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Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021

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Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya
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Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles
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World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles
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Department of Arbovirology, Emerging and Re-emerging Infectious Diseases—Uganda Virus Research Institution (UVRI), Entebbe P.O. Box 49, Uganda
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World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo
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World Health Organization-Kenya Country Office, Gigiri, Nairobi P.O. Box 45335, Kenya
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Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia
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School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry CV4 7AL, UK
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Department of Biochemistry and Biotechnology, Pwani University, Kilifi P.O. Box 195-80108, Kenya
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Department of Public Health, Pwani University, Kilifi P.O. Box 195-80108, Kenya
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Author to whom correspondence should be addressed.
Academic Editors: F. Xavier López-Labrador, Svetlana V. Trushakova, Anna Sominina, María Lourdes Guerrero and Joan Puig-Barberà
Viruses 2022, 14(6), 1318; https://doi.org/10.3390/v14061318
Received: 29 March 2022 / Revised: 13 May 2022 / Accepted: 3 June 2022 / Published: 16 June 2022
(This article belongs to the Topic Acute Respiratory Viruses Molecular Epidemiology)
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. View Full-Text
Keywords: Seychelles; SARS-CoV-2; variants of concern Seychelles; SARS-CoV-2; variants of concern
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MDPI and ACS Style

Morobe, J.M.; Pool, B.; Marie, L.; Didon, D.; Lambisia, A.W.; Makori, T.; Mohammed, K.S.; de Laurent, Z.R.; Ndwiga, L.; Mburu, M.W.; Moraa, E.; Murunga, N.; Musyoki, J.; Mwacharo, J.; Nyamako, L.; Riako, D.; Ephnatus, P.; Gambo, F.; Naimani, J.; Namulondo, J.; Tembo, S.Z.; Ogendi, E.; Balde, T.; Dratibi, F.A.; Yahaya, A.A.; Gumede, N.; Achilla, R.A.; Borus, P.K.; Wanjohi, D.W.; Tessema, S.K.; Mwangangi, J.; Bejon, P.; Nokes, D.J.; Ochola-Oyier, L.I.; Githinji, G.; Biscornet, L.; Agoti, C.N. Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021. Viruses 2022, 14, 1318. https://doi.org/10.3390/v14061318

AMA Style

Morobe JM, Pool B, Marie L, Didon D, Lambisia AW, Makori T, Mohammed KS, de Laurent ZR, Ndwiga L, Mburu MW, Moraa E, Murunga N, Musyoki J, Mwacharo J, Nyamako L, Riako D, Ephnatus P, Gambo F, Naimani J, Namulondo J, Tembo SZ, Ogendi E, Balde T, Dratibi FA, Yahaya AA, Gumede N, Achilla RA, Borus PK, Wanjohi DW, Tessema SK, Mwangangi J, Bejon P, Nokes DJ, Ochola-Oyier LI, Githinji G, Biscornet L, Agoti CN. Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021. Viruses. 2022; 14(6):1318. https://doi.org/10.3390/v14061318

Chicago/Turabian Style

Morobe, John M., Brigitte Pool, Lina Marie, Dwayne Didon, Arnold W. Lambisia, Timothy Makori, Khadija S. 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 Z. Tembo, Edwin Ogendi, Thierno Balde, Fred A. Dratibi, Ali A. Yahaya, Nicksy Gumede, Rachel A. Achilla, Peter K. Borus, Dorcas W. Wanjohi, Sofonias K. Tessema, Joseph Mwangangi, Philip Bejon, David J. Nokes, Lynette I. Ochola-Oyier, George Githinji, Leon Biscornet, and Charles N. Agoti. 2022. "Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021" Viruses 14, no. 6: 1318. https://doi.org/10.3390/v14061318

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