Genetic variability of wild-type measles viruses, circulating in the Russian Federation during the implementation of the National Measles Elimination Program, 2003–2007

Genetic characterization of wild-type measles viruses (MVs) is an important component of laboratory surveillance of measles. In this study, a phylogenetic analysis was performed of the nucleoprotein gene sequences of 228 MVs isolated in the Russian Federation between 2003 and 2007. Five genotypes, D4, D5, D6, D8, and H1, were detected. From 1999 through the first 6 months of 2003, the most prevalent genotype in the European part of Russia was D4. All genotype D4-type viruses were closely related to each other (with overall sequence diversity of ≤0.9%), suggesting the presence of a single endemic MV strain. After 2003, viruses with closely related sequences within genotype D6 (≤0.9% sequence diversity) were prevalent. During this time, there was a low level of indigenous transmission of genotype D6, and genotype D6 viruses were imported from neighbouring countries, which led to the identification of two lineages of genotype D6, i.e. D6a and D6b. Lineage D6a was closely related to viruses isolated in Turkey, Kazakhstan, and Uzbekistan, whereas lineage D6b was linked to a large outbreak in Ukraine in 2005–2006. Genotypes H1, D5 and D8 were associated with sporadic cases and clusters of transmission linked to importations. Enhanced vaccination interrupted the transmission of the previous endemic lineage D4 in 2003 and of lineage D6a in 2005, although an accumulation of susceptible individuals in the population allowed for prolonged circulation of lineage D6b. These data on MV genotype distribution, in conjunction with the epidemiological data for measles, show considerable progress in measles control and suggest that regional elimination is possible.