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

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

Natalia Palyanova  1 , Ivan Sobolev  1 , Alexander Alekseev  1 , Alexandra Glushenko  1 , Evgeniya Kazachkova  1 , Alexander Markhaev  1 , Yulia Kononova  1 , Marina Gulyaeva  1   2 , Lubov Adamenko  1 , Olga Kurskaya  1 , Yuhai Bi  3 , Yuhua Xin  4 , Kirill Sharshov  1 , Alexander Shestopalov  1
Affiliations

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

Natalia Palyanova et al. Viruses. .

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The percentage of positive cases per age group: (a) expressed as a percentage of the total number of positive cases; (b) expressed as a percentage of the total number of tested people of each corresponding age group. (a) the percentage of positive cases in each age group of the total number of positive cases. (b) the percentage of positive cases in each age group of the total number of tested people of each corresponding age group.
Figure 2
Figure 2
The percentage of symptomatic and asymptomatic people (left) and the percentage of male and female (right) among the positive for SARS-CoV-2 RNA.
Figure 3
Figure 3
The number of positive cases, expressed as a percentage of the total number of tested people per week.
Figure 4
Figure 4
The phylogenetic dendrogram performed with MrBayes 3.2.7 and based on the whole genome nucleotide sequences of SARS-CoV-2. Red label—sequences of Novosibirsk isolates; blue label—reference sequences (according to GISAID EpiCoV).
Figure 5
Figure 5
The heat map of the genetic distances between the genomes of SARS-CoV-2 isolates from Novosibirsk. The color gradient from green to red corresponds to an increase in pairwise genetic distances.
Figure 6
Figure 6
Amino acid substitutions in SARS-CoV-2 proteins from Novosibirsk according to the Wuhan reference hCoV-19/Wuhan/WIV04/2019 (WIV04).
See this image and copyright information in PMC

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