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

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

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.

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