The Development of the SARS-CoV-2 Epidemic in Different Regions of Siberia in the 2020–2022 Period

Abstract

The comparison of the development of the SARS-CoV-2 epidemic in several neighboring regions can help researchers to assess the risks and develop more effective strategies and approaches in the field of preventive medicine. We analyzed the infection and mortality statistics for the 2020–2022 period in ten individual regions of the Siberian Federal District of Russia. We also sequenced complete genomes, which allowed us to analyze the genetic diversity of SARS-CoV-2 circulated in each of the ten regions and to build a phylogenetic dendrogram for the virus variants. The ParSeq v.1.0 software was developed to automate and speed up the processing and analysis of viral genomes. At the beginning of the pandemic, in the first two waves, the B.1.1 variant (20B) dominated in all regions of the Siberian Federal District. The third and fourth waves were caused by the Delta variant. Mortality during this period was at a maximum; the incidence was quite high, but the number of deposited genomes with GISAID during this period was extremely low. The maximum incidence was at the beginning of 2022, which corresponds to the arrival of the Omicron variant in the region. The BA.5.2 variant became the dominant one. In addition, by using NextClade, we identified three recombinants in the most densely populated areas.

On the space of SARS-CoV-2 genetic sequence variants

“…To analyze the genetic sequences of SARS-CoV-2, we developed the software called ParSeq (Parser of Sequences)parser and analyzer of SARS-CoV-2 nucleotide sequences in FASTA format, which we already used while working on analysis of the SARS-CoV-2 epidemic in regions of Siberia (Palyanova et al, 2023). Its main abilities already implemented at the moment are described below:…”