Detection of SARS-CoV-2 variant 501Y.V2 in Comoros Islands in January 2021.

Charles N Agoti,Ali Ahmed Yahaya,Benjamin Tsofa,Arnold W Lambisia,Dratibi Fred Athanasius,Zaydah R De Laurent,Edward Otieno,George Githinji,Abdoulaye Diarra,Maureen W Mburu,Peter Borus,Philip Bejon,Khadija Said Mohammed ,John Mwita Morobe ,Edidah M Ong’Era,Hamza Abdou Yahaya ,Nicksy Gumede-Moeletsi ,D James Nokes,Isabella Lynette Ocholla

doi:10.12688/wellcomeopenres.16889.1

Abstract

Background. Genomic data is key in understanding the spread and evolution of SARS-CoV-2 pandemic and informing the design and evaluation of interventions. However, SARS-CoV-2 genomic data remains scarce across Africa, with no reports yet from the Indian Ocean islands. Methods. We genome sequenced six SARS-CoV-2 positive samples from the first major infection wave in the Union of Comoros in January 2021 and undertook detailed phylogenetic analysis. Results. All the recovered six genomes classified within the 501Y.V2 variant of concern (also known as lineage B.1.351) and appeared to be from 2 sub-clusters with the most recent common ancestor dated 30 th Oct-2020 (95% Credibility Interval: 06 th Sep-2020 to 10 th Dec-2020). Comparison of the Comoros genomes with those of 501Y.V2 variant of concern from other countries deposited into the GISAID database revealed their close association with viruses identified in France and Mayotte (part of the Comoros archipelago and a France, Overseas Department). Conclusions. The recovered genomes, albeit few, confirmed local transmission following probably multiple introductions of the SARS-CoV-2 501Y.V2 variant of concern during the Comoros's first major COVID-19 wave. These findings demonstrate the importance of genomic surveillance and have implications for ongoing control strategies on the islands.

Highlights

Comoros, an island country in the Indian ocean, detected its first case of SARS-CoV-2 on 30th April 2020, it experienced its first major SARS-CoV-2 outbreak in January 2021 i.e., 10 months later[1]
All the recovered six genomes classified within the 501Y.V2 variant of concern and appeared to be from 2 sub-clusters with the most recent common ancestor dated 30th Oct-2020 (95% Credibility Interval: 06th Sep-2020 to 10th Dec-2020)
Comparison of the Comoros genomes with those of 501Y.V2 variant of concern from other countries deposited into the GISAID database revealed their close association with viruses identified in France and Mayotte

Summary

Results

We assembled >80% of the SARS-CoV-2 genome from each of the six sequenced samples (Table 1). ΠComplete SARS-CoV-2 genome is 29,903 nucleotides long (Wuhan 2019 reference, accession number: NC_ 045512.2). #Experienced missing data/demographic details in the submitted forms and were not sequenced. The genomes possessed six of the eight Beta variant defining amino acid changes in the S protein (i.e., L18F, D80A, D215G, K417N, D614G, and A701V) plus a known three amino acid deletion at positions 243–245. Two additional defining amino acid changes (E484K and N501K) which were unconfirmed fell within a region that was not sequenced due to PCR amplicon drop-off. Our findings and confirmation of the presence of the SARS-CoV-2 Beta variant in Comoros samples was conveyed to Union of Comoros authorities on the 22nd January via the WHO-AFRO office to inform public health actions

Conclusions

Introduction

Methods

Discussion

Worldmeter