Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic

Natalia Palyanova; Ivan Sobolev; Alexander Alekseev; Alexandra Glushenko; Evgeniya Kazachkova; Alexander Markhaev; Yulia Kononova; Marina Gulyaeva; Lubov Adamenko; Olga Kurskaya; Yuhai Bi; Yuhua Xin; Kirill Sharshov; Alexander Shestopalov

doi:10.3390/v14092036

Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic

Viruses. 2022 Sep 14;14(9):2036. doi: 10.3390/v14092036.

Authors

Affiliations

¹ Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia.
² Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
³ CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China.
⁴ China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Abstract

In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% positive for SARS-CoV-2 cases out of the total number of diagnostic tests, and 42% of them were from asymptomatic people. We also detected two asymptomatic people, who had no confirmed contact with patients with COVID-19. The highest percentage of positive samples was observed in the 80+ group (16.3%), while among the children and adults it did not exceed 8%. Among all the people tested, 2423 came from a total of 80 different destinations and only 27 of them were positive for SARS-CoV-2. Out of all the positive samples, 15 were taken for SARS-CoV-2 sequencing. According to the analysis of the genome sequences, the SARS-CoV-2 variants isolated in the Novosibirsk region at the beginning of the pandemic belonged to three phylogenetic lineages according to the Pangolin classification: B.1, B.1.1, and B.1.1.129. All Novosibirsk isolates contained the D614G substitution in the Spike protein, two isolates werecharacterized by an additional M153T mutation, and one isolate wascharacterized by the L5F mutation.

Keywords: COVID-19; Russia; SARS-CoV-2; epidemiology; first wave; phylogeny.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
COVID-19* / epidemiology
Child
Genome, Viral
Genomics
Humans
Mutation
Pandemics
Phylogeny
Retrospective Studies
SARS-CoV-2* / genetics
Spike Glycoprotein, Coronavirus / genetics

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

This research was funded by RFBR and NSFC, CNPq, DST according to the research project 20-54-80012 of BRICS STI Framework Programme. Additionally research was partially supported by RSF according to the research project 22-24-00199 and by the State funded budget project 122012400086-2.