key: cord-0973798-vxlcie2y
authors: Morobe, J. M.; Didon, D.; Pool, B.; Lambisia, A. W.; Makori, T.; Mohammed, K. S.; de Laurent, Z. R.; Ndwiga, L.; Mburu, M. W.; Moraa, E.; Murunga, N.; Musyoki, J.; Mwacharo, J.; Nyamako, L.; Ephnatus, P.; Riako, D.; Gambo, F.; Naimani, J.; Namulondo, J.; Dratibi, F. A.; Ahmed, Y. A.; Gumede, N.; Achilla, R. A.; Borus, P. K.; Wanjohi, D. W.; Tessema, S. K.; Mwangangi, J.; Bejon, P.; Nokes, J.; Ochola-Oyier, L. I.; Githinji, G.; Biscornet, L.; Agoti, C. N.
title: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021
date: 2022-03-21
journal: nan
DOI: 10.1101/2022.03.18.22272503
sha: ff6c059b55c71ab50babdc893a6743ec171e95bf
doc_id: 973798
cord_uid: vxlcie2y

By 31st December 2021, Seychelles, an archipelago of 115 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first SARS-CoV-2 cases in Seychelles were reported on 14th March 2020, but cases remained low until January 2021, when a surge of SARS-CoV-2 cases was observed on the islands. Here, we investigated the potential drivers of the surge by genomic analysis 1,056 SARS-CoV-2 positive samples collected in Seychelles between 14th March 2020 and 31st December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1,042 of which fell within four variants of concern i.e., Alpha, Beta, Delta and Omicron. Sporadic of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (Europe origin) 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 ancestral state reconstruction approach, we estimated at least 78 independent SARS-CoV-2 introduction events into Seychelles during the study period. 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 introduction of the more transmissible SARS-CoV-2 variants into the islands.

were constituted in an additional pool, named herein pool C. After the multiplex PCR, 143 an agarose gel electrophoresis step was included to exclude samples with no visible 144 bands from further processing. 145

For each sample, the PCR products of primer pools A, B and C were combined 147 to make a total of 23μl (all of pool A (10μl), pool B (10μl) and pool C(3µl)) and cleaned 148 . CC-BY 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 

Additional quality control, clade assignment and mutation profiles were 184 obtained using the NextClade tool v1.13.2 7 using a SARS-CoV-2 reference genome 185 (accession NC_045512). All consensus sequences with a genome coverage >70% 

The global ML tree topology was used to estimate the number of viral 211 transmission events between Seychelles and the rest of the world as described 212 previously 11 . TreeTime was used to transform the ML tree topology into a dated 213 phylogenetic tree. Outlier sequences (n=208) were identified by TreeTime and 214 excluded during this process. A mugration model was fitted using the time-scaled 215 phylogenetic tree, mapping the location status of the genomes from Seychelles at both 216 . CC-BY 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 

The rise of COVID-19 cases in 2021 was preceded by a period of relaxed 225 countermeasures to curb the spread of the virus (Figure1 A and B) . Of 1,298 SARS-226

CoV-2 positive samples received at KWTRP for genome sequencing, near complete 227 genomes (>70% genome coverage) were recovered from 1,056 samples, and these 228 were used in the subsequent lineage and phylogenetic analysis (Supplementary 229 Figure 2) . A summary of the demographic details for the samples successfully 230 sequenced and those that failed are provided in Table 1 . 231 232

The recovered 1,056 genomes classified into 32 distinct Pango lineages, 28 of 234 which occurred within VOC, VOI or VUM: Alpha VOC (n=1), Beta VOC (n=1), Delta 235 VOC (n=21) and Omicron VOC (n=3) and Kappa VOI (n=1) and B.1.640.2 VUM (n=1) 236 (Table 2) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 

Genetic distance -resolved phylogeny of the Seychelles genomes, including 259 global reference sequences (n=5,179) revealed that most of the Seychelles 260 sequences were interspersed as clusters (>2 sequences) or singletons across the 261 phylogenetic trees suggesting multiple viral introductions into Seychelles (Figure 3) . 262

In the VOC/non-VOC-specific phylogenies, Delta VOC (n=863) grouped into 14 263 clusters (>2 sequences) clusters and 12 singletons on the global phylogenetic tree 264 pointing to separate introductions of the Delta VOC into the country whereas Omicron 265 VOC (n=145) clustered into 10 clusters and 11 singletons (Figures 3D and E) . is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint America. (Figure 4B ). Of the 78 detected viral imports into Seychelles, 66 occurred 291 between January and December 2021 after the rise in COVID-19 cases was 292 experienced in the Seychelles (Figure 4C) . From the analysis, we also inferred 32 293 export events from Seychelles to the rest of the world, mainly Asia (n=10) Europe 294 (n=8) and Africa (n=6). is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 

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Time-resolved global phylogeny that combined 1,056 Seychelles sequences (coloured tip labels) and 5,179 global reference sequences. B The number of viral imports and 530 exports into and out of Seychelles. C Cumulative number of viral imports and export over time into Seychelles