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© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

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.

Details

Title
Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021
Author
John Mwita Morobe 1   VIAFID ORCID Logo  ; Pool, Brigitte 2 ; Lina, Marie 2 ; Didon, Dwayne 2 ; Lambisia, Arnold W 1 ; Makori, Timothy 1 ; Khadija Said Mohammed 1   VIAFID ORCID Logo  ; de Laurent, Zaydah R 1 ; Ndwiga, Leonard 1 ; Mburu, Maureen W 1 ; Moraa, Edidah 1 ; Nickson Murunga 1 ; Musyoki, Jennifer 1 ; Mwacharo, Jedida 1 ; Nyamako, Lydia 1 ; Riako, Debra 1 ; Ephnatus, Pariken 1 ; Gambo, Faith 1 ; Naimani, Josephine 1 ; Namulondo, Joyce 3 ; Susan Zimba Tembo 4 ; Ogendi, Edwin 4 ; Balde, Thierno 5 ; Dratibi, Fred Athanasius 5 ; Ali Ahmed Yahaya 5 ; Gumede, Nicksy 5 ; Achilla, Rachel A 5 ; Borus, Peter K 6 ; Wanjohi, Dorcas W 7 ; Tessema, Sofonias K 7 ; Mwangangi, Joseph 1 ; Bejon, Philip 1 ; Nokes, David J 8   VIAFID ORCID Logo  ; Ochola-Oyier, Lynette Isabella 1   VIAFID ORCID Logo  ; Githinji, George 9   VIAFID ORCID Logo  ; Biscornet, Leon 2 ; Agoti, Charles N 10   VIAFID ORCID Logo 

 Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; [email protected] (A.W.L.); [email protected] (T.M.); [email protected] (K.S.M.); [email protected] (Z.R.d.L.); [email protected] (L.N.); [email protected] (M.W.M.); [email protected] (E.M.); [email protected] (N.M.); [email protected] (J.M.); [email protected] (J.M.); [email protected] (L.N.); [email protected] (D.R.); [email protected] (P.E.); [email protected] (F.G.); [email protected] (J.N.); [email protected] (J.M.); [email protected] (P.B.); [email protected] (D.J.N.); [email protected] (L.I.O.-O.); [email protected] (G.G.); [email protected] (C.N.A.) 
 Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Victoria P.O. Box 52, Seychelles; [email protected] (B.P.); [email protected] (L.M.); [email protected] (D.D.); [email protected] (L.B.) 
 World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles; [email protected] (J.N.); [email protected] (S.Z.T.); [email protected] (E.O.); Department of Arbovirology, Emerging and Re-emerging Infectious Diseases—Uganda Virus Research Institution (UVRI), Entebbe P.O. Box 49, Uganda 
 World Health Organization-Seychelles Country Office, Victoria P.O. Box 1217, Seychelles; [email protected] (J.N.); [email protected] (S.Z.T.); [email protected] (E.O.) 
 World Health Organization Regional Center for Africa, Brazzaville P.O. Box 06, Congo; [email protected] (T.B.); [email protected] (F.A.D.); [email protected] (A.A.Y.); [email protected] (N.G.); [email protected] (R.A.A.) 
 World Health Organization-Kenya Country Office, Gigiri, Nairobi P.O. Box 45335, Kenya; [email protected] 
 Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa P.O. Box 3243, Ethiopia; [email protected] (D.W.W.); [email protected] (S.K.T.) 
 Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; [email protected] (A.W.L.); [email protected] (T.M.); [email protected] (K.S.M.); [email protected] (Z.R.d.L.); [email protected] (L.N.); [email protected] (M.W.M.); [email protected] (E.M.); [email protected] (N.M.); [email protected] (J.M.); [email protected] (J.M.); [email protected] (L.N.); [email protected] (D.R.); [email protected] (P.E.); [email protected] (F.G.); [email protected] (J.N.); [email protected] (J.M.); [email protected] (P.B.); [email protected] (D.J.N.); [email protected] (L.I.O.-O.); [email protected] (G.G.); [email protected] (C.N.A.); School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry CV4 7AL, UK 
 Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; [email protected] (A.W.L.); [email protected] (T.M.); [email protected] (K.S.M.); [email protected] (Z.R.d.L.); [email protected] (L.N.); [email protected] (M.W.M.); [email protected] (E.M.); [email protected] (N.M.); [email protected] (J.M.); [email protected] (J.M.); [email protected] (L.N.); [email protected] (D.R.); [email protected] (P.E.); [email protected] (F.G.); [email protected] (J.N.); [email protected] (J.M.); [email protected] (P.B.); [email protected] (D.J.N.); [email protected] (L.I.O.-O.); [email protected] (G.G.); [email protected] (C.N.A.); Department of Biochemistry and Biotechnology, Pwani University, Kilifi P.O. Box 195-80108, Kenya 
10  Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi P.O. Box 230-80108, Kenya; [email protected] (A.W.L.); [email protected] (T.M.); [email protected] (K.S.M.); [email protected] (Z.R.d.L.); [email protected] (L.N.); [email protected] (M.W.M.); [email protected] (E.M.); [email protected] (N.M.); [email protected] (J.M.); [email protected] (J.M.); [email protected] (L.N.); [email protected] (D.R.); [email protected] (P.E.); [email protected] (F.G.); [email protected] (J.N.); [email protected] (J.M.); [email protected] (P.B.); [email protected] (D.J.N.); [email protected] (L.I.O.-O.); [email protected] (G.G.); [email protected] (C.N.A.); Department of Public Health, Pwani University, Kilifi P.O. Box 195-80108, Kenya 
First page
1318
Publication year
2022
Publication date
2022
Publisher
MDPI AG
e-ISSN
19994915
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2679799340
Copyright
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.