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.

Keywords: SARS-CoV-2; Seychelles; variants of concern.

Figure 1

(A) Seychelles government intervention levels as measured by the Oxford stringency index [15]. (B) An epidemic curve for Seychelles derived from the daily positive case numbers obtained from https://ourworldindata.org/coronavirus/country/seychelles (accessed on 5 May 2022). (C) Percentage of the population administered with vaccine; data obtained from https://ourworldindata.org/coronavirus/country/seychelles (accessed on 5 May 2022). (D) Monthly temporal pattern of SARS-CoV-2 lineages and variants in Seychelles among the 1056 samples sequenced from COVID-19 positive cases from the Seychelles (25 June 2020, to 31 December 2021). (E) Monthly temporal distribution of Delta VOC lineages among samples sequenced from COVID-19 positive cases from the Seychelles (25 June 2020, to 31 December 2021). (F) Monthly temporal distribution of Omicron VOC lineages among samples sequenced from COVID-19 positive cases from the Seychelles (25 June 2020, to 31 December 2021).

Figure 2

SARS-CoV-2 Pango lineages in the sequenced 1056 Seychelles samples and timing of detections (circle size scaled by number of daily detections).

Figure 3

Genetic distance-resolved lineage-specific phylogenetic trees for Omicron, Alpha, Beta, Delta VOC, and Non-VOC. Seychelles genomes are indicated with colored tip labels. (A) Phylogeny of Non-VOC that combined 14 Seychelles sequences and 875 global sequences. (B) Phylogeny of Alpha VOC that combined 5 Seychelles sequences and 246 global sequences. (C) Phylogeny of Beta VOC that combined 29 Seychelles sequences and 187 global sequences. (D) Phylogeny of Delta VOC that combined 863 Seychelles sequences and 2676 global sequences. (E) Phylogeny of Omicron VOC that combined 145 Seychelles sequences and 1195 global sequences.

Figure 4

(A) Time-resolved global phylogeny that combined 1056 Seychelles sequences (coloured tip labels) and 5179 global reference sequences. (B) The number of viral imports and exports into and out of Seychelles. (C) Cumulative number of viral imports and export over time into Seychelles.