[Nucleotide sequence and restriction fragment length polymorphism (RFLP) analysis of the long terminal repeat of human T-cell lymphotropic virus type II (HTLV-II)].

Molecular studies have demonstrated the existence of two major subtypes of human T-cell lymphotropic virus type II, HTLV-IIa and HTLV-IIb. In attempts to further classify this family of viruses we have carried out nucleotide sequence and restriction fragment length polymorphism (RFLP) analysis of the long terminal repeat (LTR), a region which has been shown in previous studies to have the greatest intra-and inter-subtype genomic divergence. Analysis of the nucleotide sequences suggested the existence of distinct phylogenetic groups in each subtype, and based on predicted differences in restriction endonuclease sites, RFLP analysis allowed the identification of four groups within the IIa subtype (a1-a4), and six within the IIb subtype (b1-b6). Nucleotide sequence analysis also suggested the possible existence of HTLV-II quasispecies. However this appeared not to be significant, and preliminary studies suggest that these would not be expected to appreciably influence the results of RFLP analysis. The validity of the RFLP method was demonstrated in an analysis of thirty-six randomly chosen samples from the blood donors from the New York City Blood Center where it could be shown that all could be successfully classified. Moreover, the RFLP analysis correctly matched the viruses in donors and recipients of contaminated blood in four situations where HTLV-II was inadvertently transmitted by transfusion. RFLP analysis of the LTR appears to be a rapid and reliable method to identify HTLV-II infection. This should prove useful in studies of the epidemiology and the characterization of viruses present both in non-indigenous in indigenous populations.