AN ISOLATE OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 ORIGINALLY CLASSIFIED AS SUBTYPE-I REPRESENTS A COMPLEX MOSAIC COMPRISING 3 DIFFERENT GROUP-M SUBTYPES (SUBTYPE-A, SUBTYPE-G, AND SUBTYPE-I)

Full-length reference clones and sequences are currently available for eight human immunodeficiency virus type 1 (HIV-I) group M subtypes (A through H), but none have been reported for subtypes I and J,which ha ve only been identified in a few individuals. Phylogenetic information for subtype I, in particular, is limited since only about 400 bp of e nv gene sequences have been determined for just two epidemiologically Linked viruses infecting a couple who were heterosexual intravenous dr ug users from Cyprus. To characterize subtype I in greater detail, we employed long-range PCR to clone a full-length provirus (94CY032.3) fr om an isolate obtained from one of the individuals originally reported to be infected with this subtype. Phylogenetic analysis of C2-V3 env gene sequences confirmed that 94CY032.3 was closely related to sequenc es previously classified as subtype I. However, analysis of the remain der of its genome revealed various regions in which 94CY032.3 was sign ificantly clustered with either subtype A or subtype G. Only sequences located in vpr and nef, as well as the middle portions of pol and env , formed independent lineages roughly equidistant from all other known subtypes. Since these latter regions most likely have a common origin , we classify them all as subtype I. These results thus indicate that the originally reported prototypic subtype I isolate 94CY032 represent s a triple recombinant (A/G/I) with at least 11 points of recombinatio n crossover. We also screened HIV-1 recombinants with regions of uncer tain subtype assignment for the presence of subtype I sequences. This analysis revealed that two of the earliest mosaics from Africa, Z321B (A/G/?) and MAL (A/D/?), contain short segments of sequence which clus tered closely with the subtype I domains of 94CY032.3. Since Z321 was isolated in 1976, subtype I as well as subtypes A and G must have exis ted in Central Africa prior to that date. The discovery of subtype I i n HIV-1 hybrids from widely distant geographic locations also suggests a more widespread distribution of this virus subtype, or at least seg ments of it, than previously recognized.