Genetic Characterization of HIV-1 Subtype A1/C/D/B/K Unique Recombinant Form from Eastern Cape, South Africa

Oladele Vincent Adeniyi*, Chikwelu Larry Obi, Daniel Ter Goon, Benson Iweriebor, Wezile Chitha, Anthony Okoh

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

HIV-1 subtype C is the predominant circulating virus in South Africa. There are reports of non-C subtypes emerging in different regions of the country, however, very little information exists on the genetic diversity of HIV in the Eastern Cape Province, despite having the third largest HIV epidemic in the country. In the current study, a near full-length genomic sequence obtained from a heterosexual woman in the Eastern Cape (ADE/CMH/0032), was analyzed using two rapid online subtyping tools; REGA and the jumping Profile Hidden Markov Model (jpHMM). There was agreement between the two tools in the assignment of the pol, Vif, and vpr regions, identified as a C/D recombinant (pol) and subtype C (vif and vpr). Some degree of agreement existed in the assignment of the Gag region, as recombinant: A1/C/B/D by REGA, and A1/C/D by jPHMM, respectively. There was disparity between the two online tools in the subtype assignment of the remaining gene regions. Phylogenetic analysis with pure subtype reference sequences showed that the query sequence clustered with a subtype C reference strain, with a low bootstrap value of 43%. This is the first report from South Africa of a putative unique recombinant as classified by rapid online subtyping tools, involving subtype A1, C, D, B, and K. However, the clinical and epidemiological implications of this variant remain unclear. Further studies are needed to fully understand the genetic diversity of HIV in the Eastern Cape.

Original languageEnglish
Pages (from-to)162-168
Number of pages7
JournalAIDS Research and Human Retroviruses
Volume37
Issue number2
DOIs
Publication statusPublished - Feb 2021

Keywords

  • Eastern Cape Province
  • South Africa
  • near full-length genome
  • unique recombinant form A1/C/D/K/B

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