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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


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.

Original languageEnglish
Article numbere4346
Issue number32
StatePublished - 1 Aug 2016
Externally publishedYes


  • Genetic complexity
  • HIV-1
  • Nigeria
  • Recombinant
  • Subtypes


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