The entire nucleotide sequence of human T-cell lymphotropic virus type II (HTLV-II) from a previously described isolate of patient NRA (HTLV-II(NRA)) was determined. Clones encoding the 5' LTR and gag, pol, env and tax/rex open reading frames were subcloned and sequenced on both strands. The provirus consisted of 8957 nucleotides and showed 95.2% homology with the HTLV-II(Mo) prototype at the nucleotide level. Less than 5% amino acid variation between HTLV-II(NRA) and HTLV-II(Mo) was observed for coding regions. Although isolate HTLV-II(NRA) had an additional 25 amino acids at the 3' end of tax/rex, this region was 96% homologous with the 5' end of HTLV-II(Mo) 3' LTR. To further investigate HTLV-II variability, a portion of the env gp46 gene derived from 9 HTLV-II infected persons was amplified by polymerase chain reaction and sequenced. Sequence was obtained for 320 nucleotides corresponding to HTLV-II(Mo) positions 5291 to 5610. Isolates similar to the HTLV-II(Mo) and HTLV-II(NRA) prototypes were identified, and sequences were highly conserved.
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