Genotypic portrait of SARS-CoV-2 in Primorsky Krai during the COVID-19 pandemic

Abstract

Introduction. The COVID-19 pandemic, etiologically related to SARS-CoV-2, was the longest-lasting pandemic for an acute respiratory disease and had a significant impact on demography, economics and politics globally. Experiences with this pandemic are significant for the sustainable development of human society. A detailed analysis of these experiences in epidemic control should include details of the pathogen evolution down to the regional level. The aim of the study was to establish the regularities of the COVID-19 epidemic process in connection with the change of the pathogen genetic variants on the territory of Primorsky Krai. Materials and methods. A retrospective epidemiological analysis of COVID-19 incidence and dynamics of circulation of SARS-CoV-2 genetic variants during the pandemic of this disease (11.03.2020–05.05.2023) in Primorsky Krai was carried out. Data was gathered from the Department of Rospotrebnadzor in Primorsky Krai, the Centre of Hygiene and Epidemiology in Primorsky Krai, as well as the G.P. Somov Research Institute of Epidemiology and Microbiology of the Russian Federation and Russian Platform for Aggregation of Information on Virus Genomes (VGARus). In particular, 1055 nucleotide sequences of full-length SARS-CoV-2 genomes from Primorsky Krai, among which 553 were sequenced at the G.P. Somov Research Institute of Epidemiology and Microbiology were included in analysis. Results. When analyzing the epidemic dynamics of COVID-19 in Primorsky Krai (2020–2023), 7 rises in incidence with different clinical and epidemiological symptoms depending on the genetic variants of the pathogen were identified. At the beginning of the pandemic in Primorsky Krai, as well as throughout Russia, Wuhan-like variants of SARS-CoV-2 were predominant, though later, Delta and Omicron genetic variants were in the majority. By the end of April — beginning of May 2023, the proportion of Omicron sub-variants (XBB.1.9.2 and XBB.1.16) in Primorsky Krai was higher than the Russian average and comparable to that in neighboring countries (Republic of Korea and Japan). Conclusion. Due to the ongoing evolution of SARS-CoV-2, the possibility of the emergence of new pathogens, the peculiarities of the geographical location as well as political and economic importance of Primorsky Krai, it is necessary to consistently improve regional capabilities for operational molecular virological monitoring.

Keywords

• sars-cov-2
• covid-19
• primorsky krai
• disease incidence
• whole genome sequencing
• genotypes