FULL-LENGTH SEQUENCE AND MOSAIC STRUCTURE OF A HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 ISOLATE FROM THAILAND

Human immunodeficiency virus type 1 isolates of envelope genotype E ar e contributing substantially to the global pandemic, These strains app ear to be mosaics, with the gag gene from clade A and the envelope fro m clade E; the parental clade E strain has not been found, Here we rep ort the first full genomic sequence of one such mosaic virus, isolate CM240 from Thailand, Multiple breakpoints between the two parental gen otypes have been found in a CM240 virus, The entire gag-pol region and most, if not all, of the accessory genes vif, vpr, tat, rev, and vpu appear to derive from clade A. The genotype switches to E shortly afte r the signal peptide of the envelope and back to clade A near the midd le of gp41; thus, the portion of the envelope that lies on the cytopla smic side of the membrane appears to be principally derived not from c lade E, as previously thought, but from clade A, Another small segment not belonging to any recognized clade and presumably also contributed by the parental E strain has been found in the long terminal repeat, It may be significant that the implied virion structure resembles a ps eudotype virus with the matrix and core from one clade and the outer e nvelope from another. In the long terminal repeat, differences were ob served between CM240 and other clades in the number of NF-kappa B bind ing sites, the sequence of the TATA box, and the putative secondary st ructure of the transactivation response region stem-loop. The mosaic s tructure of a CM240 virion is suggestive of phenotypic differences whi ch might have contributed to the emergence of this variant.