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Yakovleva A, Kovalenko G, Redlinger M, Liulchuk MG, Bortz E, Zadorozhna VI, Scherbinska AM, Wertheim JO, Goodfellow I, Meredith L, Vasylyeva TI. Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021. Sci Rep 2022; 12:15749. [PMID: 36131001 PMCID: PMC9491264 DOI: 10.1038/s41598-022-19414-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), informing evidence-based public health decision making. Ukraine has experienced four waves of the Coronavirus Disease 2019 (COVID-19) between spring 2020 and spring 2022. However, insufficient capacity for local genetic sequencing limited the potential application of SARS-CoV-2 genomic surveillance for public health response in the country. Herein, we report local sequencing of 103 SARS-CoV-2 genomes from patient samples collected in Kyiv in July-December 2021 using Oxford Nanopore technology. Together with other published Ukrainian SARS-CoV-2 genomes, our data suggest that the third wave of the epidemic in Ukraine (June-December 2021) was dominated by the Delta Variant of Concern (VOC). Our phylogeographic analysis revealed that in summer 2021 Delta VOC was introduced into Ukraine from multiple locations worldwide, with most introductions coming from Central and Eastern European countries. The wide geographic range of Delta introductions coincides with increased volume of travel to Ukraine particularly from locations outside of Europe in summer 2021. This study highlights the need to urgently integrate affordable and easily scaled pathogen sequencing technologies in locations with less developed genomic infrastructure, in order to support local public health decision making.
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Affiliation(s)
- Anna Yakovleva
- Medical Sciences Division, University of Oxford, Oxford, UK
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Ganna Kovalenko
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
| | - Matthew Redlinger
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
| | - Mariia G Liulchuk
- State Institution "L.V. Hromashevskyi Institute of Epidemiology and Infectious Diseases of the National Academy of Medical Sciences of Ukraine", Kyiv, Ukraine
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
| | - Viktoria I Zadorozhna
- State Institution "L.V. Hromashevskyi Institute of Epidemiology and Infectious Diseases of the National Academy of Medical Sciences of Ukraine", Kyiv, Ukraine
| | - Alla M Scherbinska
- State Institution "L.V. Hromashevskyi Institute of Epidemiology and Infectious Diseases of the National Academy of Medical Sciences of Ukraine", Kyiv, Ukraine
| | - Joel O Wertheim
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luke Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Tetyana I Vasylyeva
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA.
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