The subtype E of HIV-1 is primarily responsible for the heterosexual HIV-1 epidemic in Thailand. Based on limited sequence comparisons, subtype E viruses seem to be hybrids of subtypes A (gag) and E (env). No complete genomes of subtype E HIV-1 have been analyzed, and there is only 1 full-length subtype A sequence for phylogenetic comparison. Thus, virologists have performed full-length proviral sequences for subtype E viruses from Thailand (93TH253) and from the Central African Republic (CAR) (90CR402) and for a subtype A virus from Uganda (92UG037). They also sequenced the long terminal repeat (LTR) regions from 16 virus strains (clades A, C, E, F, and G). The detailed phylogenetic analyses found that subtype E HIV-1 viruses are subtype A/E recombinants with many crossover points along their genomes. The parts of the genome of subtype E origin include the extracellular portion of env, parts of vif and vpr, and most of the LTR. The remaining parts of the genome are of subtype A origin. The Thai and CPR subtype E viruses had the same pattern of A/E mosaicism, suggesting that recombination took place in Africa before the Thai subtype E HIV-1 (93TH253) spread to Asia. All subtype E viruses that also had a subtype A 5' pol region (subtype A viruses or A/D and A/E recombinants) had a unique 2-nucleotide bulge in their transaction response (TAR) elements. This suggests a possible functional linkage between the TAR region and the polymerase. Intersubtype recombination appears to be a relatively recent phenomenon. The spread of the HIV-1 epidemic and the mixing of clades have created the opportunity for coinfection and recombination. The widespread dissemination and virulence of subtype E viruses reveal that intersubtype recombination can generate potent pathogens. It is very important to study the effects of viral recombination on virus-host interaction in terms of immune protection from natural infection and vaccines.