Genomic surveillance strategy. Problems and perspectives

Abstract

The topic of epidemiologic surveillance is one of the basic concepts in the theory and practice of epidemiologic science. In Russia, generalization of the accumulated factual material and theoretical developments have allowed us to formulate a number of provisions on the nature of the epidemic process. The pandemic of a new coronavirus infection has forced adjustments in all spheres of society, including the activities of the infectious disease epidemiological surveillance system, requiring the development and implementation of innovative solutions. Based on the experience of prompt response to the tasks set by the COVID-19 pandemic, the authors raised the problem of development and implementation of a system of molecular genetic monitoring for pathogens of emerging and re-emerging infections as a priority vector of epidemiological surveillance development. The introduction of modern molecular biological technologies for the identification of pathogens with epidemic potential, taking into account their genetic diversity, into the system of epidemiologic surveillance has been substantiated based on the experience of using platform solutions created by the Central Research Institute of Epidemiology of Rospotrebnadzor. The strategy of genomic epidemiologic surveillance as a powerful tool to ensure readiness for response measures and management of the epidemic process by implementing and adjusting preventive and anti-epidemic measures was developed. The Russian platform for aggregation of information on virus genomes (VGARus) developed at the Central Research Institute of Epidemiology of Rospotrebnadzor as a technological, scientific, organizational and infrastructural base of genomic epidemiological surveillance, acting as an interdepartmental consortium, has been introduced into practice. The efficiency of VGARus was shown to assess the mutational variability of SARS-CoV-2, the influence of evolutionary development of circulating pathogens on the characteristics of the epidemic process, the implementation of operational and retrospective analysis of morbidity and prediction of the spread of genetic variants of pathogens.