A complex human immunodeficiency virus type 1 A/G/J recombinant virus isolated from a seronegative patient with AIDS from Benin, West Africa

A human immunodeficiency virus type 1 (HIV-1B76) originating from Benin (West Africa) was isolated and characterized. The patient had severe clinical AIDS and presented an unusual serological profile. Only one out of five different detection assays was able to demonstrate the presence of antibodies to HIV, whereas confirmatory assays remained indeterminate. In contrast, both plasma viral load and p24 antigen level were unusually high. HIV-1 infection was proved by viral RNA and proviral DNA amplification. HIV-1B76 partially purified lysate reacted strongly with all anti-HIV-1-positive sera from the region but B76 plasma did not react with subtype A control viral antigen. This patient is likely to have had severe acquired immune dysfunction explaining her lack of immunological reactivity. Phylogenetic analysis of the genome identified a complex HIV-1 A/G/J recombinant. The gag and pol genes, and the majority of nef, are characteristic of subtype A; the gag/pol junction, the 3′ end of pol, vpu and env genes were characteristic of subtype G; vif, vpr and the 5′ end of nef were subtype J. In addition, part of the HIV-1B76 genome had considerable sequence similarity with the previously described CRF06 cpx (BFP90) isolate. HIV-1B76 did not exhibit any remarkable replication properties or cell tropism in vitro.