AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 19, Number 11, 2003, pp. 999–1008 © Mary Ann Liebert, Inc. Recombination of HIV Type 1C (C9/C0) in Ethiopia: Possible Link of EthHIV-1C9 to Subtype C Sequences from the High-Prevalence Epidemics in India and Southern Africa GEORGIOS POLLAKIS, 1 ALMAZ ABEBE, 2 ALETTA KLIPHUIS, 1 TOBIAS F. RINKE DE WIT, 2 BITEW FISSEHA, 3 BELETE TEGBARU, 3 GIRMA TESFAYE, 4 HAILU NEGASSA, 5 YOHANNES MENGISTU, 6 ARNAUD L. FONTANET, 7 MARION CORNELISSEN, 1 and JAAP GOUDSMIT 8 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 iso- lates, and we determined recombination by the bootscanning method as implemented in the SIMPLOT pro- gram. Sequence analyses of a 2600-nucleotide fragment (including the gag gene, the protease, and the 59 half of reverse transcriptase of the pol gene) and the corresponding V1V2/C2V3 envelope regions confirmed that two distinct HIV-1C genotypes (C9 and C0) are cocirculating in Ethiopia, as shown previously by the analy- sis of the C2V3 envelope region. We have identified intrasubtype recombination between the two HIV-1C genotypes, C9 and C0, with 6 of the 30 (20%) analyzed viruses being recombinants. The C9 sequences were phylogenetically linked to the fast spreading viruses in India and southern Africa. Furthermore, all the re- combinant viruses shared the C9 V1V3 region of the envelope, suggesting that the prevalence of viruses with the C9 envelope is increasing compared to the C0 envelope. The possibility that viruses with a C9 envelope have a biological advantage over the viruses with a C0 envelope should be further investigated in biological and epidemiological studies. 999 INTRODUCTION A FRICA HAS BEEN HEAVILY AFFECTED by the human immu- nodeficiency virus type 1 (HIV-1) pandemic and despite broad genetic diversity of HIV-1, subtype C is the most preva- lent 1,2 and is responsible for close to half of the infections in sub-Saharan Africa (UNAIDS/WHO-2000). The areas most af- fected are southern countries such as South Africa and Zim- babwe and the countries of the horn of Africa where HIV-1C dominates with prevalence rates between 13% and 35% (UN- AIDS/WHO-2000). An increasing incidence of HIV-1C infec- tion has been reported in countries where nonsubtype C viruses previously dominated. 3–7 In Ethiopia the HIV/AIDS epidemic is believed to have orig- 1 Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. 2 Ethiopian-Netherlands AIDS Research Project (ENARP) at the Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia. 3 National Referral Laboratory for AIDS, EHNRI, Addis Ababa, Ethiopia. 4 Ethiopian Red Cross Society-National Blood Transfusion Service, Addis Ababa, Ethiopia. 5 AIDS/STD Control Team, Ministry of Health, Addis Ababa, Ethiopia. 6 Faculty of Medicine, Department of Microbiology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia. 7 Division of Public Health and Environment, Municipal Health Service, Amsterdam, The Netherlands. 8 Crucell, Leiden, The Netherlands.