Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

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.

Genetic characterization of HIV-1 viruses among cases with antiretroviral therapy failure in Suzhou City, China

“…Full genome sequencing can be used to confirm recombinants when viruses typing were unclassified or the results of different gene segments were inconsistent. A number of new HIV recombinants have been reported by near-full-length genome sequencing [32][33][34][35]. In this study, 12 recombinants were confirmed by performing full genome sequencing.…”

Genetic characterization of HIV-1 viruses among antiretroviral therapy failure individuals in Suzhou City, China

“…Full genome sequencing can be used to con rm recombinants when viruses typing were unclassi ed or the results of different gene segments were inconsistent. A number of new HIV recombinants have been reported by near-full-length genome sequencing [33][34][35][36]. In this study, 12 recombinants were con rmed by performing full genome sequencing.…”

Nanopore Sequencing for Characterization of HIV-1 Recombinant Forms

“…Additionally, to date, 118 circulating recombinant forms (CRFs) have also been identified according to the Los Alamos HIV sequence database ( 4 ), and unique recombinant forms (URFs) without evident transmission have also been found ( 5 ). Moreover, complex second- or third-generation CRFs resulting from further recombination of existing CRFs ( 6 , 7 ) and more diversified genotypes of HIV-1 have been observed over time ( 7 – 9 ). A recent study reported that CRFs and URFs account for 16.7% (including CRF01_AE and CRF02_AG) and 6.1% of HIV-1 infections, respectively ( 10 ).…”