title: 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.
abstract: While abundant sequence information is available from human immunodeficiency virus type 1 (HIV-1) subtypes A, B, C and CRF01_AE for HIV-1 vaccine design, sequences from West Africa are less represented. We sought to augment our understanding of HIV-1 variants circulating in 6 Nigerian cities as a step to subsequent HIV-1 vaccine development.The G/CRF02_AG multi-region hybridization assay (MHA) was developed to differentiate subtype G, CRF02_AG and their recombinants from other subtypes based on 7 HIV-1 segments. Plasma from 224 HIV-1 infected volunteers enrolled in a cohort examining HIV-1 prevalence, risk factor, and subtype from Makurdi (30), Abuja (18), Enugu (11), Kaduna (12), Tafa (95), and Ojo/Lagos (58) was analyzed using MHA. HIV-1 genomes from 42 samples were sequenced to validate the MHA and fully explore the recombinant structure of G and CRF02_AG variants.The sensitivity and specificity of MHA varied between 73-100% and 90-100%, respectively. The subtype distribution as identified by MHA among 224 samples revealed 38% CRF02_AG, 28% G, and 26% G/CRF02_AG recombinants while 8% remained nontypeable strains. In envelope (env) gp120, 38.84% of the samples reacted to a G probe while 31.25% reacted to a CRF02 (subtype A) probe. Full genome characterization of 42 sequences revealed the complexity of Nigerian HIV-1 variants.CRF02_AG, subtype G, and their recombinants were the major circulating HIV-1 variants in 6 Nigerian cities. High proportions of samples reacted to a G probe in env gp120 confirms that subtype G infections are abundant and should be considered in strategies for global HIV-1 vaccine development.
authors: US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland US Military HIV Research Program (HJF-MRI), Abuja, Nigeria Centre de Recherches Medicales de Lambarene (CERMEL) Fondation Internationale de l'Hôpital Albert Schweitzer Lambarene, Gabon United States Public Health Service, Rockville, Maryland 45 Nigerian Air Force Hospital, Makurdi, Nigeria Department of Defense HIV Program, Abuja, Nigeria.
authors: Richard A
authors: RA
authors: Heipertz
authors: Ojor
authors: O
authors: Ayemoba
authors: Eric
authors: E
authors: Sanders-Buell
authors: Kultida
authors: K
authors: Poltavee
authors: Phuc
authors: P
authors: Pham
authors: Gustavo H
authors: GH
authors: Kijak
authors: Esther
authors: E
authors: Lei
authors: Meera
authors: M
authors: Bose
authors: Shana
authors: S
authors: Howell
authors: Anne Marie
authors: AM
authors: O'Sullivan
authors: Adam
authors: A
authors: Bates
authors: Taylor
authors: T
authors: Cervenka
authors: Janelle
authors: J
authors: Kuroiwa
authors: Akindiran
authors: A
authors: Akintunde
authors: Onyekachukwu
authors: O
authors: Ibezim
authors: Abraham
authors: A
authors: Alabi
authors: Obumneke
authors: O
authors: Okoye
authors: Mark
authors: M
authors: Manak
authors: Jennifer
authors: J
authors: Malia
authors: Sheila
authors: S
authors: Peel
authors: Mohammed
authors: M
authors: Maisaka
authors: Darrell
authors: D
authors: Singer
authors: Robert J
authors: RJ
authors: O'Connell
authors: Merlin L
authors: ML
authors: Robb
authors: Jerome H
authors: JH
authors: Kim
authors: Nelson L
authors: NL
authors: Michael
authors: Ogbonnaya
authors: O
authors: Njoku
authors: Sodsai
authors: S
authors: Tovanabutra
mesh_terms: D015331:Cohort Studies; D005260:Female; D015967:Gene Expression Regulation, Viral; D015658:HIV Infections / Q000453:epidemiology / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D009549:Nigeria / Q000453:epidemiology; D010802:Phylogeny; D011110:Polymorphism, Genetic; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D011995:Recombination, Genetic; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA