Coinfection and genetic recombination between HIV-1 strains: possible biological implications in Australia and South East Asia

Abstract

It has been recognised that human immunodeficiency virus (HIV) mutates rapidly and that nucleotide substitutions, deletions, insertions, and rearrangements resulting from recombination events are the main factors that result in variation of the HIV-1 genome. Together, these processes are actively contributing to the diversity and virulence of viral forms comprising the acquired immune deficiency syndrome (AIDS) pandemic. There are 9 HIV-1 subtypes recognised (A-H and O), based on the envelope region segments. Inter-subtype recombination has been already described, whereas intra-subtype recombination has been difficult to detect. In this study, we have identified in vivo genetic recombination between HIV-1 strains belonging to subtype B in a patient who presented both intravenous drug use (IVDU) and homosexual sex as risk factors. Genetic analysis of viral strains in the hypervariable V3 region of the envelope gene indicated the presence of three distinct sequence groups categorized according to their respective tetrapeptide motifs-GPGR, GLGR and GPGK. Detailed genetic and phylogenetic analyses suggested the recombination occurring only between sequence groups with GPGR and GPGK tetrapeptide motifs. These data suggest that coinfection with closely related strains can occur in vivo, and the generation of hybrid HIV-1 genomes via genetic recombination between subtype B strains can result in further antigenic diversity which may thwart diagnosis and future vaccine efforts. Since HIV-1 subtype B is still the most commonly found subtype around the globe, the hybrid genomes between different subtype B strains may result in epidemiologic shifts and altered pathogenesis.