Epidemiological monitoring of patients with coronavirus infection based on modern molecular biological research methods in 2021-2022 in the metropolis

The characteristics of the COVID-19 epidemic process were studied according to the results of a PCR study by RT-PCR and full-genome sequencing of SARS-CoV-2 in Moscow during the year of observation from 30.07.2021 to 01.08.2022, the total volume of studies was 2 951 398. 19 091 samples were selected for subsequent study by full-genome sequencing. The evolutionary dynamics of genetic lines is noted. In the period from 07.2021 to the middle of 01.2022, the delta strain (AY.122) prevailed in Moscow, but from 12.13.2021 the first samples with the omicron strain (BA.1, BA.1.17.2) were found. In a little more than a month, these strains almost completely replaced the strains of the genetic lines (GL) «Delta«. «New» strains consistently replaced the earlier ones: from 13.12.2021 to 10.01.2022, 19 GL strains of omicron BA.1.x were identified. From 10.01.2022, a «Danish» variety of BA appeared in Moscow.2 (»Stealth Omicron«), which began to quickly displace the rest of the chapters. According to the DCLI, the sixth (since the summer of 2022) wave of infection spread is mainly determined by the «South African» strains of SARS-CoV-2 – variants of VA.4 and VA.5, which were first identified starting from 19.06.2022. The analysis of the prevalence and population composition of 1793 samples with SARS-CoV-2 for the period from 19.06. to 21.07.2022, GL BA.4.x, BA.5.x, VE.x, FF.x infected 1481 patients (82.6%). The pool of infected patients formed by the «early» generations totaled 312 patients.

During the year of observation, 13 cases of re–infection were established: 9 of them were infected with delta strains at the first disease and omicron strains at the second. Infection of two patients was also confirmed, in which in both cases COVID-19 disease was caused by «new» omicron strains.

1. Акимкин В.Г., Кузин С.Н., Семененко Т.А., Плоскирева А.А., Дубоделов Д.В., Тиванова Е.В., Пшеничная Н.Ю., Каленская А.В., Яцышина С.Б., Шипулина О.Ю., Родионова Е.Н., Петрова Н.С., Соловьева И.В., Квасова О.А., Вершинина М.А., Мамошина М.В., Клушкина В.В., Чурилова Н.С., Панасюк Я.В., Власенко Н.В., Остроушко А.А., Балмасов Е.С., Мосунов А.В. Гендерно-возрастная характеристика пациентов с COVID-19 на разных этапах эпидемии в Москве // Проблемы особо опасных инфекций. – 2020. – № 3. – С. 27-35. https://doi.org/10.21055/0370-1069-2020-3-27-35.

2. Брико Н.И., Каграманян И.Н., Никифоров В.В., Суранова Т.Г., Чернявская О.П., Полежаева Н.А. Пандемия COVID-19. Меры борьбы с ее распространением в Российской Федерации // Эпидемиология и вакцинопрофилактика. – 2020. – Т. 19. – № 2. – С. 4-12. https://doi.org/10.31631/2073-3046-2020-19-2-4-12.

3. Вечорко В.И., Аверков О.В., Зимин А.А. Новый штамм SARS-CoV-2 Омикрон – клиника, лечение, профилактика (обзор литературы) // Кардиоваскулярная терапия и профилактика. – 2022. – Т. 21. – № 6. – С. 3228. https://doi.org/10.15829/1728-8800-2022-3228.

4. Годков М.А., Шустов В.В., Кашолкина Е.А. Динамика и гендерно-возрастные особенности эпидемического процесса COVID-19 в городе Москве (итоги скринингового обследования за 1,5 года) // Лабораторная служба. –2021. – Т. 10. – № 4. – С. 30 -37. https://doi.org/10.17116/labs20211004130.

5. Данные Всемирной организации здравоохранения. [Электронный ресурс] URL: https://www.who.int/ru/activities/tracking-SARS-CoV-2variants. (Дата обращения 15 сентября 2022).

6. Araf Y., Akter F., Tang Y.D., Fatemi R., Parvez M.S.A., Zheng C., Hossain M.G. Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines // J. Med. Virol. – 2022. – Vol. 94. – N. 5. – P. 1825-1832. doi: 10.1002/jmv.27588. Epub 2022 Jan 23.

7. Chan J.F., Kok K.H., Zhu Z., Chu H., To K.K., Yuan S., Yuen K.Y. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan // Emerg. Microbes Infect. – 2020. – Vol. 9. – N. 1. – P. 221-236. doi: 10.1080/22221751.2020.1719902. Erratum in: Emerg. Microbes Infect. – 2020. – Vol. 9. – N. 1. – P. 540.

8. Gao S.J., Guo H., Luo G. Omicron variant (B.1.1.529) of SARS-CoV-2, a global urgent public health alert! // J. Med. Virol. – 2022. – Vol. 94. – N. 4. – P. 1255-1256. doi: 10.1002/jmv.27491.

9. Haseltine W.A. Birth of the omicron family: BA.1, BA.2, BA.3. Each as different as alpha is from delta. [Электронный ресурс] URL: https://www.forbes.com/sites/williamhaseltine/2022/01/26/birth-of-the-omicron-family-ba1-ba2-ba3-each-as-different-as-alpha-is-fromdelta/?sh=4b65d70f3da9. (Дата обращения 26.01.2022).

10. Joshi G., Poduri R. Omicron, a new SARS-CoV-2 variant: assessing the impact on severity and vaccines efficacy // Hum. Vaccin. Immunother. – 2022. – Vol. 18. – N. 1. – P. 2034458. doi: 10.1080/21645515.2022.2034458. Epub 2022 Mar 3.

11. Netzl A., Tureli S., LeGresley E. et al. Analysis of SARS-CoV-2 omicron neutralization data up to 2021-12-22 // BioRxiv. – 2021. [Электронный ресурс] URL: https://www.biorxiv.org/content/10.1101/2021.12.31.474032 (Дата обращения 21.09.2022).

12. Roshchina Y., Roshchin S., Rozhkova K. Determinants of COVID-19 vaccine hesitancy and resistance in Russia // Vaccine. – 2022. – Vol. 40. – N. 39. – P. 5739-5747. doi: 10.1016/j.vaccine.2022.08.042. Epub 2022 Aug 26.

13. WHO Report (2021). Enhancing Readiness for Omicron (B.1.1.529). [Электронный ресурс] URL: https://www.who.int/publications/m/item/enhancing-readiness-foromicron-(b.1.1.529)-technical-brief-and-priority-actions-for-member-states. (Дата обращения 21.01.2022).