Журнал «Актуальная инфектология» Том 9, №4, 2021
Вернуться к номеру
Molecular epidemiology of SARS-CoV-2 in Ukraine
Авторы: A. Yakovleva (1), G. Kovalenko (2), T.I. Vasylyeva (3), M. Redlinger (4), L. Meredith (2), M.G. Liulchuk (5), V.I. Zadorozhna (5), A.M. Scherbinska (5)
(1) — Medical Sciences Division, University of Oxford, Oxford, United Kingdom
(2) — Department of Pathology, University of Cambridge, Cambridge, United Kingdom
(3) — Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, United States of America
(4) — Department of Biological Sciences, University of Alaska Anchorage, Anchorage, United States of America
(5) — State Institution “L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases,
National Academy of Medical Science of Ukraine”, Kyiv, Ukraine
Рубрики: Инфекционные заболевания
Разделы: Медицинские форумы
Версия для печати
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first identified due to a cluster of acute pneumonia cases with an unknown cause in Wuhan, China in December 2019. The virus quickly spread and reached pandemic status on March, 2020; with over 200 million cases reported, and resulting in over 4.55 million deaths globally to date. Pathogen genomic sequencing has informed public health systems of virus importations, enhanced detection of transmission chains, and enabled rapid identification of novel variants of concern (VOC). Ukraine has reported 2.3 million infections, over 54,000 deaths, and an estimated 12.7 % of the population vaccinated to date. Currently, cases are rapidly doubling and are expected to reach the third wave in the winter months; however, molecular epidemiology of SARS-CoV-2 has not yet been reported in Ukraine due to lack of genomic data.
Materials and methods. We obtained SARS-CoV-2 positive patient samples with confirmed infection by RT-PCR. Viral RNA was extracted using the QIAamp Viral RNA Mini Kit (Qiagen). Samples were sequenced with the ARTIC nCoV-2019 protocol v3 (LoCost) using the NEBNext ARTIC SARS-CoV-2 Companion Kit for Oxford Nanopore (New England BioLabs). Briefly, cDNA was generated, and the full-length genome was amplified with a multiplex PCR approach consisting of 400 bp overlapping amplicons. Libraries were subsequently prepared and sequenced using the MinION flow cells version 9.4.1 (Oxford Nanopore Technologies). Genomes were assembled using the ARTIC bioinformatic pipeline with a 20x minimum coverage across all genomic areas. Pango lineage assignments were determined using the Pangolin nomenclature tool.
Results. We report 23 near full length genome sequences obtained from individuals who tested positive for SARS-CoV-2 by RT-PCR between June 2021 and July 2021 in Kyiv, Ukraine. The samples were obtained from symptomatic patients across the private laboratory in Kyiv and are thus representative of the Ukrainian epidemic. Most samples (n = 19) were of the B.1.617.2/Delta variant, two samples were classified AY.12 as a sub-lineage of the Delta variant, and two were B.1.1.7/Alpha variant.
Conclusions. Large-scale genomic sequencing of SARS-CoV-2 has enabled global tracking of pandemic dynamics. In September 2020, Alpha and Beta were amongst the first identified VOC, followed by the detection of Gamma and Delta in December 2020. VOC reportedly have higher transmission rates, severity outcomes, and potentially result in reduced vaccine efficacy. As of September 2021, transmission of the Delta variant remains predominant amongst the European Economic Area, including Ukraine. In combination with waning immunity against SARS-CoV-2, the WHO now recommends booster vaccination doses to at risk populations to enhance protection against the Delta variant.