Characterization of HIV-1 subtype B near full-length genome sequences identified at the start of HIV epidemic in South Africa

[摘要] ENGLISH SUMMARY: South Africa is home to approximately 20.0% of the global Human Immunodeficiency Virus (HIV) infected population. The first reported cases of HIV-1 in the country were described in 1982 amongst the homosexual male population. This was attributed to HIV-1 subtypes B (HIV-1B) and D (HIV-1D). Since the late 1980s HIV-1 subtype C (HIV-1C), spread mainly through heterosexual contact, has been the driving force of the epidemic. To date, only six HIV-1B near full-length genome (NFLG) sequences from South Africa are available in the Los Alamos National Laboratory database (LANL). During this study we retrieved five HIV-1B positive samples from homosexual and bi-sexual males, stored for up to 30 years, from the early 1980s, for further characterization. The NFLG amplification reactions were performed using a modern Polymerase Chain Reaction (PCR) protocol designed to target two overlapping proviral DNA HIV genome fragments, 5.5 kb and 3.7 kb in size, respectively. All positive PCR products were sequenced to characterize the viruses. The sequences were checked and edited manually using Sequencher V5. Multiple sequence alignments were created using Clustal W and Maft V7. The sequences were subtyped using the REGA V3.0, RIP V3.0 and jumping profile Hidden Markov Model (jpHMM) online subtyping programmes. Maximum likelihood phylogenetic trees were drawn using MEGA V6. Four of the five HIV-1 patient sequences were subtyped as pure HIV-1B. One sequence, ZA|85|R605, was characterized as a novel HIV-1 BD recombinant. This is the first NFLG HIV-1 BD recombinant ever described and indicates that recombination events were most likely already happening at the early stage of the South African epidemic. Two patient sequences, ZA|87|R1296 and ZA|87|R459, clusters with HIV-1B sequences from the United States of America (USA). The sequence from patient ZA|87|R68 clusters with a HIV-1B sequence from France and the sequence of ZA|87|R526 clusters with another South African HIV-1B sequence. Homosexual flight stewards, international tourists and migrants from the European and North American countries were most likely responsible for the introduction of the HIV-1B epidemic into South Africa. The findings of this study provides valuable insights from the beginning of the HIV-1 epidemic in South Africa. We highlight the importance of characterizing complete viral genomes from early archival specimens to give a more detailed picture of landmarks of the HIV/AIDS pandemic. We show that NFLG sequencing is an important tool for the identification of recombinant viral strains. This study can form the basis for continued research in our attempt to reconstruct the epidemiology and evolutionary history of HIV in South Africa. The HIV-1 epidemic is dynamic in nature and is constantly changing.

[发布机构] Stellenbosch University