Abstract
In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.
Highlights
In Korea, subtype B is the predominant variant of human immunodeficiency virus (HIV)-1, but full genome sequencing and analysis of its viral variants are lacking
near full-length genome (NFLG) were mostly classified as HIV-1 subtype B (83%; 10/12), followed by recombinant forms (17%; 2/12)
KR005 was classified as subtype A1 and subtype G recombinant, and KR050 was classified as CRF07_BC using jumping profile hidden Markov model (jpHMM)
Summary
In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005” This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. The human immunodeficiency virus (HIV) is characterized by extremely high genetic variability and rapid evolution This genetic variability results from the high mutation and recombination rate of reverse transcriptase, which lacks DNA proofreading capacity, together with high rates of viral replication. The aim of the present study was to amplify the fulllength HIV-1 genome sequences of clinical isolates in Korea, and to perform genomic characterization through multiple recombination detection methods. To reconstruct an epidemiological history of HIV-1 in Korea, we further performed a Bayesian analysis of these Korean near full genome sequences
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