# Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024

Raphaëlle Klitting, Géraldine Piorkowski, Dominique Rousset, André Cabié, Etienne Frumence, Alisé Lagrave, Anne Lavergne, Antoine Enfissi, George dos Santos, Laurence Fagour, et al.

► To cite this version:

Raphaëlle Klitting, Géraldine Piorkowski, Dominique Rousset, André Cabié, Etienne Frumence, et al.. Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024. Eurosurveillance, 2024, www.eurosurveillance.org, 29 (13), pp.2400123. 10.2807/1560-7917.es.2024.29.13.2400123. hal-04529583

HAL Id: hal-04529583

https://hal.science/hal-04529583

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# Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024

Raphaëlle Klitting, Géraldine Piorkowski, Dominique Rousset, André Cabié, Etienne Frumence, Alisé Lagrave, Anne Lavergne, Antoine Enfissi, George dos Santos, Laurence Fagour, et al.

► To cite this version:

Raphaëlle Klitting, Géraldine Piorkowski, Dominique Rousset, André Cabié, Etienne Frumence, et al.. Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024. Eurosurveillance, 2024, www.eurosurveillance.org, 29 (13), pp.2400123. 10.2807/1560-7917.es.2024.29.13.2400123. hal-04529583

HAL Id: hal-04529583

https://hal.science/hal-04529583v1

Submitted on 2 Apr 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
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RAPID COMMUNICATION

Molecular epidemiology identifies the expansion of the
DENV2 epidemic lineage from the French Caribbean
Islands to French Guiana and mainland France, 2023 to
2024

Raphaëlle Klitting¹,², Géraldine Piorkowski¹,², Dominique Rousset³, André Cabié⁴,⁵,⁶, Etienne Frumence⁷,⁸, Alisé Lagrave³, Anne Lavergne³, Antoine Enfissi³, George Dos Santos⁵,⁹, Laurence Fagour⁵,⁹, Raymond Césaire⁵,¹⁰, Marie-Christine Jaffar-Bandjee⁷,⁸, Nicolas Traversier⁷,⁸, Patrick Gérardin¹¹, Rayane Amaral², Lucie Fournier¹², Lucie Leon¹³, Frédérique Dorléans¹³, Muriel Vincent¹⁴, arbovirus genomics diagnostic laboratories working group¹⁵, Albin Fontaine²,¹⁶, Anna-Bella Failloux¹⁷, Nazli Ayhan¹,², Laura Pezzi¹,², Gilda Grard¹,², Guillaume André Durand¹,², Xavier de Lamballerie¹,²

1. National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France

2. Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France

3. Associated National Reference Center for Arboviruses, Virology unit, Institut Pasteur in French Guiana, Cayenne, French Guiana

4. Service de Maladies infectieuses et tropicales, CHU de Martinique, Fort-de-France, France

5. PCCEI, Université de Montpellier, INSERM, EFS, Montpellier, France

6. CIC Antilles Guyane, INSERM CIC1424, Fort-de-France, France

7. Associated National Reference Center for Arboviruses, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France

8. Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France

9. Laboratoire de virologie, CHU de Martinique, Fort-de-France, France

10. Pôle de biologie territoriale, CHU de Guadeloupe, Pointe-à-Pitre, France

11. CIC 1410, CHU Réunion, Saint-Pierre, France

12. Santé publique France, Saint-Maurice, France

13. Santé publique France, Cellule Antilles, Saint-Maurice, France

14. Santé publique France - La Réunion, Saint-Denis, La Réunion, France

15. The members of this group are listed under collaborators and at the end of the article

16. Institut de Recherche Biomédicale des Armées (IRBA), Unité de virologie, Marseille, France

17. Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France

Correspondence: Raphaëlle Klitting (raphaëlle.klitting@inserm.fr)

Collaborators: The collaborators are listed at the end of the article.

Citation style for this article:

Klitting Raphaëlle, Piorkowski Géraldine, Rousset Dominique, Cabié André, Frumence Etienne, Lagrave Alisé, Lavergne Anne, Enfissi Antoine, Dos Santos George, Fagour Laurence, Césaire Raymond, Jaffar-Bandjee Marie-Christine, Traversier Nicolas, Gérardin Patrick, Amaral Rayane, Fournier Lucie, Leon Lucie, Dorléans Frédérique, Vincent Muriel, arbovirus genomics diagnostic laboratories working group, Fontaine Albin, Failloux Anna-Bella, Ayhan Nazli, Pezzi Laura, Grard Gilda, Durand Guillaume André, de Lamballerie Xavier. Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024. Euro Surveill. 2024;29(13):pii=2400123. https://doi.org/10.2807/1560-7917.ES.2024.29.13.2400123

Article received on 28 Feb 2024 / Accepted on 27 Mar 2024 / Published on 28 Mar 2024

In 2023, dengue virus serotype 2 (DENV2) affected most French overseas territories. In the French Caribbean Islands, viral circulation continues with >30,000 suspected infections by March 2024. Genome sequence analysis reveals that the epidemic lineage in the French Caribbean islands has also become established in French Guiana but not Réunion. It has moreover seeded autochthonous circulation events in mainland France. To guide prevention of further inter-territorial spread and DENV introduction in non-endemic settings, continued molecular surveillance and mosquito control are essential.

In the region of the Americas, the year 2023 set an unwelcome record in terms of dengue virus (DENV) circulation, with more than 4.1million suspected infections distributed across 42 countries and territories [1]. Regarding the French Caribbean Islands, where dengue surveillance is conducted year-round, epidemics of

DENV serotype 2 (DENV2) were declared in Guadeloupe and Martinique simultaneously on 17 August 2023. Eight and 10 weeks later, the islands of Saint-Barthélemy and Saint-Martin respectively entered the epidemic phase for dengue, which was also caused by DENV2. Up to March 2024, over 30,000 suspected cases of DENV infection have been reported across all four islands [2]. In 2023, DENV2 was also active in other French overseas territories including French Guiana and the island of Réunion, both of which share strong ties with the French Caribbean Islands [3,4]. In this work, we provide evidence supporting that a single epidemic lineage circulating in Guadeloupe, Martinique, Saint-Barthélemy and Saint-Martin has become established in French Guiana but not in Réunion. Moreover, the epidemic strain appears to have caused autochthonous clusters of cases in mainland France.
# Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024

Raphaëlle Klitting¹,², Géraldine Piorkowski¹,², Dominique Rousset³, André Cabié⁴,⁵,⁶, Etienne Frumence⁷,⁸, Alisé Lagrave³, Anne Lavergne³, Antoine Enfissi³, George Dos Santos⁵,⁹, Laurence Fagour⁵,⁹, Raymond Césaire⁵,¹⁰, Marie-Christine Jaffar-Bandjee⁷,⁸, Nicolas Traversier⁷,⁸, Patrick Gérardin¹¹, Rayane Amaral², Lucie Fournier¹², Lucie Leon¹³, Frédérique Dorléans¹³, Muriel Vincent¹⁴, arbovirus genomics diagnostic laboratories working group¹⁵, Albin Fontaine²,¹⁶, Anna-Bella Failloux¹⁷, Nazli Ayhan¹,², Laura Pezzi¹,², Gilda Grard¹,², Guillaume André Durand¹,², Xavier de Lamballerie¹,²

1. National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France

2. Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France

3. Associated National Reference Center for Arboviruses, Virology unit, Institut Pasteur in French Guiana, Cayenne, French Guiana

4. Service de Maladies infectieuses et tropicales, CHU de Martinique, Fort-de-France, France

5. PCCEI, Université de Montpellier, INSERM, EFS, Montpellier, France

6. CIC Antilles Guyane, INSERM CIC1424, Fort-de-France, France

7. Associated National Reference Center for Arboviruses, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France

8. Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France

9. Laboratoire de virologie, CHU de Martinique, Fort-de-France, France

10. Pôle de biologie territoriale, CHU de Guadeloupe, Pointe-à-Pitre, France

11. CIC 1410, CHU Réunion, Saint-Pierre, France

12. Santé publique France, Saint-Maurice, France

13. Santé publique France, Cellule Antilles, Saint-Maurice, France

14. Santé publique France - La Réunion, Saint-Denis, La Réunion, France

15. The members of this group are listed under collaborators and at the end of the article

16. Institut de Recherche Biomédicale des Armées (IRBA), Unité de virologie, Marseille, France

17. Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France

Correspondence: Raphaëlle Klitting (raphaëlle.klitting@inserm.fr)

Collaborators: The collaborators are listed at the end of the article.

**Citation style for this article:**

Klitting Raphaëlle, Piorkowski Géraldine, Rousset Dominique, Cabié André, Frumence Etienne, Lagrave Alisé, Lavergne Anne, Enfissi Antoine, Dos Santos George, Fagour Laurence, Césaire Raymond, Jaffar-Bandjee Marie-Christine, Traversier Nicolas, Gérardin Patrick, Amaral Rayane, Fournier Lucie, Leon Lucie, Dorléans Frédérique, Vincent Muriel, arbovirus genomics diagnostic laboratories working group, Fontaine Albin, Failloux Anna-Bella, Ayhan Nazli, Pezzi Laura, Grard Gilda, Durand Guillaume André, de Lamballerie Xavier. Molecular epidemiology identifies the expansion of the DENV2 epidemic lineage from the French Caribbean Islands to French Guiana and mainland France, 2023 to 2024. Euro Surveill. 2024;29(13):pii=2400123. https://doi.org/10.2807/1560-7917.ES.2024.29.13.2400123

Article received on 28 Feb 2024 / Accepted on 27 Mar 2024 / Published on 28 Mar 2024

In 2023, dengue virus serotype 2 (DENV2) affected most French overseas territories. In the French Caribbean Islands, viral circulation continues with >30,000 suspected infections by March 2024. Genome sequence analysis reveals that the epidemic lineage in the French Caribbean islands has also become established in French Guiana but not Réunion. It has moreover seeded autochthonous circulation events in mainland France. To guide prevention of further inter-territorial spread and DENV introduction in non-endemic settings, continued molecular surveillance and mosquito control are essential.

In the region of the Americas, the year 2023 set an unwelcome record in terms of dengue virus (DENV) circulation, with more than 4.1 million suspected infections distributed across 42 countries and territories [1]. Regarding the French Caribbean Islands, where dengue surveillance is conducted year-round, epidemics of

DENV serotype 2 (DENV2) were declared in Guadeloupe and Martinique simultaneously on 17 August 2023. Eight and 10 weeks later, the islands of Saint-Barthélemy and Saint-Martin respectively entered the epidemic phase for dengue, which was also caused by DENV2. Up to March 2024, over 30,000 suspected cases of DENV infection have been reported across all four islands [2]. In 2023, DENV2 was also active in other French overseas territories including French Guiana and the island of Réunion, both of which share strong ties with the French Caribbean Islands [3,4]. In this work, we provide evidence supporting that a single epidemic lineage circulating in Guadeloupe, Martinique, Saint-Barthélemy and Saint-Martin has become established in French Guiana but not in Réunion. Moreover, the epidemic strain appears to have caused autochthonous clusters of cases in mainland France.
## Description of the centres collecting and analysing genomic data

To describe virus circulation in the French Caribbean islands and identify potential exchanges between these islands, French Guiana and Réunion, the French National Reference Center for arboviruses in mainland France and associated centres in the French Caribbean Islands-Guiana region and in the Indian Ocean region generated and analysed virus genome data across these territories. Moreover, as nine clusters of autochthonous DENV cases were reported in mainland France in 2023 [5], sequence data from two DENV2 clusters were generated to investigate potential links with DENV2 circulating in the French Caribbean islands.

## Finding of a single DENV2 lineage in the French Caribbean Islands with repeated viral strain exchanges between islands

DENV2 sequences derived from cases identified in the French Caribbean Islands between February 2023 and January 2024 were obtained through convenience sampling, as described in the Supplementary Material. We generated and analysed 103 nearly complete DENV2 genome sequences (>95% coding sequences (CDS)), 46 of which originated from infections in Guadeloupe, 51 from Martinique, three from Saint Barthélemy, one from Saint Martin, and two from French Caribbean Islands (exact location unknown); more information can be found in Supplementary Table 1. By inferring the phylogenetic relationships between these viral genomic sequences and a set of reference sequences representative of DENV2 genotypes, we found that all French Caribbean Island sequences belong to the cosmopolitan genotype.

To detail virus circulation between individual islands, we inferred a phylogeny based on a dataset combining all 103 virus genomes from the epidemic with all nearly complete genomes from the cosmopolitan genotype available in GenBank up to 22 November 2023 (Supplementary Table 1). In the resulting phylogenetic tree (Figure 1), French Caribbean Islands' sequences from 2023 to 2024 form a monophyletic clade (bootstrap>95), indicating that one main lineage is responsible for the current epidemic. Within this epidemic clade, sequences from Martinique and Guadeloupe are interspersed, suggesting that virus circulation involves exchanges between the two islands. Also, sequences from Saint Barthélemy are separated in different subgroups of French Caribbean sequences, suggesting that there have been multiple introductions from Martinique and/or Guadeloupe into this island. The only sequence obtained from Saint Martin Island also groups within the 2023-2024 French Caribbean clade, indicating that the epidemic lineage is also present on the island.

## The epidemic lineage emerged in 2022, following a new introduction into the French Caribbean Islands

To determine whether the epidemic clade stemmed from a new introduction or was circulating locally before the upsurge in cases, we also included in the phylogeny sequences from archived samples corresponding to infections identified during previous epidemics in the French Caribbean Islands (Supplementary Table 1). We observed that DENV2 genomes from the 2023 epidemic group with sequences from the United States (Florida 2023) and India (2021-2022) with good statistical support (bootstrap>95) rather than with French Caribbean sequences from previous years (Figure 1). In particular, they are distinct from DENV2 cosmopolitan sequences from Martinique and Guadeloupe from the years 2019 and 2020. This topology suggests that virus circulation was most likely caused by a new introduction into the French Caribbean Islands.

To date the origin of the epidemic, we selected a subset of 75 DENV2 genomes and used Bayesian inference to evaluate the time of emergence of the epidemic clade. Using the best fitted model (Supplementary Table 2), we found that the time to the most recent common ancestor of the epidemic clade dates back to September 2022 (95% highest posterior density (HPD) interval: 24 June to 26 December 2022), an estimate that aligns with the timing of the resurgence of dengue cases that was observed in Guadeloupe starting in October 2022 [6], which preluded the epidemic.

## French Caribbean Island lineage strains found in French Guiana and autochthonous clusters in mainland France but not Réunion

In 2023, DENV2 was active in other French overseas territories. In French Guiana, an epidemic of DENV is ongoing since July 2023. While DENV3 was the predominant serotype (>95% of serotyped cases) until September 2023 [7], DENV2 increased in prevalence, initially in the 'Ile de Cayenne' district [8,9], and is now present across most districts and on par with DENV3 at the level of the territory [10]. In Réunion, DENV was circulating at an endemic level in 2023 (218 cases) [11], with detections of both DENV1 and DENV2, and infections reported throughout the year. Also, mainland France recorded six clusters of autochthonous DENV2 circulation starting in July 2023 [5], with two DENV2 sequences available, one for the cluster in Limeil-Brévannes (3 cases, Île-de-France region [12]) and one for the Gardanne cluster (4 cases, Provence-Alpes-Côte d'Azur region). To determine whether the virus lineages circulating in other French territories were related to the French Caribbean Islands epidemic, we conducted a new phylogenetic analysis (Figure 2) including - in addition to the original dataset - five DENV2 genomes from cases acquired in French Guiana, 42 DENV2 genomes from cases identified in Réunion, and two DENV2 sequences from autochthonous circulation events in mainland France. The additional
## Description of the centres collecting and analysing genomic data

To describe virus circulation in the French Caribbean islands and identify potential exchanges between these islands, French Guiana and Réunion, the French National Reference Center for arboviruses in mainland France and associated centres in the French Caribbean Islands-Guiana region and in the Indian Ocean region generated and analysed virus genome data across these territories. Moreover, as nine clusters of autochthonous DENV cases were reported in mainland France in 2023 [5], sequence data from two DENV2 clusters were generated to investigate potential links with DENV2 circulating in the French Caribbean islands.

## Finding of a single DENV2 lineage in the French Caribbean Islands with repeated viral strain exchanges between islands

DENV2 sequences derived from cases identified in the French Caribbean Islands between February 2023 and January 2024 were obtained through convenience sampling, as described in the Supplementary Material. We generated and analysed 103 nearly complete DENV2 genome sequences (>95% coding sequences (CDS)), 46 of which originated from infections in Guadeloupe, 51 from Martinique, three from Saint Barthélemy, one from Saint Martin, and two from French Caribbean Islands (exact location unknown); more information can be found in Supplementary Table 1. By inferring the phylogenetic relationships between these viral genomic sequences and a set of reference sequences representative of DENV2 genotypes, we found that all French Caribbean Island sequences belong to the cosmopolitan genotype.

To detail virus circulation between individual islands, we inferred a phylogeny based on a dataset combining all 103 virus genomes from the epidemic with all nearly complete genomes from the cosmopolitan genotype available in GenBank up to 22 November 2023 (Supplementary Table 1). In the resulting phylogenetic tree (Figure 1), French Caribbean Islands' sequences from 2023 to 2024 form a monophyletic clade (bootstrap>95), indicating that one main lineage is responsible for the current epidemic. Within this epidemic clade, sequences from Martinique and Guadeloupe are interspersed, suggesting that virus circulation involves exchanges between the two islands. Also, sequences from Saint Barthélemy are separated in different subgroups of French Caribbean sequences, suggesting that there have been multiple introductions from Martinique and/or Guadeloupe into this island. The only sequence obtained from Saint Martin Island also groups within the 2023-2024 French Caribbean clade, indicating that the epidemic lineage is also present on the island.

## The epidemic lineage emerged in 2022, following a new introduction into the French Caribbean Islands

To determine whether the epidemic clade stemmed from a new introduction or was circulating locally before the upsurge in cases, we also included in the phylogeny sequences from archived samples corresponding to infections identified during previous epidemics in the French Caribbean Islands (Supplementary Table 1). We observed that DENV2 genomes from the 2023 epidemic group with sequences from the United States (Florida 2023) and India (2021-2022) with good statistical support (bootstrap>95) rather than with French Caribbean sequences from previous years (Figure 1). In particular, they are distinct from DENV2 cosmopolitan sequences from Martinique and Guadeloupe from the years 2019 and 2020. This topology suggests that virus circulation was most likely caused by a new introduction into the French Caribbean Islands.

To date the origin of the epidemic, we selected a subset of 75 DENV2 genomes and used Bayesian inference to evaluate the time of emergence of the epidemic clade. Using the best fitted model (Supplementary Table 2), we found that the time to the most recent common ancestor of the epidemic clade dates back to September 2022 (95% highest posterior density (HPD) interval: 24 June to 26 December 2022), an estimate that aligns with the timing of the resurgence of disease cases that was observed in Guadeloupe starting in October 2022 [6], which preluded the epidemic.

## French Caribbean Island lineage strains found in French Guiana and autochthonous clusters in mainland France but not Réunion

In 2023, DENV2 was active in other French overseas territories. In French Guiana, an epidemic of DENV is ongoing since July 2023. While DENV3 was the predominant serotype (>95% of serotyped cases) until September 2023 [7], DENV2 increased in prevalence, initially in the 'Ile de Cayenne' district [8,9], and is now present across most districts and on par with DENV3 at the level of the territory [10]. In Réunion, DENV was circulating at an endemic level in 2023 (218 cases) [11], with detections of both DENV1 and DENV2, and infections reported throughout the year. Also, mainland France recorded six clusters of autochthonous DENV2 circulation starting in July 2023 [5], with two DENV2 sequences available, one for the cluster in Limeil-Brévannes (3 cases, Île-de-France region [12]) and one for the Gardanne cluster (4 cases, Provence-Alpes-Côte d'Azur region). To determine whether the virus lineages circulating in other French territories were related to the French Caribbean Islands epidemic, we conducted a new phylogenetic analysis (Figure 2) including - in addition to the original dataset - five DENV2 genomes from cases acquired in French Guiana, 42 DENV2 genomes from cases identified in Réunion, and two DENV2 sequences from autochthonous circulation events in mainland France. The additional
FIGURE 1

Phylogeny of the cosmopolitan genotype of DENV2 with a focus on sequences from the French Caribbean Islands epidemic, 2023–2024 (n = 1,348 sequences)

<figure><img src="image_2.png" /></figure>

CDS: coding sequence; DENV2: dengue virus serotype 2; FCI: French Caribbean Islands.

Maximum-likelihood phylogeny of all genomes from the FCI epidemic combined with all DENV2 sequences from the cosmopolitan genotype covering more than 85% of the CDS available on GenBank up to 22 November 2023 and a set of reference sequences from other genotypes. Phylogenetic inference was performed using IQTREE2 under ModelFinder with ultrafast bootstrap approximation (1,000 replicates) [19,20]. The tree was rooted using the sylvatic genotype of DENV2. All sequences are coloured according to their geographic origin (for imported cases, the geographic origin corresponds to the source of importation identified via epidemiological surveillance, as described in Supplementary Table 1). In the main tree, bootstraps are shown for all nodes with more than 800 descendants and sequences from previous DENV2 circulation events in the French Caribbean islands are shown with arrows. In the French Caribbean Islands subtree, all nodes with a bootstrap support above 95 are highlighted with a black circle. The scale represents phylogenetic divergence, in nucleotide substitutions per site.

sequences were selected according to convenience
sampling, and information about them can be found
in Supplementary Table 3. We found that all Guianese
sequences group within the French Caribbean Islands
clade. This result, combined with serotype prevalence
data, indicates that the French Caribbean Island epi-
demic lineage is now circulating in French Guiana. In
contrast, sequences from Réunion cluster separately
from the French Caribbean Islands' clade, suggesting
that the viral strains circulating in Réunion are due to
an introduction from a distinct location. Finally, the
two sequences from autochthonous DENV2 circulation
events in Limeil-Brévannes and Gardanne are part of

the French Caribbean Islands' clade, which indicates
that these two events likely result from introductions
from the Caribbean.

Discussion

Dengue is endemo-epidemic in the French Caribbean
Islands where it has caused several epidemics over
the past decades including in 2013-2014 and in
2019-2021, during which distinct serotypes circulated
on the islands of Guadeloupe and Martinique [13,14].
In 2013-2014, DENV serotype 4 (DENV4) dominated
in Guadeloupe and DENV2 was the main serotype in
Martinique, while in 2019-2021, DENV2 was dominant
FIGURE 1

Phylogeny of the cosmopolitan genotype of DENV2 with a focus on sequences from the French Caribbean Islands epidemic, 2023–2024 (n = 1,348 sequences)

<figure><img src="image_2.png" /></figure>

CDS: coding sequence; DENV2: dengue virus serotype 2; FCI: French Caribbean Islands.

Maximum-likelihood phylogeny of all genomes from the FCI epidemic combined with all DENV2 sequences from the cosmopolitan genotype covering more than 85% of the CDS available on GenBank up to 22 November 2023 and a set of reference sequences from other genotypes. Phylogenetic inference was performed using IQTREE2 under ModelFinder with ultrafast bootstrap approximation (1,000 replicates) [19,20]. The tree was rooted using the sylvatic genotype of DENV2. All sequences are coloured according to their geographic origin (for imported cases, the geographic origin corresponds to the source of importation identified via epidemiological surveillance, as described in Supplementary Table 1). In the main tree, bootstraps are shown for all nodes with more than 800 descendants and sequences from previous DENV2 circulation events in the French Caribbean islands are shown with arrows. In the French Caribbean Islands subtree, all nodes with a bootstrap support above 95 are highlighted with a black circle. The scale represents phylogenetic divergence, in nucleotide substitutions per site.

sequences were selected according to convenience
sampling, and information about them can be found
in Supplementary Table 3. We found that all Guianese
sequences group within the French Caribbean Islands
clade. This result, combined with serotype prevalence
data, indicates that the French Caribbean Island epi-
demic lineage is now circulating in French Guiana. In
contrast, sequences from Réunion cluster separately
from the French Caribbean Islands' clade, suggesting
that the viral strains circulating in Réunion are due to
an introduction from a distinct location. Finally, the
two sequences from autochthonous DENV2 circulation
events in Limeil-Brévannes and Gardanne are part of

the French Caribbean Islands' clade, which indicates
that these two events likely result from introductions
from the Caribbean.

Discussion

Dengue is endemo-epidemic in the French Caribbean
Islands where it has caused several epidemics over
the past decades including in 2013-2014 and in
2019-2021, during which distinct serotypes circulated
on the islands of Guadeloupe and Martinique [13,14].
In 2013-2014, DENV serotype 4 (DENV4) dominated
in Guadeloupe and DENV2 was the main serotype in
Martinique, while in 2019-2021, DENV2 was dominant
Phylogeny of the cosmopolitan genotype of DENV2 with a focus on sequences from French overseas territories, 2023–2024 (n = 1,394)

<figure><img src="image_3.png" /></figure>

CDS: coding sequence; DENV2: dengue virus serotype 2; ISO: country International Organization for Standardization 3 code.

Maximum-likelihood phylogeny of all genomes from the French Caribbean Islands epidemic combined with sequences, from French Guiana, from Réunion island, from mainland France, and with all DENV2 sequences from the cosmopolitan genotype covering more than 85% of the CDS available on GenBank up to 22 November 2023. Phylogenetic inference was performed using IQTREE2 under ModelFinder with ultrafast bootstrap approximation (1,000 replicates) [19,20]. The tree was rooted using the sylvatic genotype of DENV2. All sequences are coloured according to their geographic origin (for imported cases, the geographic origin corresponds to the source of importation). In the main tree, bootstrap values are shown for all nodes with more than 800 descendants and sequences from Réunion islands (2023) not present in the subtree are shown with arrows (with the ISO code 3 of the of travel location when applicable). In the subtree, all nodes with more than 35 leaves and with a bootstrap support above 95 are highlighted with a black circle. The scale represents phylogenetic divergence, in nucleotide substitutions per site.

in Guadeloupe and DENV serotype 3 (DENV3) was the main serotype in Martinique. Here, we identify circulation dynamics which differ markedly from those past epidemics, with one main lineage present both in Guadeloupe and Martinique and a phylogenetic tree topology suggestive of exchanges between both islands. The successful spread of DENV2 on the island Guadeloupe only 2 years following a previous DENV2 epidemic is unexpected considering the broad and recent homotypic immunity in the island population, and in a context where other serotypes are actively circulating in Central America (including in French Guiana), notably DENV3 [1]. The past and current DENV2

lineages being quite distant phylogenetically, potential antigenic differences might explain the temporal proximity between the past and current circulation events. Other explanations may however apply, including a particularly high transmission efficiency of the current epidemic lineage.

In this work, we show that the epidemic clade stems from a new introduction in the French Caribbean Islands, but locating the source of this introduction is challenging in part because of limited genomic sampling around the French Caribbean Islands. We find that the closest relative to strains of the French
Phylogeny of the cosmopolitan genotype of DENV2 with a focus on sequences from French overseas territories, 2023–2024 (n = 1,394)

<figure><img src="image_3.png" /></figure>

CDS: coding sequence; DENV2: dengue virus serotype 2; ISO: country International Organization for Standardization 3 code.

Maximum-likelihood phylogeny of all genomes from the French Caribbean Islands epidemic combined with sequences, from French Guiana, from Réunion island, from mainland France, and with all DENV2 sequences from the cosmopolitan genotype covering more than 85% of the CDS available on GenBank up to 22 November 2023. Phylogenetic inference was performed using IQTREE2 under ModelFinder with ultrafast bootstrap approximation (1,000 replicates) [19,20]. The tree was rooted using the sylvatic genotype of DENV2. All sequences are coloured according to their geographic origin (for imported cases, the geographic origin corresponds to the source of importation). In the main tree, bootstrap values are shown for all nodes with more than 800 descendants and sequences from Réunion islands (2023) not present in the subtree are shown with arrows (with the ISO code 3 of the of travel location when applicable). In the subtree, all nodes with more than 35 leaves and with a bootstrap support above 95 are highlighted with a black circle. The scale represents phylogenetic divergence, in nucleotide substitutions per site.

in Guadeloupe and DENV serotype 3 (DENV3) was the main serotype in Martinique. Here, we identify circulation dynamics which differ markedly from those past epidemics, with one main lineage present both in Guadeloupe and Martinique and a phylogenetic tree topology suggestive of exchanges between both islands. The successful spread of DENV2 on the island Guadeloupe only 2 years following a previous DENV2 epidemic is unexpected considering the broad and recent homotypic immunity in the island population, and in a context where other serotypes are actively circulating in Central America (including in French Guiana), notably DENV3 [1]. The past and current DENV2

lineages being quite distant phylogenetically, potential antigenic differences might explain the temporal proximity between the past and current circulation events. Other explanations may however apply, including a particularly high transmission efficiency of the current epidemic lineage.

In this work, we show that the epidemic clade stems from a new introduction in the French Caribbean Islands, but locating the source of this introduction is challenging in part because of limited genomic sampling around the French Caribbean Islands. We find that the closest relative to strains of the French
Caribbean Islands epidemic clade is a strain from Florida collected in July 2023, which itself appears to be closely related to strains sampled in India in 2021. While the closest phylogenetic relative of the French Caribbean Islands epidemic clade strains appears to have been sampled in Florida, this location is not a likely geographic origin of the epidemic. Local DENV case numbers are usually limited in Florida [15], especially compared with other countries neighbouring the French Caribbean Islands, such as Honduras, Panama, and the Dominican Republic, which reported DENV2 circulation over recent years (2021–2022) according to the Pan American Health Organization (PAHO) [16,17]. The source of the epidemic affecting the French Caribbean Islands is likely located elsewhere, possibly in Central America, from where it may have also caused one – or more – local circulation events in Florida.

Our study presents several limitations. Here, we used
near-complete (>95%) CDSs to infer phylogenetic rela-
tionships among DENV genomes. The absence of up
to 5% of the CDS and of the 3' and 5' untranslated
regions (UTRs) of the genome may result in a loss of
resolution in the tree topology [18]. This is neverthe-
less expected to have minimal impact on the parts of
the tree with strong statistical support and thus on
the conclusions of the study. Moreover, the limited
number of sequences available for French Guiana may
limit our ability to infer with certainty the directional-
ity of the DENV2 lineage circulation between the French
Caribbean islands and French Guiana. Our results are
however, also supported by serotype prevalence data
that indicate that DENV2 prevalence was extremely
low in French Guiana before October 2023, making
an importation from a location with high DENV2 case
numbers to a location with low DENV2 case numbers
much more likely than the opposite. Finally, our analy-
sis of autochthonous DENV2 transmission events in
Limeil-Brévannes and in Gardanne relies on a single
sequence for each of the clusters, as the remainder of
the cases were either negative by PCR or exhibited viral
loads incompatible with sequencing. The three cases
from Limeil-Brévannes belonged to the same family
[12] and all four cases from Gardanne were located
within a 1km radius. Given the size of the clusters
and the spatio-temporal vicinity among the few cases
involved, it is likely that for each of these two clusters,
un-sequenced cases share viruses of the same phylo-
genetic lineage as the sequenced case. In addition, as
the French Caribbean islands constituted – by far – the
most frequent source of imported cases in mainland
France in 2023, it is also the most likely source of
autochthonous circulation events independent of any
sequence data analysis [5].

Conclusion

In this work, we use virus genomic data to detail cir-
culation dynamics during the French Caribbean Islands
epidemic. We identify a change in local circulation
trends compared with previous epidemics in the French
Caribbean Islands and show that the lineage linked to

this epidemic appears to have become established in
French Guiana amidst an epidemic of DENV3. Finally,
we provide evidence suggesting that strains belonging
to the French Caribbean Island epidemic lineage also
fuelled autochthonous DENV2 circulation events in
mainland France, with at least two local DENV2 clus-
ters involved. These results highlight the strong epide-
miological connections between French territories and
call for increased efforts in genetic monitoring to gain
additional insights into those inter-territorial exchange
dynamics and inform public health strategies, such as
immunisation strategies, blood donor screening, infor-
mation to travellers, or vector surveillance and control.

Arbovirus genomics diagnostic laboratories working
group members' affiliations

Laboratoire Cerba, Frépillon, France: Laura Verdurme; Infectious Diseases Department, Eurofins-Biomnis Lyon, France: Marie Hervo, Alexia Barbry; Cerballiance Martinique: Pierre Bancons; Centre de ressource biologique de la Martinique, CHU de Martinique, France: Valérie Suez-Panama, Isabelle Komla-Soukha; Centre Hospitalier de l'Ouest Guyanais, Saint-Laurent-du-Maroni, French Guiana: Jean-François Carod; Laboratoire, Centre Hospitalier de Cayenne, Cayenne, French Guiana: Pr Magalie Demar; Laboratoires Eurofins Guyane: Didier Musso et Alain Berlioz- Arthaud; Laboratoires Eurofins Martinique: Sandra Fabienne, Kate Lebouteiller, Esther Christine et Michèle Adélaïde, Fabrice Ghisalberti; Centre Hospitalier Ouest Réunion: Anne Ligneureux; Inovie Laboratory (Réunion): Céline Ben Cimon; Cerballiance (Réunion): Mahery Ramiandrisoa; Medical biology laboratory of Saint-Benoît (Réunion): Geoffrey Masson; Bioaustral Laboratory (Réunion): Paul Séraphin.

Ethical statement

This study was part of national public health surveil-
lance program of the National Reference Centre (NRC) for
Arboviruses supervised by the National Public Health Agency
(Santé Publique France, SPF). Therefore, as an epidemiologi-
cal record, consultation with ethics committee was not re-
quired. Samples involved in this study were chosen among
human plasma and serum specimens received as part of
standard diagnostic and expertise activities of the associ-
ated arboviruses NRC in Reunion Island's Hospital. Samples
transferred to the NRC are submitted with a form that in-
cludes the patient's consent (non-opposition clause). No
additional clinical specimens were collected for the purpose
of the study. Human samples and cultures originating from
human samples were anonymised, with no or minimal risk
to patients within the terms of the European General Data
Protection Regulation and the French National Commission
on Informatics and Liberty (CNIL).

Funding statement

This work was supported by the ARBOGEN project, funded
by the MSDAVENIR foundation. The activity of the National
Reference Centers is supported by the French national
health agency (Santé publique France). The activity of the
UVE is supported by its supervising institutional bodies (Aix-
Marseille Université, Université di Corsica, Institut national
de la santé et de la recherche médicale, Institut de recherche
pour le développement, Institut de Recherche Biomédicale
des Armées).
Caribbean Islands epidemic clade is a strain from Florida collected in July 2023, which itself appears to be closely related to strains sampled in India in 2021. While the closest phylogenetic relative of the French Caribbean Islands epidemic clade strains appears to have been sampled in Florida, this location is not a likely geographic origin of the epidemic. Local DENV case numbers are usually limited in Florida [15], especially compared with other countries neighbouring the French Caribbean Islands, such as Honduras, Panama, and the Dominican Republic, which reported DENV2 circulation over recent years (2021–2022) according to the Pan American Health Organization (PAHO) [16,17]. The source of the epidemic affecting the French Caribbean Islands is likely located elsewhere, possibly in Central America, from where it may have also caused one – or more – local circulation events in Florida.

Our study presents several limitations. Here, we used
near-complete (>95%) CDSs to infer phylogenetic rela-
tionships among DENV genomes. The absence of up
to 5% of the CDS and of the 3' and 5' untranslated
regions (UTRs) of the genome may result in a loss of
resolution in the tree topology [18]. This is neverthe-
less expected to have minimal impact on the parts of
the tree with strong statistical support and thus on
the conclusions of the study. Moreover, the limited
number of sequences available for French Guiana may
limit our ability to infer with certainty the directional-
ity of the DENV2 lineage circulation between the French
Caribbean islands and French Guiana. Our results are
however, also supported by serotype prevalence data
that indicate that DENV2 prevalence was extremely
low in French Guiana before October 2023, making
an importation from a location with high DENV2 case
numbers to a location with low DENV2 case numbers
much more likely than the opposite. Finally, our analy-
sis of autochthonous DENV2 transmission events in
Limeil-Brévannes and in Gardanne relies on a single
sequence for each of the clusters, as the remainder of
the cases were either negative by PCR or exhibited viral
loads incompatible with sequencing. The three cases
from Limeil-Brévannes belonged to the same family
[12] and all four cases from Gardanne were located
within a 1km radius. Given the size of the clusters
and the spatio-temporal vicinity among the few cases
involved, it is likely that for each of these two clusters,
un-sequenced cases share viruses of the same phylo-
genetic lineage as the sequenced case. In addition, as
the French Caribbean islands constituted – by far – the
most frequent source of imported cases in mainland
France in 2023, it is also the most likely source of
autochthonous circulation events independent of any
sequence data analysis [5].

Conclusion

In this work, we use virus genomic data to detail cir-
culation dynamics during the French Caribbean Islands
epidemic. We identify a change in local circulation
trends compared with previous epidemics in the French
Caribbean Islands and show that the lineage linked to

this epidemic appears to have become established in
French Guiana amidst an epidemic of DENV3. Finally,
we provide evidence suggesting that strains belonging
to the French Caribbean Island epidemic lineage also
fuelled autochthonous DENV2 circulation events in
mainland France, with at least two local DENV2 clus-
ters involved. These results highlight the strong epide-
miological connections between French territories and
call for increased efforts in genetic monitoring to gain
additional insights into those inter-territorial exchange
dynamics and inform public health strategies, such as
immunisation strategies, blood donor screening, infor-
mation to travellers, or vector surveillance and control.

Arbovirus genomics diagnostic laboratories working
group members' affiliations

Laboratoire Cerba, Frépillon, France: Laura Verdurme; Infectious Diseases Department, Eurofins-Biomnis Lyon, France: Marie Hervo, Alexia Barbry; Cerballiance Martinique: Pierre Bancons; Centre de ressource biologique de la Martinique, CHU de Martinique, France: Valérie Suez-Panama, Isabelle Komla-Soukha; Centre Hospitalier de l'Ouest Guyanais, Saint-Laurent-du-Maroni, French Guiana: Jean-François Carod; Laboratoire, Centre Hospitalier de Cayenne, Cayenne, French Guiana: Pr Magalie Demar; Laboratoires Eurofins Guyane: Didier Musso et Alain Berlioz- Arthaud; Laboratoires Eurofins Martinique: Sandra Fabienne, Kate Lebouteiller, Esther Christine et Michèle Adélaïde, Fabrice Ghisalberti; Centre Hospitalier Ouest Réunion: Anne Ligneureux; Inovie Laboratory (Réunion): Céline Ben Cimon; Cerballiance (Réunion): Mahery Ramiandrisoa; Medical biology laboratory of Saint-Benoît (Réunion): Geoffrey Masson; Bioaustral Laboratory (Réunion): Paul Séraphin.

Ethical statement

This study was part of national public health surveil-
lance program of the National Reference Centre (NRC) for
Arboviruses supervised by the National Public Health Agency
(Santé Publique France, SPF). Therefore, as an epidemiologi-
cal record, consultation with ethics committee was not re-
quired. Samples involved in this study were chosen among
human plasma and serum specimens received as part of
standard diagnostic and expertise activities of the associ-
ated arboviruses NRC in Reunion Island's Hospital. Samples
transferred to the NRC are submitted with a form that in-
cludes the patient's consent (non-opposition clause). No
additional clinical specimens were collected for the purpose
of the study. Human samples and cultures originating from
human samples were anonymised, with no or minimal risk
to patients within the terms of the European General Data
Protection Regulation and the French National Commission
on Informatics and Liberty (CNIL).

Funding statement

This work was supported by the ARBOGEN project, funded
by the MSDAVENIR foundation. The activity of the National
Reference Centers is supported by the French national
health agency (Santé publique France). The activity of the
UVE is supported by its supervising institutional bodies (Aix-
Marseille Université, Université di Corsica, Institut national
de la santé et de la recherche médicale, Institut de recherche
pour le développement, Institut de Recherche Biomédicale
des Armées).
## Data availability

All virus sequences are accessible either on Genbank (accessions specified in the supplementary materials) or on Github (https://github.com/rklitting/D2_BR_FCI_epidemic). The xml and tree files used in this study are available on Github (same repository as above).

## Acknowledgements

We thank Thomas Canivez and Manon Gueulen from the National Reference Center for Arboviruses for their valuable technical contribution.

## Conflict of interest

None declared.

## Authors' contributions

Conceived and designed the study: RK, XdL, GG, GAD; Sample collection: AC, GDS, DR, ALagrave, EF, M-CJ-B, AF, A-BF, FD, LL, MV, NT, AÉ, PG, RC, LFagour, arbovirus genomics diagnostic laboratories working group; Data processing and analysis: RK, GP, LP, NA, RA, LFournier, DR, A Lagrave, EF, MC-J-B, ALavergne. Drafting the manuscript: RK, XdL. All authors gave final approval of the version to be submitted.

## References

1. World Health Organization (WHO). Disease Outbreak News; Dengue - Global situation. Geneva: WHO; 21 December 2023. Available from: https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON498

2. Santé Publique France (SPF). Dengue aux Antilles. Point au 14 Mars 2024. Saint-Maurice: SPF. French. [Accessed 20 March 2024]. Available from: https://www.santepubliquefrance.fr/regions/antilles/documents/bulletin-regional/2024/dengue-aux-antilles.-point-au-14-mars-2024

3. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 23 novembre 2023. French. [Accessed 20 March 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/dengue-en-guyane.-point-au-23-novembre-2023

4. Santé Publique France (SPF). Dengue à la Réunion - Bilan 2023. French. [Accessed 20 March 2024]. Available online: https://www.santepubliquefrance.fr/regions/ocean-indien/documents/bulletin-regional/2024/dengue-a-la-reunion.-bilan-2023

5. Santé Publique France (SPF). Chikungunya, dengue et zika - Données de la surveillance renforcée en France métropolitaine en 2023. Saint-Maurice: SPF. French. [Accessed 29 Jan 2024]. Available from: https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-a-transmission-vectorielle/chikungunya/articles/donnees-en-france-métropolitaine/chikungunya-dengue-et-zika-donnees-de-la-surveillance-renforcee-en-france-métropolitaine-en-2023

6. Santé Publique France (SPF). Dengue aux Antilles. Point au 30 novembre 2022. Saint-Maurice: SPF. French. [Accessed 29 Jan 2024]. Available from: https://www.santepubliquefrance.fr/regions/antilles/documents/bulletin-regional/2022/surveillance-de-la-dengue-aux-antilles.-point-au-30-novembre-2022

7. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 31 août 2023. French. [Accessed 20 March 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/situation-epidemiologique-de-la-dengue-en-guyane.-point-au-31-aout-2023

8. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 9 novembre 2023. French. [Accessed 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/dengue-en-guyane.-point-au-9-novembre-2023

9. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 23 novembre 2023. French. [Accessed 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/dengue-en-guyane.-point-au-23-novembre-2023

10. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 29 février 2024. French. [Accessed on 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2024/dengue-en-guyane.-point-au-29-fevrier-2024

11. Santé Publique France (SPF). Dengue à la Réunion - Bilan 2023. French. [Accessed 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/ocean-indien/documents/bulletin-regional/2024/dengue-a-la-reunion.-bilan-2023

12. Fournet N, Voiry N, Rozenberg J, Bassi C, Cassonnet C, Karch A, et al. investigation team. A cluster of autochthonous dengue transmission in the Paris region - detection, epidemiology and control measures, France, October 2023. Euro Surveill. 2023;28(49):2300641. https://doi.org/10.2807/1560-7917. ES.2023.28.49.2300641 PMID: 38062947

13. Garcia-Van Smévoorde M, Piorkowski G, Emboulé L, Dos Santos G, Loraux C, Guyomard-Rabenirina S, et al. Phylogenetic Investigations of Dengue 2019-2021 Outbreak in Guadeloupe and Martinique Caribbean Islands. Pathogens. 2023;12(9):1182. https://doi.org/10.3390/pathogens12091182 PMID: 37764990

14. Santé Publique France (SPF). Bulletin de veille sanitaire Antilles-Guyane. n°2-3 - Mars 2015. Saint-Maurice: SPF. French. [Accessed 31 May 2023]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2015/bulletin-de-veille-sanitaire-antilles-guyane.-n-2-3-mars-2015

15. Jones FK, Morrison AM, Santiago GA, Rysava K, Zimler RA, Heberlein LA, et al. Florida Department of Health Bureau of Public Health Laboratory Team,2. Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022-April 2023. Emerg Infect Dis. 2024;30(2):376-9. https://doi.org/10.3201/eid3002.231615 PMID: 38232709

16. Pan American Health Organization (PAHO). Annual arbovirus bulletin 2022. [Accessed on 29 Jan 2024]. Washington DC: PAHO. Available from: https://www3.paho.org/data/index.php/en/mnu-topics/indicadores-dengue-en/annual-arbovirus-bulletin-2022.html

17. Pan American Health Organization (PAHO). Annual arbovirus bulletin 2021. Washington DC: PAHO. [Accessed 29 Jan 2024]. Available from: https://www3.paho.org/data/index.php/en/mnu-topics/indicadores-dengue-en/annual-arbovirus-bulletin-2021.html

18. Dudas G, Bedford T. The ability of single genes vs full genomes to resolve time and space in outbreak analysis. BMC Evol Biol. 2019;19(1):232. https://doi.org/10.1186/s12862-019-1567-0 PMID: 31878875

19. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268-74. https://doi.org/10.1093/molbev/msu300 PMID: 25371430

20. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020;37(5):1530-4. https://doi.org/10.1093/molbev/msaa015 PMID: 32011700

## License, supplementary material and copyright

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made.

Any supplementary material referenced in the article can be found in the online version.

This article is copyright of the authors or their affiliated institutions, 2024.
## Data availability

All virus sequences are accessible either on Genbank (accessions specified in the supplementary materials) or on Github (https://github.com/rklitting/D2_BR_FCI_epidemic). The xml and tree files used in this study are available on Github (same repository as above).

## Acknowledgements

We thank Thomas Canivez and Manon Gueulen from the National Reference Center for Arboviruses for their valuable technical contribution.

## Conflict of interest

None declared.

## Authors' contributions

Conceived and designed the study: RK, XdL, GG, GAD; Sample collection: AC, GDS, DR, ALagrave, EF, M-CJ-B, AF, A-BF, FD, LL, MV, NT, AÉ, PG, RC, LFagour, arbovirus genomics diagnostic laboratories working group; Data processing and analysis: RK, GP, LP, NA, RA, LFournier, DR, A Lagrave, EF, MC-J-B, ALavergne. Drafting the manuscript: RK, XdL. All authors gave final approval of the version to be submitted.

## References

1. World Health Organization (WHO). Disease Outbreak News; Dengue - Global situation. Geneva: WHO; 21 December 2023. Available from: https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON498

2. Santé Publique France (SPF). Dengue aux Antilles. Point au 14 Mars 2024. Saint-Maurice: SPF. French. [Accessed 20 March 2024]. Available from: https://www.santepubliquefrance.fr/regions/antilles/documents/bulletin-regional/2024/dengue-aux-antilles.-point-au-14-mars-2024

3. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 23 novembre 2023. French. [Accessed 20 March 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/dengue-en-guyane.-point-au-23-novembre-2023

4. Santé Publique France (SPF). Dengue à la Réunion - Bilan 2023. French. [Accessed 20 March 2024]. Available online: https://www.santepubliquefrance.fr/regions/ocean-indien/documents/bulletin-regional/2024/dengue-a-la-reunion.-bilan-2023

5. Santé Publique France (SPF). Chikungunya, dengue et zika - Données de la surveillance renforcée en France métropolitaine en 2023. Saint-Maurice: SPF. French. [Accessed 29 Jan 2024]. Available from: https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-a-transmission-vectorielle/chikungunya/articles/donnees-en-france-métropolitaine/chikungunya-dengue-et-zika-donnees-de-la-surveillance-renforcee-en-france-métropolitaine-en-2023

6. Santé Publique France (SPF). Dengue aux Antilles. Point au 30 novembre 2022. Saint-Maurice: SPF. French. [Accessed 29 Jan 2024]. Available from: https://www.santepubliquefrance.fr/regions/antilles/documents/bulletin-regional/2022/surveillance-de-la-dengue-aux-antilles.-point-au-30-novembre-2022

7. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 31 août 2023. French. [Accessed 20 March 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/situation-epidemiologique-de-la-dengue-en-guyane.-point-au-31-aout-2023

8. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 9 novembre 2023. French. [Accessed 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/dengue-en-guyane.-point-au-9-novembre-2023

9. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 23 novembre 2023. French. [Accessed 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2023/dengue-en-guyane.-point-au-23-novembre-2023

10. Santé Publique France (SPF). Dengue. Point Epidémiologique, Guyane, 29 février 2024. French. [Accessed on 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2024/dengue-en-guyane.-point-au-29-fevrier-2024

11. Santé Publique France (SPF). Dengue à la Réunion - Bilan 2023. French. [Accessed 20 Mar 2024]. Available from: https://www.santepubliquefrance.fr/regions/ocean-indien/documents/bulletin-regional/2024/dengue-a-la-reunion.-bilan-2023

12. Fournet N, Voiry N, Rozenberg J, Bassi C, Cassonnet C, Karch A, et al. investigation team. A cluster of autochthonous dengue transmission in the Paris region - detection, epidemiology and control measures, France, October 2023. Euro Surveill. 2023;28(49):2300641. https://doi.org/10.2807/1560-7917. ES.2023.28.49.2300641 PMID: 38062947

13. Garcia-Van Smévoorde M, Piorkowski G, Emboulé L, Dos Santos G, Loraux C, Guyomard-Rabenirina S, et al. Phylogenetic Investigations of Dengue 2019-2021 Outbreak in Guadeloupe and Martinique Caribbean Islands. Pathogens. 2023;12(9):1182. https://doi.org/10.3390/pathogens12091182 PMID: 37764990

14. Santé Publique France (SPF). Bulletin de veille sanitaire Antilles-Guyane. n°2-3 - Mars 2015. Saint-Maurice: SPF. French. [Accessed 31 May 2023]. Available from: https://www.santepubliquefrance.fr/regions/guyane/documents/bulletin-regional/2015/bulletin-de-veille-sanitaire-antilles-guyane.-n-2-3-mars-2015

15. Jones FK, Morrison AM, Santiago GA, Rysava K, Zimler RA, Heberlein LA, et al. Florida Department of Health Bureau of Public Health Laboratory Team,2. Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022-April 2023. Emerg Infect Dis. 2024;30(2):376-9. https://doi.org/10.3201/eid3002.231615 PMID: 38232709

16. Pan American Health Organization (PAHO). Annual arbovirus bulletin 2022. [Accessed on 29 Jan 2024]. Washington DC: PAHO. Available from: https://www3.paho.org/data/index.php/en/mnu-topics/indicadores-dengue-en/annual-arbovirus-bulletin-2022.html

17. Pan American Health Organization (PAHO). Annual arbovirus bulletin 2021. Washington DC: PAHO. [Accessed 29 Jan 2024]. Available from: https://www3.paho.org/data/index.php/en/mnu-topics/indicadores-dengue-en/annual-arbovirus-bulletin-2021.html

18. Dudas G, Bedford T. The ability of single genes vs full genomes to resolve time and space in outbreak analysis. BMC Evol Biol. 2019;19(1):232. https://doi.org/10.1186/s12862-019-1567-0 PMID: 31878875

19. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268-74. https://doi.org/10.1093/molbev/msu300 PMID: 25371430

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