Molecular and genetic characteristics from phylogenetic analysis of Russian and foreign variants of measles virus 2020–2024

Introduction. Over the past two years, there has been an increase in measles morbidity in Russia and other countries. In order to assess the heterogeneity of clinically significant strains of Measles morbillivirus to reveal the sources of infection and transmission routes strains, a molecular genetic study thus becomes an urgent task. In this paper, a genetic identification of clinical strains of measles virus detected in 2023–2024 is compared with global variants as well as Russian strains detected in previous years. Materials and methods. Forty measles virus genome sequences isolated from nasopharyngeal swab samples obtained in Moscow and Novosibirsk in 2023–2024 were included in the study. The data were then compared with strains collected in Russia in May 2023 and deposited at the Central Research Institute of Epidemiology, as well as strains collected in 2020 and 2021 in Moscow. Results. The nucleotide sequences of studied Measles morbillivirus strains were categorized into different phylogenetic groups within genotype D8. For samples of genotype B3 collected in 2020 and 2023, a comparative analysis was performed to identify the region of origin. Phylogenetic analysis of Russian and foreign variants of measles virus suggests that strains currently circulating in Russia may be a variety of strains that had previously circulated in other countries and independently spread to Russia in 2023. After analyzing the most frequent nucleotide substitutions in various measles virus genes, the most variable genes were identified to provide a basis for the extension of phylogenetic analysis. Conclusions. The proposed approach to molecular genetic testing of complete and partial genome sequences of clinical isolate of measles virus detected in 2023–2024 in Moscow and Novosibirsk made it possible to identify strain subgroups that differ in origin. The comparison of the Measles morbillivirus strains sequenced in the present research with global sequences allowed us to detect similar sequences identified both in 2023 and in previous years in various countries of the world. The analysis of epidemiologically significant strains of Measles morbillivirus shows that N gene can be used to reliably determine the main genotype; however, this approach is not sufficient for studying the transmission pathways of the virus.