Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

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.

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.

Background: The emergence of the Omicron variant of concern in late 2021 led to a resurgence of SARS-CoV-2 infections globally. By September 2022, Seychelles had experienced two major surges of SARS-CoV-2 infections driven by the Omicron variant. Here, we examine the genomic epidemiology of Omicron in the Seychelles between November 2021 and September 2022. Methods: We analysed 618 SARS-CoV-2 Omicron genomes identified in the Seychelles between November 2021 and September 2022 to infer virus introductions and local transmission patterns using phylogenetics and the ancestral state reconstruction approach. We then evaluated the impact of government coronavirus 2019 (COVID-19) countermeasures on the estimated number of viral introductions during the study period. Results: The genomes classified into 43 distinct Pango lineages. The first surge in Omicron cases (beginning November 2021 and peaking in January 2022) was predominated by the BA.1.1 lineage (59%) co-circulating with 11 other Omicron lineages. In the second surge (between April and June 2022), four lineages (BA.2, BA.2.10, BA.2.65 and BA.2.9) co-circulated and these were swiftly replaced by BA.5 subvariants in July 2022, which remained predominant through to September 2022. In the latter period, sporadic detections of BA.5 subvariants BQ.1, BE and BF were observed. We estimated 109 independent Omicron importations into Seychelles over the 11-month period, most of which occurred between December 2021 and March 2022 when strict government restrictions (SI>50%) were still in force. The districts Anse Royale, and Baie St. Anne Praslin appeared to be the major dispersal points fuelling local transmission. Conclusions: Our results suggest that the waves of Omicron infections in the Seychelles were driven by multiple lineages and multiple virus introductions. The introductions were followed by substantial local spread and successive lineage displacement that mirrored the global patterns.