Genetic relatedness of Sindbis virus strains from Europe, Middle East, and Africa.

The relatedness of 40 strains of Sindbis virus (SIN) from Europe, the Middle East, and Africa was investigated by limited sequencing within the gene encoding the E2 glycoprotein corresponding to amino acid residues 117 to 229 and encompassing one of the major neutralization epitopes. Phylogenetic analyses using distance matrix and parsimonious methods identified two major genetic clusters of western SIN strains, although the variability was less than that of the corresponding region for Venezuelan equine encephalomyelitis virus with a maximum divergence of 12.4% versus 28.5%, respectively. One cluster comprising 19 strains included the HR derivate of the Egypt SIN prototype, AR339, and strains from Israel, Saudi-Arabia, Italy, Slovak Republic, Azerbaijan, as well as three Swedish strains. Another cluster of 17 strains included the Ockelbo virus (OCK) prototype, Edsbyn 5/82, and the majority of SIN strains from northern Europe including strains from Sweden, Norway, and Karelia, as well as two strains from South Africa. A third cluster, supported by the Neighbor joining method, was made up of four strains from South Africa, Uganda, and Cameroon. Residue 212, either Ser or Thr, previously appointed important for the differences in neutralization assays between SIN and Edsbyn 5/82, respectively, correlated with the two major genetic clusters, but was a Thr for two of the three Swedish strains in the SIN prototype cluster, and a Ser in one Swedish and one Karelian strain in the OCK cluster. The finding of strains similar to prototype SIN in Middle Sweden and of strains in South Africa relating to the northern cluster of SIN strains supports the notion of the dispersal of SIN by migrating birds as previously suggested for New World alphaviruses.