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COVID-19: evolution of the pandemic in Russia. Report II: dynamics of the circulation of SARS-CoV-2 genetic variants

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1. Title Title of document COVID-19: evolution of the pandemic in Russia. Report II: dynamics of the circulation of SARS-CoV-2 genetic variants
2. Creator Author's name, affiliation, country Vasily G. Akimkin; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Anna Yu. Popova; Federal Service for Supervision of Consumer Rights Protection and Human Welfare; Россия
2. Creator Author's name, affiliation, country Kamil F. Khafizov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Dmitry V. Dubodelov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Svetlana V. Ugleva; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Tatyana A. Semenenko; National Research Center of Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya; Россия
2. Creator Author's name, affiliation, country Antonina A. Ploskireva; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Alexander V. Gorelov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Natalia Yu. Pshenichnaya; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Elena B. Yezhlova; Federal Service for Supervision of Consumer Rights Protection and Human Welfare; Россия
2. Creator Author's name, affiliation, country Alexander N. Letyushev; Federal Service for Supervision of Consumer Rights Protection and Human Welfare; Россия
2. Creator Author's name, affiliation, country Yulia V. Demina; Federal Service for Supervision of Consumer Rights Protection and Human Welfare; Россия
2. Creator Author's name, affiliation, country Vladimir V. Kutyrev; Russian Research Anti-Plague Institute "Microbe"; Россия
2. Creator Author's name, affiliation, country Rinat A. Maksyutov; State Research Centre of Virology and Biotechnology “Vector”; Россия
2. Creator Author's name, affiliation, country Vadim M. Govorun; Institute of Disinfectology; Россия
2. Creator Author's name, affiliation, country Ivan A. Dyatlov; State Research Center for Applied Microbiology and Biotechnology; Россия
2. Creator Author's name, affiliation, country Areg A. Totolian; Pasteur St. Petersburg Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Alexandr N. Kulichenko; Stavropol Research Anti-Plague Institute; Россия
2. Creator Author's name, affiliation, country Sergey V. Balakhonov; Irkutsk Research Anti-Plague Institute of Siberia and the Far East; Россия
2. Creator Author's name, affiliation, country Nikolay V. Rudakov; Omsk Research Institute of Natural Focal Infections; Россия
2. Creator Author's name, affiliation, country Olga E. Trotsenko; Khabarovsk Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Alexey K. Noskov; Rostov-on-Don Researsh Anti-Plague Institute; Россия
2. Creator Author's name, affiliation, country Natalia N. Zaitseva; Nizhny Novgorod Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Andrey V. Toporkov; Volgograd Research Anti-Plague Institute; Россия
2. Creator Author's name, affiliation, country Dmitry A. Lioznov; Smorodintsev Research Institute of Influenza; Россия
2. Creator Author's name, affiliation, country Elena E. Andreeva; Federal Service for Supervision of Consumer Rights Protection and Human Welfare for the City of Moscow; Россия
2. Creator Author's name, affiliation, country Olga M. Mikailova; Federal Service for Supervision of Consumer Rights Protection and Human Welfare in the Moscow Region; Россия
2. Creator Author's name, affiliation, country Andrey G. Komarov; Diagnostic Center (Center for Laboratory Research) of the Department of Health of the City of Moscow; Россия
2. Creator Author's name, affiliation, country Vasily Yu. Ananyev; Federal Center for Hygiene and Epidemiology; Россия
2. Creator Author's name, affiliation, country Vladimir V. Moldovanov; Center for Hygiene and Epidemiology in the City of Moscow; Россия
2. Creator Author's name, affiliation, country Denis Yu. Logunov; National Research Center of Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya; Россия
2. Creator Author's name, affiliation, country Vladimir A. Gushchin; National Research Center of Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya; Россия
2. Creator Author's name, affiliation, country Vladimir G. Dedkov; Pasteur St. Petersburg Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Anna S. Cherkashina; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Stanislav N. Kuzin; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Elena V. Tivanova; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Larisa Yu. Kondrasheva; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Valeria V. Saenko; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Semyon Yu. Selezov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Gasan A. Gasanov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Nino Kh. Svanadze; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Maxim B. Glazov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Aleksey A. Ostroushko; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Konstantin O. Mironov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Anna S. Esman; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Natalia A. Osina; Russian Research Anti-Plague Institute "Microbe"; Россия
2. Creator Author's name, affiliation, country Sergei A. Bodnev; State Research Centre of Virology and Biotechnology “Vector”; Россия
2. Creator Author's name, affiliation, country Andrey B. Komissarov; Smorodintsev Research Institute of Influenza; Россия
2. Creator Author's name, affiliation, country Daria М. Danilenko; Smorodintsev Research Institute of Influenza; Россия
2. Creator Author's name, affiliation, country Aleksandr G. Bogun; State Research Center for Applied Microbiology and Biotechnology; Россия
2. Creator Author's name, affiliation, country Yuriy P. Skryabin; State Research Center for Applied Microbiology and Biotechnology; Россия
2. Creator Author's name, affiliation, country Kristina V. Lopatovskaya; Irkutsk Research Anti-Plague Institute of Siberia and the Far East; Россия
2. Creator Author's name, affiliation, country Sergey V. Shtrek; Omsk Research Institute of Natural Focal Infections; Россия
2. Creator Author's name, affiliation, country Anna S. Volynkina; Stavropol Research Anti-Plague Institute; Россия
2. Creator Author's name, affiliation, country Anna S. Gladkikh; Pasteur St. Petersburg Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Valeria О. Kotova; Khabarovsk Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Alexey S. Vodopyanov; Rostov-on-Don Researsh Anti-Plague Institute; Россия
2. Creator Author's name, affiliation, country Nadezhda A. Novikova; Nizhny Novgorod Research Institute of Epidemiology and Microbiology; Россия
2. Creator Author's name, affiliation, country Anna S. Speranskaya; Institute of Disinfectology; Россия
2. Creator Author's name, affiliation, country Andrey E. Samojlov; Institute of Disinfectology; Россия
2. Creator Author's name, affiliation, country Alexey D. Neverov; Central Research Institute for Epidemiology; Россия
2. Creator Author's name, affiliation, country Ivan M. Shpak; Volgograd Research Anti-Plague Institute; Россия
3. Subject Discipline(s)
3. Subject Keyword(s) COVID-19; incidence; epidemic process; SARS-CoV-2; sequencing; genetic variant
4. Description Abstract

Background. The ongoing pandemic of the novel coronavirus infection (COVID-19) draws attention to the significance of molecular and genetic monitoring of the SARS-CoV-2 spread among the population of the Russian Federation. The aim of the study was to analyze the dynamics of circulation of SARS-CoV-2 genetic variants in Russia.

Materials and methods. The analysis of the circulation dynamics for SARS-CoV-2 genetic variants in Russia was carried out, covering the period from 28/12/2020 to 26/6/2022. The analysis included the data from Rospotrebnadzor Report No. 970 "Information about Infectious Diseases in Individuals with Suspected Novel Coronavirus Infection" and the Virus Genome Aggregator of Russia (VGARus). The presence of SARS-CoV-2 RNA was confirmed by the real-time reverse transcription polymerase chain reaction. The primer panels developed at the Central Research Institute of Epidemiology were used for amplification of genomic fragments and the subsequent sequencing.

Results and discussion. Using the Russian VGARus platform developed by the Central Research Institute of Epidemiology, we received the data on mutational variability of SARS-CoV-2. By monitoring the circulation of SARS-CoV-2 genetic variants in Russia from 28/12/2020 to 26/6/2022, we found that Delta and Omicron genetic variants prevailed at different stages of the epidemic.

Conclusion. The data of molecular and genetic studies are an essential component of epidemiological surveillance, being critically important for making executive decisions aimed at prevention of further spread of SARS-CoV-2 and laying the groundwork for creating new vaccines.
5. Publisher Organizing agency, location Central Research Institute for Epidemiology
6. Contributor Sponsor(s)
7. Date (DD-MM-YYYY) 24.09.2022
8. Type Status & genre Peer-reviewed Article
8. Type Type Research Article
9. Format File format
10. Identifier Uniform Resource Identifier https://microbiol.crie.ru/jour/article/view/1303
10. Identifier Digital Object Identifier (DOI) 10.36233/0372-9311-295
11. Source Title; vol., no. (year) Journal of microbiology, epidemiology and immunobiology; Vol 99, No 4 (2022)
12. Language English=en ru
13. Relation Supp. Files Fig. 1. Dynamics of genetic variants of SARS-CoV-2 and COVID-19 incidence rates (per 100,000 population) in Russia (2020–2022). (543KB)
Fig. 2. The distribution of genetic variants in biomaterial specimens collected from 28/12/2020 to 26/6/2022. (62KB)
Fig. 3. Subvariants of the Delta lineage (B.1.617.2+AY.*) isolated in Russia. (91KB)
Fig. 4. Subvariants of the B.1.617.2. (Delta) lineage, except for basic variant B.1.617.2 and subvariants AY.122, AY.126, AY.121, AY.43 isolated in Russia. (297KB)
Fig. 5. Dynamics of subvariants of the Delta lineage (B.1.617.2+AY.*), which were isolated in Russia, based on the data from the national VGARus database. (302KB)
Fig. 6. Subvariants of the Omicron lineage (B.1.1.529+BA.*), which were isolated in Russia, based on the data from the national VGARus database as of 26/6/2022. (53KB)
Fig. 7. Dynamics of subvariants of the Omicron lineage (B.1.1.529 + BA.*), which were isolated in Russia, based on the data from the national VGARus database. (345KB)
Fig. 1. Dynamics of genetic variants of SARS-CoV-2 and COVID-19 incidence rates (per 100,000 population) in Russia (2020–2022). (544KB)
Fig. 2. The distribution of genetic variants in biomaterial specimens collected from 28/12/2020 to 26/6/2022. (74KB)
Fig. 3. Subvariants of the Delta lineage (B.1.617.2+AY.*) isolated in Russia. (60KB)
Fig. 4. Subvariants of the B.1.617.2. (Delta) lineage, except for basic variant B.1.617.2 and subvariants AY.122, AY.126, AY.121, AY.43 isolated in Russia. (297KB)
Fig. 5. Dynamics of subvariants of the Delta lineage (B.1.617.2+AY.*), which were isolated in Russia, based on the data from the national VGARus database. (295KB)
Fig. 6. Subvariants of the Omicron lineage (B.1.1.529+BA.*), which were isolated in Russia, based on the data from the national VGARus database as of 26/6/2022. (50KB)
Fig. 7. Dynamics of subvariants of the Omicron lineage (B.1.1.529 + BA.*), which were isolated in Russia, based on the data from the national VGARus database. (303KB)
14. Coverage Geo-spatial location, chronological period, research sample (gender, age, etc.)
15. Rights Copyright and permissions Copyright (c) 2022 Akimkin V.G., Popova A.Y., Khafizov K.F., Dubodelov D.V., Ugleva S.V., Semenenko T.A., Ploskireva A.A., Gorelov A.V., Pshenichnaya N.Y., Yezhlova E., Letyushev A.N., Demina Y.V., Kutyrev V.V., Maksyutov R.A., Govorun V.M., Dyatlov I.A., Totolian A.A., Kulichenko A.N., Balakhonov S.V., Rudakov N.V., Trotsenko O.E., Noskov A.K., Zaitseva N.N., Toporkov A.V., Lioznov D.A., Andreeva E.E., Mikailova O.M., Komarov A.G., Ananyev V.Y., Moldovanov V.V., Logunov D.Y., Gushchin V.A., Dedkov V.G., Cherkashina A.S., Kuzin S.N., Tivanova E.V., Kondrasheva L.Y., Saenko V.V., Selezov S.Y., Gasanov G.A., Svanadze N.K., Glazov M.B., Ostroushko A.A., Mironov K.O., Esman A.S., Osina N.A., Bodnev S.A., Komissarov A.B., Danilenko D.M., Bogun A.G., Skryabin Y.P., Lopatovskaya K.V., Shtrek S.V., Volynkina A.S., Gladkikh A.S., Kotova V.O., Vodopyanov A.S., Novikova N.A., Speranskaya A.S., Samojlov A.E., Neverov A.D., Shpak I.M.
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