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

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.

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

“…The description of epidemiological processes is of fundamental importance both for epidemiology, virology, genetics and social sciences. One of the features of the current pandemic is a large number of asymptomatic carriers of the infection [ 6 , 16 ] actively spreading the virus among a wide range of people because the carrier, unlike a sick person, does not reduce their social activity. Timely measures taken to limit contacts and travel between regions have significantly reduced the peak incidence in the beginning of the pandemic [ 2 , 28 ].…”

“…In the Siberian Federal District, as in Novosibirsk [ 16 ], the beginning of the first wave lagged behind the European part of Russia. In the first three waves, the federal districts were involved in the epidemic more slowly than in the fourth and, especially, in the fifth wave, when the rise in incidence was rapid, the next week after Moscow, and simultaneously in all federal districts [ 28 ] and the world.…”

“…The nucleotide sequences of the SARS-CoV-2 variants circulated in the Siberian Federal District in the 2020–2022 period were obtained by next-generation sequencing (NGS) in the WHO National Influenza Centre (Research Institute of Influenza) and the Federal Research Center of Fundamental and Translational Medicine [ 16 ], and most of them were deposited in the GISAID database. The selection of samples for sequencing was based on obtaining from several healthcare institutions located in different regions of the Siberian Federal District.…”

“…In our previous work, we analyzed the beginning of the pandemic in the Novosibirsk region [ 16 ]. At the initial stage of the pandemic in the Novosibirsk region on 1 April 2020, in our laboratory, 13,699 samples of biological material were collected from people who showed symptoms of acute respiratory illness and who had contact with patients with a confirmed diagnosis of COVID-19, from people who crossed the Russian border and from healthcare professionals.…”

Editorial for SARS-CoV-2 and COVID-19 Topical Collection

“…The fifth section covers the epidemiology of SARS-CoV-2 and includes four communication articles describing viral shedding among re-positive SARS-CoV-2 individuals in the Republic of Korea (26), the lack of evidence for SARS-CoV-2 spillover in free-living neotropical non-human primates in Brazil (27), the neutralizing activity of serum against the B.1.17, B.1.351, and P.1 SARS-CoV-2 VoCs in hospitalized COVID-19 patients (28), and SARS-CoV-2 re-infection in a healthcare worker despite the presence of neutralizing antibodies (29). This section also includes two case reports describing the first detection of the SARS-CoV-2 B.1.1.7 VoC in an asymptomatic dog in Spain (30) and a genomic surveillance of SARS-CoV-2 in Lebanon (31), and eleven original research articles describing different aspects of the epidemiology of SARS-CoV-2 (32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42).…”