Identification of a complex env subtype E HIV type 1 virus from the Democratic Republic of Congo, recombinant with A, G, H, J, K, and unknown subtypes

Up to now, all known env subtype E viruses (CRF01-AE) have had the same mos aic structure with subtype A, and no other env subtype E HIV-1 viruses with non-A subtypes in their genomes have been described. In this report we des cribe the full-length genome sequence of an env subtype E isolate with a re combinant genome different from the prototype CRF01-AE strains. The 97CD-KT B49 strain, obtained from a tuberculosis patient in Kinshasa, has a complex mosaic genome involving subtypes A, E, G, H, J, K, and several unknown fra gments. The U sequences formed well-separated clusters together with previo usly described unknown fragments from CRF04-cpx (subtype I), and from Z321, the oldest intersubtype recombinant isolated in 1976 in the Democratic Rep ublic of Congo. The complex recombinant virus from our study is not an isol ated strain; partial sequencing of a second strain, 97CD-KFE45, confirmed t he breakpoints observed in the 97CD-KTB49 strain in the regions sequenced. The complexity of these recombinant strains suggests a longstanding presenc e of subtype E in Central Africa.