Dynamics of SARS-CoV-2 lineages in French Guiana in 2020-2021: 4 epidemic waves with cross-influences from Europe and South America

Abstract

Since the first cases of SARS-CoV-2 infection in Wuhan in December 2019, this RNA virus gave rise to different viral lineages with different virological, epidemiological and immunological properties. Here we describe the dynamics of circulation of SARS-CoV-2 lineages in an Amazonian South American French overseas territory, French Guiana (FG). The data analyzed are based on the general epidemic course, and genomic surveillance data come from whole genome sequencing (WGS) as well as typing PCRs. From March 2020 to October 2021, four COVID-19 epidemic waves were observed in FG with an evolution of viral lineages influenced by virus introductions from continental France and above all by land-based introductions from neighbouring countries. The third epidemic wave from March to June 2021 was driven by a predominant Gamma introduced from Brazil and a less frequent Alpha introduced from France. This coexistence was completely substituted by Delta that initiated the fourth epidemic wave.

Keywords: Dynamics of circulation; French Guiana; Genomic surveillance; SARS-CoV2 variants; Variant of concern.

Fig. 1

The first four epidemic waves of SARS-CoV-2 in French Guiana and coverage by genomic sequencing and typing PCRs. Epidemiological curve showing the progression of weekly COVID-19 numbers in French Guiana. Four epidemic waves have been registered, with the first peaking in June/July 2020. The grey bars show the overall sampling of SARS-CoV2 genomes, while the black curve depicts the number of samples (among the positives) tested for variant key mutations by typing PCRs. The sudden fall of typing PCR numbers in week 21–22 is due to the time laboratories needed to switch from the old type of typing PCR kits to the new one.

Fig. 2

Variant frequencies in French Guiana from December 2020 until August 2021. (a) Results from typing PCRs with 2 periods distinguished by the mutations screened: Period 1- From January to May 2021, detection of a set of key mutations as defined by French national guidelines allowed to distinguish non-VOC (in grey) from VOC variants: Alpha suspicion in blue, and Gamma suspicion in pink. Due to the absence of significant Beta circulation (sequencing results), all N501Y plus E484K positives were considered Gamma suspicions. Period 2 - From June to September 2021, the typing PCR kits detected E484K and L452R key mutations, allowing to distinguish the four VOC (the only variants still circulating during this period as confirmed by the sequencing results): Alpha suspicion (absence of E484K and L452R) in blue, Gamma suspicion (presence of E484K) in pink and Delta suspicion (presence of L452R) in green. (b) WGS data. An average of 109 samples were sequenced each month, except for December 2020 with only 3 samples. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

The introduction of Alpha, Gamma and Delta variants. (a) 7 days incidence showing the 6 epidemic waves of SARS-CoV-2 circulation in FG between March 2020 and August 2022. Box B and D are the periods of time that is zoomed upon in Figs. 3 (b) and (d) (b) The introduction and dissemination of VOC Alpha and VOC Gamma. The underlying data are an addition of typing PCR and genome sequencing data of week 2021–03 until 2021–16. The dashed line box is the same time period as the box labelled B in graph (a). (c) Epidemiological investigation of the first Alpha and Gamma cases. Cases that confirmed a travel history in the last 14 days were distinguished from cases with presumably autochthonous infection. (d) The introduction and dissemination of Delta variant from week 2021–27 on, as shown by typing PCR data.

Fig. 4

Time-calibrated phylogeny of SARS-CoV-2 in French Guiana. The phylogeny was inferred using 912 complete or near complete sequences from French Guiana, with 5099 international genomes for contextualization. The tips corresponding to sequences from French Guiana are highlighted, and colored according to their clade. All SARS-CoV-2 sequences available on the GISAID EpiCov database as if January 30th, 2021 were retrieved, and included in a phylogenetic analysis using the Nextstrain pipeline (https://github.com/nextstrain/ncov). Within Nextstrain, a random subsampling approach capping a maximum number of sequences was used. The acknowledgement of contributing and originating laboratories for all sequences used in this analysis is provided in Supplemental Table 2.