title: Recombination of HIV type 1C (C'/C") in Ethiopia: possible link of EthHIV-1C' to subtype C sequences from the high-prevalence epidemics in India and Southern Africa.
abstract: The magnitude and complexity of the HIV-1 genetic diversity are major challenges for vaccine development. Investigation of the genotypes circulating in areas of high incidence, as well as their interactions, will be a milestone in the development of an efficacious vaccine. Because HIV-1 subtype C (HIV-1C) is responsible for most of the 36 million infections worldwide we investigated the HIV-1C strains circulating in Ethiopia in a retrospective, cross-sectional study. Serum samples from HIV-1-positive individuals were collected in seven Ethiopian cities and towns. Nucleotide sequences of the gag, pol, and env genes were analyzed. We performed phylogenetic analysis by the neighbor-joining and maximum-likelihood methods with sequences from 30 isolates, and we determined recombination by the bootscanning method as implemented in the SIMPLOT program. Sequence analyses of a 2600-nucleotide fragment (including the gag gene, the protease, and the 5' half of reverse transcriptase of the pol gene) and the corresponding V1V2/C2V3 envelope regions confirmed that two distinct HIV-1C genotypes (C' and C") are cocirculating in Ethiopia, as shown previously by the analysis of the C2V3 envelope region. We have identified intrasubtype recombination between the two HIV-1C genotypes, C' and C", with 6 of the 30 (20%) analyzed viruses being recombinants. The C' sequences were phylogenetically linked to the fast spreading viruses in India and southern Africa. Furthermore, all the recombinant viruses shared the C' V1V3 region of the envelope, suggesting that the prevalence of viruses with the C' envelope is increasing compared to the C" envelope. The possibility that viruses with a C' envelope have a biological advantage over the viruses with a C" envelope should be further investigated in biological and epidemiological studies.
authors.affiliation: Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. g.pollakis@amc.uva.nl
authors.forename: Georgios
authors.initials: G
authors.lastname: Pollakis
authors.forename: Almaz
authors.initials: A
authors.lastname: Abebe
authors.forename: Aletta
authors.initials: A
authors.lastname: Kliphuis
authors.forename: Tobias F Rinke
authors.initials: TF
authors.lastname: De Wit
authors.forename: Bitew
authors.initials: B
authors.lastname: Fisseha
authors.forename: Belete
authors.initials: B
authors.lastname: Tegbaru
authors.forename: Girma
authors.initials: G
authors.lastname: Tesfaye
authors.forename: Hailu
authors.initials: H
authors.lastname: Negassa
authors.forename: Yohannes
authors.initials: Y
authors.lastname: Mengistu
authors.forename: Arnaud L
authors.initials: AL
authors.lastname: Fontanet
authors.forename: Marion
authors.initials: M
authors.lastname: Cornelissen
authors.forename: Jaap
authors.initials: J
authors.lastname: Goudsmit
mesh_terms: D000353:Africa, Southern / Q000453:epidemiology; D000818:Animals; D003430:Cross-Sectional Studies; D004196:Disease Outbreaks; D005002:Ethiopia / Q000453:epidemiology; D005260:Female; D015686:Gene Products, env / Q000235:genetics; D015683:Gene Products, gag / Q000235:genetics; D015684:Gene Products, pol / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D007194:India / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D011995:Recombination, Genetic; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA
chemical_list: D015686:Gene Products, env; D015683:Gene Products, gag; D015684:Gene Products, pol