Management of genomic surveillance for respiratory viral infections circulating in the territory of the city of Moscow

Introduction. Outbreaks of respiratory viral infections have an economic impact on the healthcare system and pose a threat to public well-being. Monitoring for the incidence of acute respiratory viral infections in a metropolitan area, especially during the COVID-19 pandemic, was in dire need of an adequate tool to identify mutations and variants that evade vaccine immunity and initiate an increase in incidence. Genomic surveillance was required for a timely response. Purpose of the study. Management of the Moscow Genomic Center for genomic surveillance for acute respiratory viral infections and COVID-19, with an assessment of the results during seasonal outbreaks in the capital. Materials and methods. With the support of the Moscow City Health Department, management and logistics measures were developed and implemented, the NGS testing program in patient samples on a planned basis and during the period of increased incidence of acute respiratory viral infections and COVID-19, technical procedures for high-throughput sequencing were developed, the security of data exchange and biosafety of medical personnel were ensured. Results. The Moscow Genome Center was established within the structure of the Moscow City Health Department. For the period from October 2023 to April 2024, targeted NGS data (a panel of thirty two pathogens, 6528 samples were tested): SARS-COV-2 dominated the entire period, the incidence of influenza A (H3N2) increased sharply from the beginning of December and decreased sharply by the end of January. Sars-CoV-2 genetic lineage rotation: XBB lineage dominated (most represented: XBB.1.16, XBB.1.16.11) from October to the end of January, then JN lineage prevailed (most represented: JN.1, also found: JN.1.13, JN.1.18, JN.1.19, JN.1.4). Influenza A strain rotation: H3N2 (A/Massachusetts/01/2020) and H3N2 (A/Massachusetts/38/2019) dominated from December to February. Research limitations. A targeted panel of 32 respiratory viruses most common in the Moscow population was used for NGS. Incomplete coverage of the entire viriome is a conditional limitation. Conclusion. Representative, high-quality and continuous genetic surveillance has been managed in the capital. The Moscow Genome Center has successfully implemented the NGS Testing Program and support for the Russian Genomic Resource of Microorganisms VGARus.