Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic
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...
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MDPI AG
2022-09-01
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| Online Access: | https://www.mdpi.com/1999-4915/14/9/2036 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Natalia Palyanova |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T22:13:20Z |
| format | Article |
| id | doaj.art-6485d597e1624887b669a44ce51756d5 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T22:13:20Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6485d597e1624887b669a44ce51756d52023-11-23T19:28:29ZengMDPI AGViruses1999-49152022-09-01149203610.3390/v14092036Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the PandemicNatalia Palyanova0Ivan Sobolev1Alexander Alekseev2Alexandra Glushenko3Evgeniya Kazachkova4Alexander Markhaev5Yulia Kononova6Marina Gulyaeva7Lubov Adamenko8Olga Kurskaya9Yuhai Bi10Yuhua Xin11Kirill Sharshov12Alexander Shestopalov13Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaCAS 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, ChinaChina General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaLaboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, RussiaIn 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.https://www.mdpi.com/1999-4915/14/9/2036SARS-CoV-2first waveRussiaepidemiologyCOVID-19phylogeny |
| spellingShingle | 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 Viruses SARS-CoV-2 first wave Russia epidemiology COVID-19 phylogeny |
| title | Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic |
| title_full | Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic |
| title_fullStr | Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic |
| title_full_unstemmed | Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic |
| title_short | Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic |
| title_sort | genomic and epidemiological features of covid 19 in the novosibirsk region during the beginning of the pandemic |
| topic | SARS-CoV-2 first wave Russia epidemiology COVID-19 phylogeny |
| url | https://www.mdpi.com/1999-4915/14/9/2036 |
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