rise of the South: Human Progress in a Diverse World. http://hdr.undp.org/sites/default/files/reports/14/hdr2013-en-complete. pdf. Accessed December 28, 2015
4. Excler JL, Robb ML, Kim JH. Prospects for a globally effective HIV-1 vaccine. Vaccine 2015;33(suppl 4):D4-12
5. Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, et al. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med 2009;361:2209-20
6. Barouch DH, Stephenson KE, Borducchi EN, et al. Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys. Cell 2013;155:531-9
7. Pitisuttithum P, Gilbert P, Gurwith M, et al. Randomized, double-blind, placebo-controlled efficacy trial of a bivalent recombinant glycoprotein 120 HIV-1 vaccine among injection drug users in Bangkok, Thailand. J Infect Dis 2006;194:1661-71
8. Flynn NM, Forthal DN, Harro CD, et al. Placebo-controlled phase 3 trial of a recombinant glycoprotein 120 vaccine to prevent HIV-1 infection. J Infect Dis 2005;191:654-65
9. Guenaga J, de Val N, Tran K, et al. Well-ordered trimeric HIV-1 subtype B and C soluble spike mimetics generated by negative selection display native-like properties. PLoS Pathog 2015;11:e1004570
10. Pugach P, Ozorowski G, Cupo A, et al. A native-like SOSIP.664 trimer based on an HIV-1 subtype B env gene. J Virol 2015;89:3380-95
11. Buchbinder SP, Mehrotra DV, Duerr A, et al. Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial. Lancet (London, England) 2008;372:1881-93
12. Gray GE, Allen M, Moodie Z, et al. Safety and efficacy of the HVTN 503/Phambili study of a clade-B-based HIV-1 vaccine in South Africa: a double-blind, randomised, placebo-controlled test-of-concept phase 2b study. Lancet Infect Dis 2011;11:507-15
13. Barouch DH, Michael NL. Accelerating HIV-1 vaccine efficacy trials. Cell 2014;159:969-72
14. Los Alamos National Laboratory. HIV Sequence Database. http://www. hiv.lanl.gov/content/sequence/HIV/mainpage.html. Accessed December 28, 2015
15. Taylor BS, Sobieszczyk ME, McCutchan FE, et al. The challenge of HIV-1 subtype diversity. New Engl J Med 2008;358:1590-602
16. Diallo K, Zheng DP, Rottinghaus EK, et al. Viral genetic diversity and polymorphisms in a Cohort of HIV-1-infected patients eligible for initiation of antiretroviral therapy in Abuja, Nigeria. AIDS Res Hum Retroviruses 2015;31:564-75
17. Agwale SM, Zeh C, Robbins KE, et al. Molecular surveillance of HIV-1 field strains in Nigeria in preparation for vaccine trials. Vaccine 2002;20:2131-9
18. Ajoge HO, Gordon ML, de Oliveira T, et al. Genetic characteristics, coreceptor usage potential and evolution of Nigerian HIV-1 subtype G and CRF02 AG isolates. PLoS ONE 2011;6:e17865
19. Ajoge HO, Gordon ML, Ibrahim S, et al. Drug resistance pattern of HIV type 1 isolates sampled in 2007 from therapy-naive pregnant women in North-Central Nigeria. AIDS Res Hum Retroviruses 2012;28:115-8
20. Chaplin B, Eisen G, Idoko J, et al. Impact of HIV type 1 subtype on drug resistance mutations in Nigerian patients failing first-line therapy. AIDS Res Hum Retroviruses 2011;27:71-80
21. Charurat M, Nasidi A, Delaney K, et al. Characterization of acute HIV-1 infection in high-risk Nigerian populations. J Infect Dis 2012;205: 1239-47
22. Hawkins CA, Chaplin B, Idoko J, et al. Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria. J Acquir Immun Defic Syndr 2009; 52:228-34
23. Montavon C, Toure-Kane C, Nkengasong JN, et al. CRF06-cpx: a new circulating recombinant form of HIV-1 inWest Africa involving subtypes A, G, K, and J. J Acquir Immun Defic Syndr 2002;29:522-30
24. Ojesina AI, Mullins C, Imade G, et al. Characterization of HIV type 1 reverse transcriptase mutations in infants infected by mothers who received peripartum nevirapine prophylaxis in Jos, Nigeria. AIDS Res Hum Retroviruses 2007;23:1587-92
25. Ojesina AI, Sankale JL, Odaibo G, et al. Subtype-specific patterns in HIV Type 1 reverse transcriptase and protease in Oyo State, Nigeria: implications for drug resistance and host response. AIDS Res Hum Retroviruses 2006;22:770-9
26. Peeters M, Esu-Williams E, Vergne L, et al. Predominance of subtype A and G HIV type 1 in Nigeria, with geographical differences in their distribution. AIDS Res Hum Retroviruses 2000;16:315-25
27. Sankale JL, Langevin S, Odaibo G, et al. The complexity of circulating HIV type 1 strains in Oyo state, Nigeria. AIDS Res Hum Retroviruses 2007;23:1020-5
28. McCutchan FE, Carr JK, Bajani M, et al. Subtype G and multiple forms of A/G intersubtype recombinant human immunodeficiency virus type 1 in Nigeria. Virology 1999;254:226-34
29. Carr JK, Salminen MO, Albert J, et al. Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants. Virology 1998;247:22-31
30. Kijak GH, Sanders-Buell E, Wolfe ND, et al. Development and application of a high-throughput HIV type 1 genotyping assay to identify CRF02 AG in West/West Central Africa. AIDS Res Hum Retroviruses 2004;20:521-30
31. Vidal N, Diop H, Montavon C, et al. A novel multiregion hybridization assay reveals high frequency of dual inter-subtype infections among HIVpositive individuals in Cameroon,West Central Africa. Infect Genet Evol 2013;14:73-82
32. Delatorre E, Mir D, Bello G. Spatiotemporal dynamics of the HIV-1 subtype G epidemic in West and Central Africa. PLoS ONE 2014;9: e98908
33. Hoelscher M, Dowling WE, Sanders-Buell E, et al. Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multiregion hybridization assay. AIDS (London, England) 2002;16:2055-64
34. Hierholzer J, Montano S, Hoelscher M, et al. Molecular epidemiology of HIV Type 1 in Ecuador, Peru, Bolivia, Uruguay, and Argentina. AIDS Res Hum Retroviruses 2002;18:1339-50
35. Kijak GH, Tovanabutra S, Sanders-Buell E, et al. Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2. Virology 2007;358:178-91
36. Heipertz RAJr, Sanders-Buell E, Kijak G, et al. Molecular epidemiology of early and acute HIV type 1 infections in the United States Navy and Marine Corps, 2005-2010. AIDS Res Hum Retroviruses 2013;29: 1310-20
37. Rozanov M, Plikat U, Chappey C, et al. A web-based genotyping resource for viral sequences. Nucleic Acids Res 2004;32:W654-9
38. Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731-9
39. Schultz AK, ZhangM, Bulla I, et al. jpHMM: improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res 2009;37: W647-651