sredobЗдоровье населения и среда обитания – ЗНиСОPublic Health and Life Environment – PH&LE2219-52382619-0788ФБУЗ ФЦГиЭ Роспотребнадзора10.35627/2219-5238/2024-32-3-63-69sredob-1879Research ArticleЭПИДЕМИОЛОГИЯEPIDEMIOLOGYГеномный мониторинг вируса SARS-CоV-2, циркулировавшего на территории Кыргызской Республики в 2020–2021 гг.Genome Monitoring of SARS-CoV-2 Circulating in the Kyrgyz Republic in 2020–2021https://orcid.org/0009-0005-9065-6744ДжумакановаА. БDzhumakanovaA. B.

Джумаканова Айгуль Бейшебаевна – начальник Центра лабораторных испытаний Департамента профилактики заболеваний и Госсанэпиднадзора МЗ КР.

ул. Фрунзе, д. 535, Бишкек, 720033

Aigul B. Dzhumakanova - Head of the Testing Laboratory Center, Department of Disease Prevention and State Sanitary and Epidemiological Surveillance of the Ministry of Health of the Kyrgyz Republic.

535 Frunze Street, Bishkek, 720033

aigul.dzumakanova.dgsn@mail.ruДепартамент профилактики заболеваний и государственного санитарно-эпидемиологического надзора Министерства здравоохранения Кыргызской РеспубликиКыргызстанDepartment of Disease Prevention and State Sanitary and Epidemiological Surveillance of the Ministry of Health of the Kyrgyz RepublicKyrgyzstan2024290320243236369Copyright © Джумаканова А.Б., 20242024Джумаканова А.Б.Dzhumakanova A.B.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://zniso.fcgie.ru/jour/article/view/1879 

 

Введение

Введение. РНК-содержащий вирус тяжелого острого респираторного заболевания SARS-CoV-2 быстро распространился по миру вследствие адаптации к хозяину путем генетической эволюции. Появление геновариантов с мутациями, повышающими контагиозность и трансмиссивность, могут негативно влиять на эффективность программ борьбы с заболеванием и снизить эффективность вакцинации.

Цель исследования

Цель исследования: выявление доминирующих геновариантов вируса SARS-CoV-2, циркулирующих на территории Кыргызской Республики в 2020–2021 гг.

Материалы и методы

Материалы и методы. Геномный мониторинг был проведен на положительных мазках из носоглотки. Диагностику COVID-19 проводили методом ПЦР в реальном времени с обратной транскрипцией (ОТ-ПЦР) на различных коммерческих тест-системах.

Определение геновариантов (n = 15) проводилось методом высокопроизводительного секвенирования на приборе MiSeq по протоколу ARTIC v3. Изучение мутационной изменчивости вируса SARS-CoV-2 проводили посредством кластерного анализа аминокислотных замен в S-белке по методу Уорда. Нуклеотидные последовательности из Кыргызстана (n = 15), России (n = 16), Индии (n = 2) и Китая (n = 2) выравнивали с помощью MAFFT. Филогенетическое дерево было создано с помощью метода максимального правдоподобия (ML) в IQ-TREE v1.6.12 с использованием

процессов Nextstrain

процессов Nextstrain. Корнем дерева считались образцы SARS-CoV-2 Wuhan/Hu-1/2019 и Wuhan/WH01/2019, загруженными из базы данных GenBank®.

Результаты

Результаты. Филогенетический анализ полученных данных выявил, что доминирующим геновариантом VOC был В.1.1.7 (Alpha), на долю которого приходилось 36,4 % (12/33), также был выявлен B.1.351 (Веtа) VOC, на долю которого приходилось 6,1 % (2/33). При исследовании образцов на наличие аминокислотных замен в S-белке обнаружено, что изоляты B.1.1.7 Alpha (Британский) кластеризуются на две отдельные ветви.

Заключение

Заключение. Изучение частоты и влияния мутаций на патогенетические свойства вируса, а также анализ преобладающих геновариантов вируса позволят своевременно принимать меры по противодействию распространению вируса SARS-CoV-2 в стране. В связи с этим необходим постоянный геномный мониторинг за циркулирующими геновариантами COVID-19.

Introduction

Introduction: The RNA-containing severe acute respiratory syndrome virus SARS-CoV-2 has spread rapidly around the world by adaptation to the host through genetic evolution. The emergence of variants with genetic mutations that increase contagiousness and transmission may hamper the effectiveness of disease control programs and efficacy of vaccination.

Objective

Objective: To establish dominant SARS-CoV-2 variants circulating in the Kyrgyz Republic in 2020–2021.

Materials and methods

Materials and methods: Genomic monitoring was carried out based on positive results of testing nasopharyngeal swabs. SARS-CoV-2 was detected by a real-time reverse transcription –polymerase chain reaction (RT-PCR) assay using registered commercial test kits. Genetic variants (n = 15) were determined by high-throughput sequencing on a MiSeq device (Illumina, USA) using the COVID-19 ARTIC v3 protocol. Mutational variability of SARS-CoV-2 was examined using a cluster analysis of amino acid substitutions in the S protein applying Ward’s method. Nucleotide sequences from Kyrgyzstan (n = 15), Russia (n = 16), India (n = 2), and China (n = 2) were aligned using MAFFT. IQ-TREE v1.6.12 was used to infer the phylogenetic tree by maximum likelihood applying Nextstrain processes. Isolates Wuhan/Hu-1/2019 and Wuhan/WH01/2019 downloaded from the GenBank® database were considered to be the root of the tree (reference).

Results

Results: Phylogenetic data analysis revealed that SARS-CoV-2 B.1.1.7 (Alpha) was the dominant VOC variant, the proportion of which was as high as 36.4 % (12/33); B.1.351 (Beta) was also found (6.1 % or 2/33). When samples were examined for amino acid substitutions in the S-protein, B.1.1.7 Alpha (British) isolates were found to cluster into two distinct branches.

Conclusion

Conclusion: The study of the frequency and influence of mutations on pathogenetic properties of the virus, as well as the analysis of the predominant variants of the virus will allow timely measures to be taken to counteract the spread of SARS-CoV-2 in the country. In this regard, continuous genome monitoring of circulating COVID-19 variants is necessary.

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The authors declare that there are no conflicts of interest present.