An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia
The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021–early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that t...
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MDPI AG
2023-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/7/1415 |
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| author | Galya V. Klink Daria Danilenko Andrey B. Komissarov Nikita Yolshin Olga Shneider Sergey Shcherbak Elena Nabieva Nikita Shvyrev Nadezhda Konovalova Alyona Zheltukhina Artem Fadeev Kseniya Komissarova Andrey Ksenafontov Tamila Musaeva Veronika Eder Maria Pisareva Petr Nekrasov Vladimir Shchur Georgii A. Bazykin Dmitry Lioznov |
| author_facet | Galya V. Klink Daria Danilenko Andrey B. Komissarov Nikita Yolshin Olga Shneider Sergey Shcherbak Elena Nabieva Nikita Shvyrev Nadezhda Konovalova Alyona Zheltukhina Artem Fadeev Kseniya Komissarova Andrey Ksenafontov Tamila Musaeva Veronika Eder Maria Pisareva Petr Nekrasov Vladimir Shchur Georgii A. Bazykin Dmitry Lioznov |
| author_sort | Galya V. Klink |
| collection | DOAJ |
| description | The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021–early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between 16–29 December 2021, which was the earliest known instance of a large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR-positive. Among the 118 residents for whom the variant had been tested by whole-genome sequencing, 111 (94.1%) were found to carry the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported a previous infection of COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sub-lineage of the Omicron variant. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint Petersburg and has spread to other regions of Russia and even to other countries. The rapid spread of the Omicron variant in a population with preexisting immunity to previous variants underlines its propensity for immune evasion. |
| first_indexed | 2024-03-11T00:34:13Z |
| format | Article |
| id | doaj.art-6e50a175cade43e6a04bbb717fe5981a |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T00:34:13Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6e50a175cade43e6a04bbb717fe5981a2023-11-18T21:43:23ZengMDPI AGViruses1999-49152023-06-01157141510.3390/v15071415An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, RussiaGalya V. Klink0Daria Danilenko1Andrey B. Komissarov2Nikita Yolshin3Olga Shneider4Sergey Shcherbak5Elena Nabieva6Nikita Shvyrev7Nadezhda Konovalova8Alyona Zheltukhina9Artem Fadeev10Kseniya Komissarova11Andrey Ksenafontov12Tamila Musaeva13Veronika Eder14Maria Pisareva15Petr Nekrasov16Vladimir Shchur17Georgii A. Bazykin18Dmitry Lioznov19A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaCity Hospital #40, 197706 Saint-Petersburg, RussiaA.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, RussiaInternational Laboratory of Statistical and Computational Genomics, HSE University, 101000 Moscow, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaInternational Laboratory of Statistical and Computational Genomics, HSE University, 101000 Moscow, RussiaA.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, RussiaThe Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021–early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between 16–29 December 2021, which was the earliest known instance of a large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR-positive. Among the 118 residents for whom the variant had been tested by whole-genome sequencing, 111 (94.1%) were found to carry the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported a previous infection of COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sub-lineage of the Omicron variant. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint Petersburg and has spread to other regions of Russia and even to other countries. The rapid spread of the Omicron variant in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.https://www.mdpi.com/1999-4915/15/7/1415SARS-CoV-2Russiafounder effectBA.1.1superspreadingoutbreak |
| spellingShingle | Galya V. Klink Daria Danilenko Andrey B. Komissarov Nikita Yolshin Olga Shneider Sergey Shcherbak Elena Nabieva Nikita Shvyrev Nadezhda Konovalova Alyona Zheltukhina Artem Fadeev Kseniya Komissarova Andrey Ksenafontov Tamila Musaeva Veronika Eder Maria Pisareva Petr Nekrasov Vladimir Shchur Georgii A. Bazykin Dmitry Lioznov An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia Viruses SARS-CoV-2 Russia founder effect BA.1.1 superspreading outbreak |
| title | An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia |
| title_full | An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia |
| title_fullStr | An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia |
| title_full_unstemmed | An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia |
| title_short | An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia |
| title_sort | early sars cov 2 omicron outbreak in a dormitory in saint petersburg russia |
| topic | SARS-CoV-2 Russia founder effect BA.1.1 superspreading outbreak |
| url | https://www.mdpi.com/1999-4915/15/7/1415 |
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