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

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.

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

“…The circulation period of VOCs Alpha, Delta, and Omicron was similar to that of west Africa. 86 – 88 The same VOC circulation pattern has been found in central Africa. 68 , 69 , 89 …”

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

“…Scaling up sequencing in Africa has provided a wealth of information on how the pandemic unfolded on the continent. The epidemic has largely been spatially heterogeneous across Africa, but most countries have experienced multiple waves of infection (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29), with substantial local and regional diversity in the first wave and to a lesser extent in the second wave, followed by successive sweeps of the continent with Delta and Omicron (Fig. 1A).…”

“…23 Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan. 24 General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan. 25 41 Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.…”

“…23 Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan. 24 General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan. 25 MRC Unit The Gambia at LSHTM, Fajara, Gambia.…”

Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018-2021

“…16.1 was then used to calculate the mean read depth and breadth of coverage of the sequences using the BAM files generated from the RABV ARTIC pipeline [18]. Sequences for phylogenetic analysis were selected based on the following criteria: whole genome coverage (where depth at each position >20X) is greater than 70% [19], and the breadth of coverage (where depth at each position >1X) obtained via SAMtools is greater than 90% [11]. Bammix version 1.0.0 was used to search for nucleotide mixtures among samples suspected to be contaminated during the sequencing run using filters on base quality (q>7), mapping quality (m>40), depth of coverage (>20X), base proportion (>25%), and read position (30-11620bp) [20].…”