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. 2022 Dec:106:105381.
doi: 10.1016/j.meegid.2022.105381. Epub 2022 Oct 26.

Genomic evolution of SARS-CoV-2 in Reunion Island

David A Wilkinson  1 , Alizé Mercier  2 , Magali Turpin  3 , Marie-Alice Simbi  4 , Jonathan Turpin  4 , Camille Lebarbenchon  3 , Maya Cesari  5 , Marie-Christine Jaffar-Bandjee  6 , Laurence Josset  7 , Luce Yemadje-Menudier  2 , Bruno Lina  7 , Patrick Mavingui  8
Affiliations

Genomic evolution of SARS-CoV-2 in Reunion Island

David A Wilkinson et al. Infect Genet Evol. 2022 Dec.

Abstract

Island communities are interesting study sites for microbial evolution during epidemics, as their insular nature reduces the complexity of the population's connectivity. This was particularly true on Reunion Island during the first half of 2021, when international travel was restricted in order to mitigate the risk for SARS-CoV-2 introductions. Concurrently, the SARS-CoV-2 Beta variant became dominant and started to circulate at high levels for several months before being completely replaced by the Delta variant as of October 2021. Here, we explore some of the particularities of SARS-CoV-2 genomic evolution within the insular context of Reunion Island. We show that island isolation allowed the amplification and expansion of unique genetic lineages that remained uncommon across the globe. Islands are therefore potential hotspots for the emergence of new genetic variants, meaning that they will play a key role in the continued evolution and propagation of COVID-19 as the pandemic persists.

Keywords: Evolution; Genomics; Reunion Island; SARS-CoV-2.

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Conflict of interest statement

Declaration of Competing Interest The authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Summary of the epidemiological and genomic classification data from Reunion 2021–2022. Panels display (from top to bottom): 1) Weekly numbers of reported cases, and the ratio between imported and autochthonous cases (black line), 2) Weekly proportions of genomes attributed to different variants of concern, 3–7) Weekly numbers of sequenced genomes attributed to different PANGO lineages, data are displayed separately for each major variant of concern.
Fig. 3
Fig. 3
Phylogenetic analyses of SAR-CoV-2 genomes from Reunion 2021–2022. a) Timetree phylogeny, leaves are coloured by variant of concern, shaded regions represent 6-month intervals.
Fig. 2
Fig. 2
Comparison of lineage B.1.622 to its closest genetic relatives in GISAID.
Fig. 4
Fig. 4
Dynamics of VOCs in Reunion 2021–2022. TOP) Proportion of all sequenced isolates belonging to each VOC. BOTTOM) Total measured genetic diversity of main lineages over time. Boxplots show the distribution in the number of mutations between isolates belonging to the same VOC sequenced on the same week. Throughout, week number is measured relative to the start of each “wave” of variant circulation, as follows: Beta started in week one of 2021, Delta started in week 27 of 2021 and Omicron started in week 48 of 2021, the first observation of Alpha was in week 3 of 2021.
Fig. 5
Fig. 5
Substitution rate estimates for SARS-CoV-2 genomes from Reunion 2021–2022. a) Overall linear correlation between root-to-tip distance in phylogenetic analyses and collection date for all SARS-CoV-2 genomes. b) Individual correlations between root-to-tip distance and collection date for all variants of concern. c) Average substitutions per site per year calculated for each major variant of concern, error bars represent the 95% confidence intervals of the linear regression for each correlation.
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