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

被引：4

作者：

Morobe, John Mwita ^{[1
]}

Pool, Brigitte ^{[2
]}

Marie, Lina ^{[2
]}

Didon, Dwayne ^{[2
]}

Lambisia, Arnold W. ^{[1
]}

Makori, Timothy ^{[1
]}

Mohammed, Khadija Said ^{[1
]}

de Laurent, Zaydah R. ^{[1
]}

Ndwiga, Leonard ^{[1
]}

Mburu, Maureen W. ^{[1
]}

Moraa, Edidah ^{[1
]}

Murunga, Nickson ^{[1
]}

Musyoki, Jennifer ^{[1
]}

Mwacharo, Jedida ^{[1
]}

Nyamako, Lydia ^{[1
]}

Riako, Debra ^{[1
]}

Ephnatus, Pariken ^{[1
]}

Gambo, Faith ^{[1
]}

Naimani, Josephine ^{[1
,4
]}

Namulondo, Joyce ^{[3
]}

Tembo, Susan Zimba ^{[3
]}

Ogendi, Edwin ^{[3
]}

Balde, Thierno ^{[5
]}

Dratibi, Fred Athanasius ^{[5
]}

Yahaya, Ali Ahmed ^{[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. ^{[1
,8
,9
]}

Ochola-Oyier, Lynette Isabella ^{[1
]}

Githinji, George ^{[1
,10
]}

Biscornet, Leon ^{[2
]}

Agoti, Charles N. ^{[1
,11
]}

机构：

[1] Kenya Med Res Inst Wellcome Trust Res Programme K, POB 230-80108, Kilifi, Kenya

[2] Minist Hlth, Publ Hlth Author, Seychelles Publ Hlth Lab, POB 52, Victoria, Seychelles

[3] World Hlth Org Seychelles Country Off, POB 1217, Victoria, Seychelles

[4] Uganda Virus Res Inst UVRI, Dept Arbovirol Emerging & Reemerging Infect Dis, POB 49, Entebbe, Uganda

[5] World Hlth Org Reg Ctr Africa, POB 06, Brazzaville, Rep Congo

[6] World Hlth Org Kenya Country Off, POB 45335, Nairobi, Kenya

[7] Africa Ctr Dis Control & Prevent Africa CDC, POB 3243, Addis Ababa, Ethiopia

[8] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England

[9] Univ Warwick, Zeeman Inst Syst Biol & Infect Dis Epidemiol Res, Coventry CV4 7AL, W Midlands, England

[10] Pwani Univ, Dept Biochem & Biotechnol, POB 195-80108, Kilifi, Kenya

[11] Pwani Univ, Dept Publ Hlth, POB 195-80108, Kilifi, Kenya

来源：

VIRUSES-BASEL | 2022年 / 14卷 / 06期

基金：

美国国家卫生研究院; 英国惠康基金;

关键词：

Seychelles; SARS-CoV-2; variants of concern;

D O I：

10.3390/v14061318

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

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.

引用

页数：15

共 29 条

[1] Agoti C. N., 2021, medRxiv, DOI [10.1101/2021.07.01.21259583, DOI 10.1101/2021.07.01.21259583]
[2] [Anonymous], 2022, SARS COV 2 VAR CLASS
[3] Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization
Cele, Sandile
Jackson, Laurelle
Khoury, David S.
Khan, Khadija
Moyo-Gwete, Thandeka
Tegally, Houriiyah
San, James Emmanuel
Cromer, Deborah
Scheepers, Cathrine
Amoako, Daniel G.
Karim, Farina
Bernstein, Mallory
Lustig, Gila
Archary, Derseree
Smith, Muneerah
Ganga, Yashica
Jule, Zesuliwe
Reedoy, Kajal
Hwa, Shi-Hsia
Giandhari, Jennifer
Blackburn, Jonathan M.
Gosnell, Bernadett, I
Karim, Salim S. Abdool
Hanekom, Willem
von Gottberg, Anne
Bhiman, Jinal N.
Lessells, Richard J.
Moosa, Mahomed-Yunus S.
Davenport, Miles P.
de Oliveira, Tulio
Moore, Penny L.
Sigal, Alex
[J]. NATURE, 2022, 602 (7898) : 654 - +
[4] Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
Geoghegan, Jemma L.
Ren, Xiaoyun
Storey, Matthew
Hadfield, James
Jelley, Lauren
Jefferies, Sarah
Sherwood, Jill
Paine, Shevaun
Huang, Sue
Douglas, Jordan
Mendes, Fabio K.
Sporle, Andrew
Baker, Michael G.
Murdoch, David R.
French, Nigel
Simpson, Colin R.
Welch, David
Drummond, Alexei J.
Holmes, Edward C.
Duchene, Sebastian
de Ligt, Joep
[J]. NATURE COMMUNICATIONS, 2020, 11 (01)
[5] Gong S.Y., 2021, BIORXIV, DOI [10.1016/j.virol.2021.09.001, DOI 10.1016/J.VIROL.2021.09.001]
[6] Nextstrain: real-time tracking of pathogen evolution
Hadfield, James
Megill, Colin
Bell, Sidney M.
Huddleston, John
Potter, Barney
Callender, Charlton
Sagulenko, Pavel
Bedford, Trevor
Neher, Richard A.
[J]. BIOINFORMATICS, 2018, 34 (23) : 4121 - 4123
[7] Iketani S., 2022, BIORXIV, DOI [10.1038/s41586-022-04594-4, DOI 10.1038/S41586-022-04594-4]
[8] Lee K, 2009, GLOB INST, P1
[9] Minimap2: pairwise alignment for nucleotide sequences
Li, Heng
[J]. BIOINFORMATICS, 2018, 34 (18) : 3094 - 3100
[10] Lyngse FP, PREPRINT, DOI [DOI 10.1101/2022.01.28.22270044, 10.1101/2022.01.28.22270044.]

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