Genetic variation within the premembrane coding region of dengue viruses from the Yucatan peninsula of Mexico.

Single-strand conformation polymorphism (SSCP) and sequence analyses were used to characterize genetic polymorphisms and phylogenetic relationships, respectively, among dengue (DEN) viruses isolated between 1980 and 1997 from Yucatan, Mexico and surrounding states. Amplified cDNAs from the premembrane (prM) coding region of the DEN viruses were characterized by SSCP. There were six distinct haplotypes of DEN-1 viruses, four haplotypes of DEN-2, four haplotypes of DEN-3, and eight haplotypes of DEN-4. The diversity index for DEN-3 isolates was significantly lower than that of the other serotypes, probably reflecting the recent introduction of this viral serotype into Mexico. The SSCP was a sensitive (84.5%) and specific (95.5%) technique for identifying nucleotide substitutions. Sequence analyses provided insight into the phylogenetic relationships of the DEN strains isolated in Yucatan. One DEN-2 isolate from 1996 was demonstrated to cluster with viruses of the Sri Lanka genotype, none of which have been detected before in the Americas.