key: cord-1037725-3hi3mmjj
authors: Agoti, C. N.; Githinji, G.; Mohammed, K. S.; Lambisia, A. W.; de Laurent, Z. R.; Mburu, M. W.; Ong'era, E. M.; Morobe, J. M.; Otieno, E.; Yahaya, H. A.; Abdallah, K. S.; Diarra, A.; Yahaya, A. A.; Athanasius, D. F.; Gumede-Moeletsi, N.; Tsofa, B.; Borus, P.; Bejon, P.; Nokes, J. D.; Ocholla, I. L.
title: Detection of SARS-CoV-2 variant 501Y.V2 in Comoros Islands in January 2021
date: 2021-04-13
journal: nan
DOI: 10.1101/2021.04.08.21254321
sha: c48ec444e8abf9a5f4c844a176f534c56c41928f
doc_id: 1037725
cord_uid: 3hi3mmjj

Phylogenetic analysis of six SARS-CoV-2 genomes collected from the Comoros islands confirmed local circulation of the 501Y.V2 variant of concern during the countrys first major SARS-CoV-2 wave in January 2021. These findings demonstrate the importance of SARS-CoV-2 genomic surveillance and have implications for ongoing COVID-19 control strategies on the islands.

Towards the end of 2020, in widely different geographical locations globally, three SARS-CoV-51 2 variants of concern (501Y.V1, 501Y.V2 and 501Y.V3) emerged that appeared to be 52 considerably more transmissible and with potential to facilitate immune escape or cause more 53 severe disease than the prior SARS-CoV-2 variants (2-4). The three variants possessed several 54 defining amino acid changes, most of them occurring within the spike (S) protein (5) . The S 55 protein contains the domain that binds the virus to the human host cell receptor and is a key 56 target for several vaccines (6). 57

The study 59

To investigate if the variants of concern had a role in the rising number of SARS-CoV-2 cases in 60 the Comoros in January 2021, 11 positive nasopharyngeal/oropharyngeal swab samples were 61 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted April 13, 2021. ; https://doi.org/10.1101/2021.04.08.21254321 doi: medRxiv preprint 3 sent to KEMRI-Wellcome Trust Programme (KWTRP) in Kilifi, Kenya, for genome analysis. 62 KWTRP is one of the 12 designated WHO-AFRO /Africa-CDC specialized and regional 63 reference laboratories for SARS-CoV-2 sequencing in Africa (7). The samples had been 64 collected between 5 th and 11 th January 2021 from two islands (Ngazidja and Mohéli), Table. On Ethical statement: The genomes generated were part of a regional collaborative COVID-19 116 public health rapid response. This manuscript therefore provides context on the genome data 117 already available on GISAID. The whole genome sequencing study protocol was reviewed and 118 approved by the Scientific and Ethics Review Committee (SERU) that sits at the Kenya Medical 119

Research Institute (KEMRI) headquarters in Nairobi (SERU # 4035). 120 121 Acknowledgements: We thank the WHO-AFRO and the WHO Kenya and Comoros country 122 offices for facilitating sharing of the positive samples that were sequenced; Further, we thank all 123 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 13, 2021. 

Countries / Comoros / Coronaviris. Coronavirus

Increased mortality in 149 community-tested cases of SARS-CoV-2 lineage B.1.1.7

SARS-CoV-2 variant of concern with mutations in spike glycoprotein

Genomics and 153 epidemiology of a novel SARS-CoV-2 lineage in Manaus

A Guide to Emerging SARS-CoV-2 Variants. The scientist

Structural genetics of circulating variants affecting Likelihood tree of the clade containing the newly sequenced Comoros genomes. c. Root-to-tip 182 divergence among the analysed 81 501Y

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 13, 2021. 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 13, 2021. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted April 13, 2021. ; https://doi.org/10.1101/2021.04.08.21254321 doi: medRxiv preprint