RNA fingerprinting as a method for distinguishing dengue 1 virus strains

Virion RNAs of 12 geographically distinct dengue type 1 (DEN-1) virus isolates were clearly unique by RNA fingerprinting. Isolates from the same geographic area were very similar but differed from those of other areas, allowing us to establish three geographical groupings based upon percent shared oligonucleotides. Three Caribbean strains were virtually identical (85-91% homologous oligonucleotides) whereas Pacific/S.E. Asian strains exhibited considerably less homology to one another (44-49%). The Pacific/S.E. Asian strains exhibited little relationship (20-30%) to the Caribbean and African strains. A Sri Lankan isolate displayed a relatively high degree of homology to Nigerian isolates (60-66% homologous oligonucleotides), suggesting that the Sri Lanka DEN-1 infection originated from Africa. A 1978 Nigerian DEN-1 isolate and the 1969 Sri Lankan strain each exhibited greater than 50% homology with a 1977 Jamaican strain. The similarities observed between the African/Sri Lankan and Jamaican strains suggest that the DEN-1 virus which caused the 1977 Jamaican epidemic may have originated from Africa or Sri Lanka. The RNA fingerprint is a unique characteristic of DEN-1 strains from a particular geographic region, suggesting this technique as a useful tool for dengue epidemiological investigations.