Sequence Note Genetic Diversity of HIV Type 1 in Likasi, Southeast of the Democratic Republic of Congo

To investigate the prevalence of subtypes A and C, and the existence of recombinants of both subtypes in the southeast of the Democratic Republic of Congo (DRC), blood samples were collected from 27 HIV-infected individuals in Likasi, located in an area bordering close to Zambia, and analyzed phylogenetically. Out of the 24 strains with a positive PCR profile for pol-IN and env-C2V3, 15 (62.5%) had a discordant subtype or CRF designation: one subtype A/G (pol/env), four A/U (unclassified), three G/A, one G/CRF01, three H/A, one J/C, one CRF02 (G)/A, and one U/A. Nine (37.5%) strains had a concordant subtype or CRF designation: five subtype A, two C, one D, and one CRF02/G. The remaining three samples negative for PCR with env-C2V3 primers used in this study were further analyzed with env-gp41 primers and revealed the presence of two profiles: two J/J (pol-IN/env-gp41) and one C/G. These data highlight the presence of a high proportion (16/27, 59.3%) of recombinant strains and a low prevalence (4.1 and 7.4%) of subtype C based on env-C2V3 and polIN analyses, respectively, in Likasi. In addition, this is the first report that CRF02_AG exists in DRC, though the epidemiological significance of the existence of CRF02_AG in DRC remains unknown. HUMAN IMMUNODEFICIENCY VIRUS TYPE-1 (HIV-1) has been classified into three major phylogenetic groups, termed M (major), N (non-M, non-O), and O (outlier).1 The vast majority of variants found worldwide and responsible for the AIDS pandemic belong to group M.2,3 Phylogenetic analysis of group M has further led to its subclassification into nine pure subtypes, A–D, F–H, J, and K and subsubtypes A1, A2, F1, and F2.2 Recently, it was realized that a significant fraction of HIV-1 isolates, 10–40% or more, exhibit a shift in subtypes when different regions of their genome are analyzed.3 Currently, some of the mosaic HIV-1 genomes play a major role in the global AIDS epidemics and are designated as circulating recombinant forms (CRFs), CRF01-CRF16. Although subtypes A, C, and CRF02_AG are most prevalent in Africa, the distribution of CRF/subtype is very heterogeneous.2–7 The proportion of CRF02_AG among subtype A strains based on env sequences decreases from west to central Africa, with an absence of CRF02_AG in the Democratic Republic of Congo (DRC).2,8,9 The profile of HIV-1 endemic in DRC, such as high number of cocirculating HIV-1 subtypes, possible recombinant viruses, and unclassified strains, is consistent with that of an old and mature epidemic of HIV-1.5 The DRC is bordered on the southeast by Zambia. The majority (95%) of the HIV-1 strains circulating in Zambia are subtype C, although HIV-1 group M subtypes A, D, G, and J as well as group O have been identified.2,3,10,11 1Department of Viral Infection and International Health, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan. 2Laboratoire de virologie, INRB, Kinshasa, Republique Democratique du Congo. 3Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan. 4Cité Louis Pasteur-Laboratoire National de Santé Publique, Brazaville 120, Congo. 5Department of Laboratory Science, School of Health Sciences, Kanazawa University, Kanazawa 920-8640, Japan. 5381_10_p1352-1357 12/8/04 9:07 AM Page 1352