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Genomic epidemiology of SARS-CoV-2 in Seychelles, 2020–2021
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(2022) Genomic epidemiology of SARS-CoV-2 in Seychelles, 2020–2021. Viruses, 14 (6). 1318. doi:10.3390/v14061318 ISSN 1999-4915.
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Official URL: https://doi.org/10.3390/v14061318
Abstract
Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.
| Item Type: | Journal Article | ||||||||||||
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| Subjects: | R Medicine > RA Public aspects of medicine | ||||||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||||
| SWORD Depositor: | Library Publications Router | ||||||||||||
| Library of Congress Subject Headings (LCSH): | COVID-19 (Disease) , COVID-19 (Disease) -- Epidemiology -- Seychelles, Communicable diseases -- Transmission -- Seychelles | ||||||||||||
| Journal or Publication Title: | Viruses | ||||||||||||
| Publisher: | MDPI AG | ||||||||||||
| ISSN: | 1999-4915 | ||||||||||||
| Official Date: | 16 June 2022 | ||||||||||||
| Dates: |
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| Volume: | 14 | ||||||||||||
| Number: | 6 | ||||||||||||
| Article Number: | 1318 | ||||||||||||
| DOI: | 10.3390/v14061318 | ||||||||||||
| Status: | Peer Reviewed | ||||||||||||
| Publication Status: | Published | ||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
| Date of first compliant deposit: | 14 July 2022 | ||||||||||||
| Date of first compliant Open Access: | 14 July 2022 | ||||||||||||
| RIOXX Funder/Project Grant: |
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