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Perez LJ, Yamaguchi J, Weiss S, Carlos C, Meyer TV, Rodgers MA, Phoompoung P, Suputtamongkol Y, Cloherty GA, Berg MG. Climate, inter-serotype competition and arboviral interactions shape dengue dynamics in Thailand. Commun Biol 2025; 8:601. [PMID: 40216923 PMCID: PMC11992266 DOI: 10.1038/s42003-025-07999-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 03/25/2025] [Indexed: 04/14/2025] Open
Abstract
The incidence and global spread of dengue are reaching alarming levels. Thailand represents a critical disease epicenter and demands an understanding of the environmental and evolutionary pressures that sustain DENV transmission. Unlike most affected countries experiencing recurrent outbreaks of the same serotype or replacement of one serotype for another, Thailand is an ecological niche for all four serotypes. Favorable climate and mosquito vector availability maintain a landscape defined by stable, endemic circulation of genotypes, with minimal genetic variation attributed to sporadic, external introductions. This equilibrium is achieved through inter-serotype competition, characterized by reproductive fitness levels that maintain infections (Re>1) and elevated evolutionary rates ( ~ 10-4), which steadily increase the genetic diversity of each serotype. This conclusion is reinforced by the identification of numerous positively selected mutations, skewed in the direction of non-structural proteins conferring replication and transmission advantages versus those present in structural proteins evading neutralizing antibodies. Precipitous drops in DENV cases following outbreaks of Chikungunya suggest that interactions with other arboviruses also impact DENV dynamics through vector competition, replication inhibition or partial cross-protection. Thailand is a major exporter of DENV cases and novel emergent lineages gaining fitness here are likely to spread internationally. Surveillance is therefore paramount to monitor diversification trends and take measures to avoid the establishment of similar sustained, local transmission in other countries.
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Affiliation(s)
- Lester J Perez
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA.
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA.
| | - Julie Yamaguchi
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
| | - Sonja Weiss
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
| | - Christiane Carlos
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
| | - Todd V Meyer
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
| | - Mary A Rodgers
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
| | - Pakpoom Phoompoung
- Faculty of Medicine, Siriraj Hospital Mahidol University, Bangkok, Thailand
| | | | - Gavin A Cloherty
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
| | - Michael G Berg
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Lake Bluff, IL, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Lake Bluff, IL, USA
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Lagrave A, Enfissi A, Tirera S, Pierre Demar M, Jaonasoa J, Carod JF, Ramavoson T, Succo T, Carvalho L, Devos S, Dorleans F, Leon L, Berlioz-Arthaud A, Musso D, Klitting R, de Lamballerie X, Lavergne A, Rousset D. The Genetic Evolution of DENV2 in the French Territories of the Americas: A Retrospective Study from the 2000s to the 2024 Epidemic, Including a Comparison of Amino Acid Changes with Vaccine Strains. Vaccines (Basel) 2025; 13:264. [PMID: 40266131 PMCID: PMC11945534 DOI: 10.3390/vaccines13030264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 04/24/2025] Open
Abstract
BACKGROUND Dengue virus type 2 (DENV2) is endemic to hyperendemic in the French territories of the Americas (FTAs), including French Guiana, Guadeloupe, Martinique, Saint-Barthelemy, and Saint-Martin. In 2023-2024, French Guiana, Martinique, and Guadeloupe experienced unprecedented dengue epidemics partly associated with this serotype. In response, we conducted a retrospective study of the diversity of DENV2 strains circulating in the FTAs from 2000 to 2024. METHODS To this end, we selected DENV2 samples from the collection at the National Research Center for Arboviruses in French Guiana (NRCA-FG) and sequenced them using Oxford Nanopore Technologies (ONT)-based next-generation sequencing (NGS). RESULTS Phylogenetic analysis revealed that (i) the 77 DENV2 sequences from the FTAs belong to two distinct genotypes-Asian American and Cosmopolitan; (ii) from the 2000s up to the 2019 epidemic in French Guiana, all sequenced strains belonged to the Asian American genotype; (iii) and from 2019 to 2020, strains circulating in Martinique and Guadeloupe belonged to the Cosmopolitan genotype, specifically the Indian subcontinent sublineage, while (iv) strains from the 2023-2024 outbreak in Martinique, Guadeloupe, and French Guiana fall within a distinct sublineage of the same genotype-Other Cosmopolitan. Additionally, we analyzed amino acid (AA) changes in FTA sequences compared to the Dengvaxia® and Qdenga® vaccines. The analysis of amino acid changes in FTA sequences compared to the vaccines (Dengvaxia® and Qdenga®) identified 42 amino acid changes in the prM/E regions (15 in the prM region and 27 in the E region) relative to CYD-2 Dengvaxia® and 46 amino acid changes in the prM/E regions relative to Qdenga®, including 16 in the prM region and 30 in the E region. Some of these AA changes are shared across multiple genotypes and sublineages, with 8 substitutions in the prM region and 18 in the E region appearing in both analyses. This raises questions about the potential impact of these changes on vaccine efficacy. CONCLUSION Overall, these findings provide a current overview of the genomic evolution of DENV2 in the FTA, which is crucial for developing more effective prevention and control strategies and for selecting future vaccines tailored to circulating strains.
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Affiliation(s)
- Alisé Lagrave
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Antoine Enfissi
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Sourakhata Tirera
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Magalie Pierre Demar
- Laboratoire Centre Hospitalier de Cayenne, Cayenne, French Guiana; (M.P.D.); (J.J.)
| | - Jean Jaonasoa
- Laboratoire Centre Hospitalier de Cayenne, Cayenne, French Guiana; (M.P.D.); (J.J.)
| | - Jean-François Carod
- Department of Biology, West French Guiana Hospital Center, Saint-Laurent-du-Maroni, French Guiana; (J.-F.C.); (T.R.)
| | - Tsiriniaina Ramavoson
- Department of Biology, West French Guiana Hospital Center, Saint-Laurent-du-Maroni, French Guiana; (J.-F.C.); (T.R.)
| | - Tiphanie Succo
- Santé Publique France, Cellule Guyane, Cayenne, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Luisiane Carvalho
- Santé Publique France, Cellule Guyane, Cayenne, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Sophie Devos
- Santé Publique France, Cellule Guyane, Cayenne, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Frédérique Dorleans
- Santé Publique France, Cellule Antilles, French Caribbean Islands; (F.D.); (L.L.)
| | - Lucie Leon
- Santé Publique France, Cellule Antilles, French Caribbean Islands; (F.D.); (L.L.)
| | | | - Didier Musso
- Laboratoires Eurofins Guyane, French Guiana; (A.B.-A.); (D.M.)
| | - Raphaëlle Klitting
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France; (R.K.); (X.d.L.)
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Xavier de Lamballerie
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France; (R.K.); (X.d.L.)
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Anne Lavergne
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Dominique Rousset
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
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3
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Sacchetto L, Bernardi V, Brancini ML, Marques BDC, Negri A, Vasilakis N, Estofolete CF, Nogueira ML. Early insights of dengue virus serotype 3 (DENV-3) re-emergence in São Paulo, Brazil. J Clin Virol 2025; 176:105763. [PMID: 39848015 DOI: 10.1016/j.jcv.2025.105763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 12/04/2024] [Accepted: 01/14/2025] [Indexed: 01/25/2025]
Abstract
BACKGROUND In dengue hyperendemic regions, the evolution of the virus is marked by frequent virus introduction/reintroduction and clade replacement events, occasionally linked to an epidemic outbreak. From 2023 onwards, an increase in the detection of DENV-3 cases has been reported in different regions of Brazil. Thus, molecular and genomic surveillance of circulating DENV strains is crucial for public health preparedness and response efforts for the disease. OBJECTIVES This work aimed to characterize and provide preliminary insights into dengue virus serotype 3 (DENV-3) re-emergence in São Paulo state, Brazil. STUDY DESIGN We conducted active arbovirus molecular surveillance on samples from patients with acute febrile illness combined with next-generation sequencing and phylogenetic analyses. RESULTS We detected and characterized DENV-3 circulation in São Paulo, Brazil, since late 2023. The genomes clustered within genomes recently (2022-2024) identified in Florida, the Caribbean region, and Brazil. CONCLUSIONS Our results demonstrate the resurgence of DENV-3 in the region since 2009, raising concerns about a potential outbreak in regions with a high epidemic history.
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Affiliation(s)
- Lívia Sacchetto
- Departmento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Victória Bernardi
- Departmento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Marini L Brancini
- Departmento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de C Marques
- Departmento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Andreia Negri
- Departamento de Vigilância Epidemiológica, São José do Rio Preto, São Paulo, Brazil
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Cassia F Estofolete
- Departmento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil.
| | - Maurício L Nogueira
- Departmento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
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4
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Zavaleta-Monestel E, Rojas-Chinchilla C, Molina-Sojo P, Murillo-Castro MF, Rojas-Molina JP, Martínez-Vargas E. Impact of Climate Change on the Global Dynamics of Vector-Borne Infectious Diseases: A Narrative Review. Cureus 2025; 17:e77972. [PMID: 39996198 PMCID: PMC11849761 DOI: 10.7759/cureus.77972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2025] [Indexed: 02/26/2025] Open
Abstract
Climate change has significantly altered the dynamics of vector-borne infectious diseases, favoring their proliferation and geographic expansion. Factors such as rising temperatures, the frequency of extreme weather events, and uncontrolled urbanization have increased the incidence of diseases such as dengue, Zika, chikungunya, malaria, and Lyme disease, especially in vulnerable regions with limited infrastructure. This article presents a narrative review based on recent scientific literature (2018-2025) to assess the impact of climate change on vector distribution, co-infections, and control strategies. The evidence collected highlights how changing climate conditions, combined with socioeconomic, political, and demographic factors, exacerbate public health crises and complicate mitigation efforts. It is concluded that facing this challenge requires a comprehensive strategy that combines environmental management, technological innovation, epidemiological surveillance, and community educational programs, promoting a coordinated global response to reduce the associated risks.
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Napit R, Elong Ngono A, Mihindukulasuriya KA, Pradhan A, Khadka B, Shrestha S, Droit L, Paredes A, Karki L, Khatiwada R, Tamang M, Chalise BS, Rawal M, Jha BK, Wang D, Handley SA, Shresta S, Manandhar KD. Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak. BMC Genomics 2024; 25:998. [PMID: 39449117 PMCID: PMC11515306 DOI: 10.1186/s12864-024-10879-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 10/08/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. METHODS AND RESULTS During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+ participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. CONCLUSION These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
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Affiliation(s)
- Rajindra Napit
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Annie Elong Ngono
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Aunji Pradhan
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Binod Khadka
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Smita Shrestha
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lata Karki
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rabindra Khatiwada
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Mamata Tamang
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Bimal Sharma Chalise
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | - Manisha Rawal
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | | | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sujan Shresta
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, USA.
| | - Krishna Das Manandhar
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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6
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Bouzidi HS, Sen S, Piorkowski G, Pezzi L, Ayhan N, Fontaine A, Canivez T, Geulen M, Amaral R, Grard G, Durand GA, de Lamballerie X, Touret F, Klitting R. Genomic surveillance reveals a dengue 2 virus epidemic lineage with a marked decrease in sensitivity to Mosnodenvir. Nat Commun 2024; 15:8667. [PMID: 39384752 PMCID: PMC11464713 DOI: 10.1038/s41467-024-52819-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 09/23/2024] [Indexed: 10/11/2024] Open
Abstract
Dengue fever is the most important arbovirosis for public health, with more than 5 million cases worldwide in 2023. Mosnodenvir is the first anti-dengue compound with very high preclinical pan-serotype activity, currently undergoing phase 2 clinical evaluation. Here, by analyzing dengue virus (DENV) genomes from the 2023-2024 epidemic in the French Caribbean Islands, we show that they all exhibit mutation NS4B:V91A, previously associated with a marked decrease in sensitivity to mosnodenvir in vitro. Using antiviral activity tests on four clinical and reverse-genetic strains, we confirm a marked decrease in mosnodenvir sensitivity for DENV-2 ( > 1000 fold). Finally, combining phylogenetic analysis and experimental testing for resistance, we find that virus lineages with low sensitivity to mosnodenvir due to the V91A mutation likely emerged multiple times over the last 30 years in DENV-2 and DENV-3. These results call for increased genomic surveillance, in particular to track lineages with resistance mutations. These efforts should allow to better assess the activity profile of DENV treatments in development against circulating strains.
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Affiliation(s)
- Hawa Sophia Bouzidi
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Selin Sen
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Laura Pezzi
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Nazli Ayhan
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Albin Fontaine
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Institut de Recherche Biomédicale des Armées (IRBA), Unité de virologie, Marseille, France
| | - Thomas Canivez
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Manon Geulen
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Rayane Amaral
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Guillaume André Durand
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France.
| | - Raphaëlle Klitting
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France.
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France.
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7
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Hill V, Cleemput S, Pereira JS, Gifford RJ, Fonseca V, Tegally H, Brito AF, Ribeiro G, de Souza VC, Brcko IC, Ribeiro IS, De Lima ITT, Slavov SN, Sampaio SC, Elias MC, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, Lima ARJ, Oliveira TD, Grubaugh ND. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLoS Biol 2024; 22:e3002834. [PMID: 39283942 PMCID: PMC11426435 DOI: 10.1371/journal.pbio.3002834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/26/2024] [Indexed: 09/25/2024] Open
Abstract
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we propose adding 2 sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present assignment tools to show that the proposed lineages are useful for regional, national, and subnational discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - James Siqueira Pereira
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, United Kingdom
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Vagner Fonseca
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Gabriela Ribeiro
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Vinicius Carius de Souza
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Isabela Carvalho Brcko
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Igor Santana Ribeiro
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | | | - Svetoslav Nanev Slavov
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Maria Carolina Elias
- Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil
| | - Vi Thuy Tran
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tuyen Huynh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Richard Salvato
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference, Hamburg, Germany
- National Reference Center for Tropical Infectious Diseases. Bernhard, Hamburg, Germany
| | - Tatiana S Gregianini
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Fernanda M S Godinho
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mariana Leguia
- Genomics Laboratory, Pontificia Universidad Católica del Peru, Lima, Peru
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Gaspary Mwanyika
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Applied Sciences, Mbeya University of Science and Technology (MUST), Mbeya, Tanzania
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Roma, Italy
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Luiz C J Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | | | | | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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8
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Lagrave A, Enfissi A, Tirera S, Demar MP, Jaonasoa J, Carod JF, Ramavoson T, Succo T, Carvalho L, Devos S, Dorleans F, Leon L, Berlioz-Arthaud A, Musso D, Lavergne A, Rousset D. Re-Emergence of DENV-3 in French Guiana: Retrospective Analysis of Cases That Circulated in the French Territories of the Americas from the 2000s to the 2023-2024 Outbreak. Viruses 2024; 16:1298. [PMID: 39205272 PMCID: PMC11360160 DOI: 10.3390/v16081298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/04/2024] Open
Abstract
French Guiana experienced an unprecedented dengue epidemic during 2023-2024. Prior to the 2023-2024 outbreak in French Guiana, DENV-3 had not circulated in an epidemic manner since 2005. We therefore studied retrospectively the strains circulating in the French Territories of the Americas (FTA)-French Guiana, Guadeloupe, and Martinique-from the 2000s to the current epidemic. To this end, DENV-3 samples from the collection of the National Reference Center for Arboviruses in French Guiana (NRCA-FG) were selected and sequenced using next-generation sequencing (NGS) based on Oxford Nanopore Technologies, ONT. Phylogenetic analysis showed that (i) the 97 FTA sequences obtained all belonged to genotype III (GIII); (ii) between the 2000s and 2013, the regional circulation of the GIII American-I lineage was the source of the FTA cases through local extinctions and re-introductions; (iii) multiple introductions of lineages of Asian origin appear to be the source of the 2019-2021 epidemic in Martinique and the 2023-2024 epidemic in French Guiana. Genomic surveillance is a key factor in identifying circulating DENV genotypes, monitoring strain evolution, and identifying import events.
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Affiliation(s)
- Alisé Lagrave
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Antoine Enfissi
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Sourakhata Tirera
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Magalie Pierre Demar
- Laboratoire Centre Hospitalier de Cayenne, Cayenne 97300, French Guiana; (M.P.D.); (J.J.)
| | - Jean Jaonasoa
- Laboratoire Centre Hospitalier de Cayenne, Cayenne 97300, French Guiana; (M.P.D.); (J.J.)
| | - Jean-François Carod
- Department of Biology, West French Guiana Hospital Center, Saint-Laurent-du-Maroni 97320, French Guiana; (J.-F.C.); (T.R.)
| | - Tsiriniaina Ramavoson
- Department of Biology, West French Guiana Hospital Center, Saint-Laurent-du-Maroni 97320, French Guiana; (J.-F.C.); (T.R.)
| | - Tiphanie Succo
- Santé Publique France, Cellule Guyane, Cayenne 97300, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Luisiane Carvalho
- Santé Publique France, Cellule Guyane, Cayenne 97300, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Sophie Devos
- Santé Publique France, Cellule Guyane, Cayenne 97300, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Frédérique Dorleans
- Santé Publique France, Cellule Antilles, French Caribbean Islands; (F.D.); (L.L.)
| | - Lucie Leon
- Santé Publique France, Cellule Antilles, French Caribbean Islands; (F.D.); (L.L.)
| | | | - Didier Musso
- Laboratoires Eurofins Guyane, French Guiana; (A.B.-A.); (D.M.)
| | - Anne Lavergne
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Dominique Rousset
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
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9
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Phadungsombat J, Nakayama EE, Shioda T. Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses 2024; 16:1046. [PMID: 39066210 PMCID: PMC11281397 DOI: 10.3390/v16071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics.
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Affiliation(s)
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (J.P.); (E.E.N.)
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10
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Napit R, Ngono AE, Mihindukulasuriya KA, Pradhan A, Khadka B, Shrestha S, Droit L, Paredes A, Karki L, Khatiwada R, Tamang M, Chalise BS, Rawal M, Jha B, Wang D, Handley SA, Shresta S, Manandhar KD. Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597008. [PMID: 38895410 PMCID: PMC11185532 DOI: 10.1101/2024.06.02.597008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. Methods and Results During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1 + participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. Conclusion These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
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11
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Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CBF, Morrison A, Michael SF, Grubaugh ND. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nat Commun 2024; 15:3508. [PMID: 38664380 PMCID: PMC11045810 DOI: 10.1038/s41467-024-47774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.
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Affiliation(s)
- Emma Taylor-Salmon
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Marshall Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Sarah Eysoldt
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Alezaundra Garcia
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Nicadia Gilles
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Andrew Hagy
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Elizabeth Kassens
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Pamela Colarusso
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Amanda Davis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Samantha Baudin
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | - Edhelene Rico
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | | | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Jorge L Muñoz-Jordán
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gilberto A Santiago
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Laura E Adams
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Melanie Spillane
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Bureau for Global Health, United States Agency for International Development, Arlington, VA, USA
| | - Volha Katebi
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert Paulino-Ramírez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Sayira Mueses
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Armando Peguero
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Nelissa Sánchez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Francesca F Norman
- National Referral Unit for Tropical Diseases, Infectious Diseases Department, CIBER de Enfermedades Infecciosas, IRYCIS, Hospital Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Juan-Carlos Galán
- Microbiology Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Section of Infectious Diseases, Boston University School of Medicine, Center for Emerging Infectious Disease Policy and Research, Boston University, and National Emerging Infectious Disease Laboratory, Boston, MA, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Andrea Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA.
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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12
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Klitting R, Piorkowski G, Rousset D, Cabié A, Frumence E, Lagrave A, Lavergne A, Enfissi A, Dos Santos G, Fagour L, Césaire R, Jaffar-Bandjee MC, Traversier N, Gérardin P, Amaral R, Fournier L, Leon L, Dorléans F, Vincent M, Fontaine A, Failloux AB, Ayhan N, Pezzi L, Grard G, Durand GA, de Lamballerie X. 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; 29:2400123. [PMID: 38551097 PMCID: PMC10979529 DOI: 10.2807/1560-7917.es.2024.29.13.2400123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024] Open
Abstract
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.
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Affiliation(s)
- Raphaëlle Klitting
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Géraldine Piorkowski
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Dominique Rousset
- Associated National Reference Center for Arboviruses, Virology unit, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - André Cabié
- Service de Maladies infectieuses et tropicales, CHU de Martinique, Fort-de-France, France
- PCCEI, Université de Montpellier, INSERM, EFS, Montpellier, France
- CIC Antilles Guyane, INSERM CIC1424, Fort-de-France, France
| | - Etienne Frumence
- Associated National Reference Center for Arboviruses, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Alisé Lagrave
- Associated National Reference Center for Arboviruses, Virology unit, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - Anne Lavergne
- Associated National Reference Center for Arboviruses, Virology unit, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - Antoine Enfissi
- Associated National Reference Center for Arboviruses, Virology unit, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - George Dos Santos
- PCCEI, Université de Montpellier, INSERM, EFS, Montpellier, France
- Laboratoire de virologie, CHU de Martinique, Fort-de-France, France
| | - Laurence Fagour
- PCCEI, Université de Montpellier, INSERM, EFS, Montpellier, France
- Laboratoire de virologie, CHU de Martinique, Fort-de-France, France
| | - Raymond Césaire
- Pôle de biologie territoriale, CHU de Guadeloupe, Pointe-à-Pitre, France
- PCCEI, Université de Montpellier, INSERM, EFS, Montpellier, France
| | - Marie-Christine Jaffar-Bandjee
- Associated National Reference Center for Arboviruses, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Nicolas Traversier
- Associated National Reference Center for Arboviruses, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | | | - Rayane Amaral
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | | | - Lucie Leon
- Santé publique France, Cellule Antilles, Saint-Maurice, France
| | | | - Muriel Vincent
- Santé publique France - La Réunion, Saint-Denis, La Réunion, France
| | - Albin Fontaine
- Institut de Recherche Biomédicale des Armées (IRBA), Unité de virologie, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Anna-Bella Failloux
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France
| | - Nazli Ayhan
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Laura Pezzi
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Gilda Grard
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Guillaume André Durand
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Xavier de Lamballerie
- National Reference Center for Arboviruses, Inserm-IRBA, Marseille, France
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
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