Characterization of a highly replicative intergroup M/O human immunodeficiency virus type 1 recombinant isolated from a Cameroonian patient

A Cameroonian patient with antibodies reacting simultaneously to human immu nodeficiency virus type 1 (HIV-1) group O- and group M-specific V3-loop pep tides was identified. In order to confirm that this patient was coinfected with both viruses, PCRs with O- and M-specific discriminating primers corre sponding to different regions of the genome were carried out with both prim ary lymphocyte DNA and the corresponding viral strains isolated from three consecutive patient samples. The PCR data suggested that this patient is co infected with a group M virus and a recombinant M/O virus. Indeed, only typ e M gag sequences could be amplified, while for the env region, both type M and O sequences were amplified, from plasma or from DNA extracted from pri mary lymphocytes. Sequence analysis of a complete recombinant genome isolat ed from the second sample (97CA-MP645 virus isolate) revealed two intergrou p breakpoints, one in the vpr gene and the second in the long terminal repe at region around the TATA box. Comparison of the type M sequences shared by the group M and the recombinant M/O viruses showed that these sequences we re closely related, with only 3% genetic distance, suggesting that the M vi rus was one of the parental viruses. In this report we describe for the fir st time a recombination event in vivo between viruses belonging to two diff erent groups, leading to a replicative virus. Recombination between strains with such distant lineages (65% overall homology) may contribute substanti ally to the emergence of new HIV-1 variants. We documented that this virus replicates well and became predominant in vitro. At this time, group O viru ses represent a minority of the strains responsible for the HIV-1 pandemic. If such recombinant intergroup viruses gained better fitness, inducing cha nges in their biological properties compared to the parental group O virus, the prevalences of group O sequences could increase rapidly. This will hav e important implications for diagnosis of HIV-1 infections by serological a nd molecular tests, as well as fur antiviral treatment.