Genomic Characterization of HIV-1 Bc Recombinant Viruses

Abstract The Human Immunodeficiency Virus 1 (HIV-1) is characterized by high rates of genetic diversity, being classified into groups, subtypes and recombinant forms. To date, 14 Circulating Recombinant Forms (CRFs) of subtypes B and C have been identified, three of them in 2021: CRF108_BC in Spain, CRF110_BC and CRF118_BC in China. This study investigated the genetic diversity among circulating BC recombinant viruses. Near-Full Length Genomes (NFLG) of 225 BC strains were retrieved from the Los Alamos database. Recombination and phylogenetic analysis were conducted using bioinformatics tools. Sequences were obtained from 17 countries between 1992 and 2018. Fourteen CRFs and 82 distinct Unique Recombinant Forms (URFs) recombination patterns were identified. Preferential recombination points were found in pol (66.7%) and env (62.5%) genes, while subtype C is the predominant genetic form in gag, vif, vpr, tat, rev, tat 2, rev 2, nef and 3'-LTR genomic regions. Specific positions in pol and env genes maintain the B subtype, which may be related to the acquisition of adaptive advantage over subtype C.