Genomic insights into early SARS-CoV-2 strains isolated in Reunion Island

Abstract

The relative isolation of many island communities provides some protection from the COVID-19 pandemic, as imported cases can be limited and traced effectively. Until recently, this was true for the population of the French overseas department, Reunion Island, where only limited numbers of autochthonous cases were observed prior to August 2020. Since the report of the first case of COVID-19, contact tracing has been carried out for each new case identified in Reunion Island to identify transmission and clusters. To contribute to the public health response and understand the diffusion of SARS-Cov-2 strains in Reunion Island, we established in-house genome sequencing capability in Reunion using Oxford nanopore technology (MinION) as an inexpensive option for genomic typing of SARS-CoV-2 lineages on the island, and cross-validated typing results between viral isolation methods and different sequencing technologies. The results of our work during the early phase of the epidemics are presented herein.Article Summary LineThe COVID-19 pandemic has had an unprecedented impact on the global community. Here we provide epidemiological and genomic details of the early stages of the pandemic on Reunion Island.

Differentiating COVID-19 and dengue from other febrile illnesses in co-epidemics: Development and internal validation of COVIDENGUE scores

“…On Reunion Island, the first wave of SARS-CoV-2 circulation ended in June 2020 as a result of the influence of the first national lockdown. The second wave began in August 2020 during the winter season of the region and was concomitant to the spread of the D614G mutation in Europe [ 7 ]. Since this period, SARS-CoV-2 transmission has been mainly autochthonous and successively maintained through the circulation of both South African (B.1.351/501Y.V2) and the Indian (B.1.617/21APR-02) variants of concerns (VOCs).…”

“…On Reunion Island, a French overseas territory located in the southwestern Indian ocean region known to have host one of the largest chikungunya outbreaks [ 5 ], dengue virus (DENV) is endemic with annual epidemics occurring since 2015 [ 6 ]. Moreover COVID-19, which emerged in March 2020, has established an autochthonous transmission since August 2020 [ 7 ].…”

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

“…These RBD mutations coupled with four amino acid substitutions (i.e., A67V, T95I, and L212) and three deletion (67-70, 142-144 and 211) and an insertion (EPE at position 214) in the N-terminal domain (NTD) are linked to reduced sensitivity of Omicron to reduced sensitivity to convalescent and post-vaccination sera 21,22 Our findings are consistent with findings from Island countries such Comoros, Reunion Islands and New Zealand, where this countries were able to contain the first pandemic wave starting in March 2020, due COVID-19 strict countermeasures such as ban on international arrivals, which may have led to limited viral introductions into the islands, or perhaps viral introductions during the early phase of the pandemic did not results to community transmission due to government countermeasure on COVID-19 such as countrywide lockdown or self-isolation of the entire population 24,25 . Surge of COVID-19 cases in Islandic populations appears to be majorly driven by introductions of VOCs.…”

“…Our findings are consistent with findings from Island countries such Comoros, Reunion Islands and New Zealand, where this countries were able to contain the first pandemic wave starting in March 2020, due COVID-19 strict countermeasures such as ban on international arrivals, which may have led to limited viral introductions into the islands, or perhaps viral introductions during the early phase of the pandemic did not results to community transmission due to government countermeasure on COVID-19 such as countrywide lockdown or self-isolation of the entire population 24,25 . Surge of COVID-19 cases in Islandic populations appears to be majorly driven by introductions of VOCs.…”

Differentiating COVID-19 and dengue from other febrile illnesses in co-epidemics: Development and internal validation of COVIDENGUE scores

“…On Reunion Island, the first wave of SARS-CoV-2 circulation ended in June 2020 as a result of the influence of the first national lockdown. The second wave began in August 2020 during the winter season of the region and was concomitant to the spread of the D614G mutation in Europe [7]. Since this period, SARS-CoV-2 transmission has been mainly autochthonous and successively maintained through the 16 circulation of both South African (B.1.351/501Y.V2) and the Indian (B.1.617/21APR-02) variants of concerns (VOCs).…”