Viruses (Jun 2022)
Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021
- John Mwita Morobe,
- Brigitte Pool,
- Lina Marie,
- Dwayne Didon,
- Arnold W. Lambisia,
- Timothy Makori,
- Khadija Said Mohammed,
- Zaydah R. de Laurent,
- Leonard Ndwiga,
- Maureen W. Mburu,
- Edidah Moraa,
- Nickson Murunga,
- Jennifer Musyoki,
- Jedida Mwacharo,
- Lydia Nyamako,
- Debra Riako,
- Pariken Ephnatus,
- Faith Gambo,
- Josephine Naimani,
- Joyce Namulondo,
- Susan Zimba Tembo,
- Edwin Ogendi,
- Thierno Balde,
- Fred Athanasius Dratibi,
- Ali Ahmed Yahaya,
- Nicksy Gumede,
- Rachel A. Achilla,
- Peter K. Borus,
- Dorcas W. Wanjohi,
- Sofonias K. Tessema,
- Joseph Mwangangi,
- Philip Bejon,
- David J. Nokes,
- Lynette Isabella Ochola-Oyier,
- George Githinji,
- Leon Biscornet,
- Charles N. Agoti
Affiliations
- John Mwita Morobe
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles
- Lina Marie
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles
- Dwayne Didon
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles
- Arnold W. Lambisia
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Timothy Makori
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Khadija Said Mohammed
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Zaydah R. de Laurent
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Leonard Ndwiga
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Maureen W. Mburu
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Edidah Moraa
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Nickson Murunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Jennifer Musyoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Jedida Mwacharo
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Lydia Nyamako
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Debra Riako
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Pariken Ephnatus
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Faith Gambo
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Josephine Naimani
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Joyce Namulondo
- World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles
- Susan Zimba Tembo
- World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles
- Edwin Ogendi
- World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles
- Thierno Balde
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo
- Fred Athanasius Dratibi
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo
- Ali Ahmed Yahaya
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo
- Nicksy Gumede
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo
- Rachel A. Achilla
- World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo
- Peter K. Borus
- World Health Organization-Kenya Country Office, Gigiri, Nairobi P.O. Box 45335, Kenya
- Dorcas W. Wanjohi
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia
- Sofonias K. Tessema
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia
- Joseph Mwangangi
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- David J. Nokes
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Lynette Isabella Ochola-Oyier
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- George Githinji
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles
- Charles N. Agoti
- Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
- DOI
- https://doi.org/10.3390/v14061318
- Journal volume & issue
-
Vol. 14,
no. 6
p. 1318
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.
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