THE HETEROSEXUAL HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 EPIDEMIC IN THAILAND IS CAUSED BY AN INTERSUBTYPE (A E) RECOMBINANT OF AFRICAN ORIGIN/

Since 1989, human immunodeficiency virus type 1 (HIV-1) has spread exp losively through the heterosexual population in Thailand. This epidemi c is caused primarily by viruses classified as ''subtype E'', which, o n the basis of limited sequence comparisons, appear to represent hybri ds of subtypes A (gag) and E (env). However, the true evolutionary ori gins of ''subtype E'' viruses are still obscure since no complete geno mes have been analyzed, and only one full length subtype A sequence ha s been available for phylogenetic comparison. In this study, we determ ined full-length proviral sequences for ''subtype E'' viruses from Tha iland (93TH253) and the Central African Republic (90CR402) and for a s ubtype A virus from Uganda (92UG037). We also sequenced the long termi nal repeat (LTR) regions from 16 virus strains representing clades A, C, E, F, and G, Detailed phylogenetic analyses of these sequences indi cated that ''subtype E'' viruses do indeed represent A/E recombinants with multiple points of crossover along their genomes. The extracellul ar portion of env, parts of vif and vpr, as well as most of the LTR ar e of subtype E origin, whereas the remainder of the genome is of subty pe A origin. The possibility that the discordant phylogenetic position s of ''subtype E'' viruses in gag- and env-derived trees are the resul t of unusual rates or patterns of evolution was also considered but wa s ruled out on the basis of two lines of evidence: (i) phylogenetic tr ees constructed for synonymous and nonsynonymous substitutions yielded the same discordant branching orders for ''subtype E'' gag and env ge ne sequences, thus excluding selection-driven evolution, and (ii) mult iple crossovers in the viral genome are most consistent with the copy choice model of recombination and have been observed in other document ed examples of HIV-1 intersubtype recombination. Thai and CAR ''subtyp e E'' viruses exhibited the same pattern of A/E mosaicism, indicating that the recombination event occurred in Africa prior to the spread of virus to Asia. Finally, all ''subtype E'' viruses were found to conta in a distinctive two-nucleotide bulge in their transactivation respons e (TAR) elements. This feature was present only in viruses which also contained a subtype A 5' pol region (i.e., subtype A viruses or A/D an d A/E recombinants), raising the possibility of a functional linkage b etween the TAR region and the polymerase. The implications of epidemic spread of a recombinant HIV-1 strain to viral natural history and. va ccine development are discussed.