1
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Brook CE, Rozins C, Bohl JA, Ahyong V, Chea S, Fahsbender L, Huy R, Lay S, Leang R, Li Y, Lon C, Man S, Oum M, Northrup GR, Oliveira F, Pacheco AR, Parker DM, Young K, Boots M, Tato CM, DeRisi JL, Yek C, Manning JE. Climate, demography, immunology, and virology combine to drive two decades of dengue virus dynamics in Cambodia. Proc Natl Acad Sci U S A 2024; 121:e2318704121. [PMID: 39190356 PMCID: PMC11388344 DOI: 10.1073/pnas.2318704121] [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: 11/03/2023] [Accepted: 07/31/2024] [Indexed: 08/28/2024] Open
Abstract
The incidence of dengue virus disease has increased globally across the past half-century, with highest number of cases ever reported in 2019 and again in 2023. We analyzed climatological, epidemiological, and phylogenomic data to investigate drivers of two decades of dengue in Cambodia, an understudied endemic setting. Using epidemiological models fit to a 19-y dataset, we first demonstrate that climate-driven transmission alone is insufficient to explain three epidemics across the time series. We then use wavelet decomposition to highlight enhanced annual and multiannual synchronicity in dengue cycles between provinces in epidemic years, suggesting a role for climate in homogenizing dynamics across space and time. Assuming reported cases correspond to symptomatic secondary infections, we next use an age-structured catalytic model to estimate a declining force of infection for dengue through time, which elevates the mean age of reported cases in Cambodia. Reported cases in >70-y-old individuals in the 2019 epidemic are best explained when also allowing for waning multitypic immunity and repeat symptomatic infections in older patients. We support this work with phylogenetic analysis of 192 dengue virus (DENV) genomes that we sequenced between 2019 and 2022, which document emergence of DENV-2 Cosmopolitan Genotype-II into Cambodia. This lineage demonstrates phylogenetic homogeneity across wide geographic areas, consistent with invasion behavior and in contrast to high phylogenetic diversity exhibited by endemic DENV-1. Finally, we simulate an age-structured, mechanistic model of dengue dynamics to demonstrate how expansion of an antigenically distinct lineage that evades preexisting multitypic immunity effectively reproduces the older-age infections witnessed in our data.
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Affiliation(s)
- Cara E Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
| | - Carly Rozins
- Department of Science, Technology, and Society, York University, Toronto, ON M3J 1P3, Canada
| | - Jennifer A Bohl
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20892
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Sophana Chea
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
| | | | - Rekol Huy
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh 120801, Cambodia
| | - Sreyngim Lay
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
| | - Rithea Leang
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh 120801, Cambodia
| | - Yimei Li
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
| | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
| | - Somnang Man
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh 120801, Cambodia
| | - Mengheng Oum
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
| | - Graham R Northrup
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Fabiano Oliveira
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20892
| | - Andrea R Pacheco
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
| | - Daniel M Parker
- Department of Population Health and Disease Prevention, University of California, Irvine, CA 92697
- Department of Epidemiology and Biostatistics, University of California, Irvine, CA 92697
| | - Katherine Young
- Department of Biological Sciences, University of Texas, El Paso, TX 79968
| | - Michael Boots
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | | | | | - Christina Yek
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20892
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
| | - Jessica E Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20892
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, NIH, Phnom Penh 120801, Cambodia
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2
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Vi TT, Thi Hue Kien D, Thi Long V, Dui LT, Tuyet Nhu VT, Thi Giang N, Thi Xuan Trang H, Yacoub S, Simmons CP. A serotype-specific and tiled amplicon multiplex PCR method for whole genome sequencing of dengue virus. J Virol Methods 2024; 328:114968. [PMID: 38796133 DOI: 10.1016/j.jviromet.2024.114968] [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: 01/24/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Dengue fever, a mosquito-borne viral disease of significant public health concern in tropical and subtropical regions, is caused by any of the four serotypes of the dengue virus (DENV1-4). Cutting-edge technologies like next-generation sequencing (NGS) are revolutionizing virology, enabling in-depth exploration of DENV's genetic diversity. Here, we present an optimized workflow for full-genome sequencing of DENV 1-4 utilizing tiled amplicon multiplex PCR and Illumina sequencing. Our assay, sequenced on the Illumina MiSeq platform, demonstrates its ability to recover the full-length dengue genome across various viral abundances in clinical specimens with high-quality base coverage. This high quality underscores its suitability for precise examination of intra-host diversity, enriching our understanding of viral evolution and holding potential for improved diagnostic and intervention strategies in regions facing dengue outbreaks.
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Affiliation(s)
- Tran Thuy Vi
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam
| | - Duong Thi Hue Kien
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam.
| | - Vo Thi Long
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam
| | - Le Thi Dui
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam
| | - Vu Thi Tuyet Nhu
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam
| | - Nguyen Thi Giang
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam
| | - Huynh Thi Xuan Trang
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Wellcome Trust Africa Asia Programme, District 5, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, University of Oxford, UK
| | - Cameron P Simmons
- World Mosquito Program, Monash University, Clayton, Melbourne, VIC 3168, Australia
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3
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Agbodzi B, Sado Yousseu FB, Nemg Simo FB, Kumordjie S, Yeboah C, Mosore MT, Bentil RE, Coatsworth HG, Attram N, Nimo-Paintsil S, Fox AT, Bonney JHK, Ampofo W, Dinglasan RR, Sanders T, Wiley MR, Demanou M, Letizia AG. Whole genome sequencing of outbreak strains from 2017 to 2018 reveals an endemic clade of dengue 1 virus in Cameroon. Emerg Microbes Infect 2023; 12:2281352. [PMID: 37933502 PMCID: PMC10732222 DOI: 10.1080/22221751.2023.2281352] [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: 07/23/2023] [Accepted: 11/04/2023] [Indexed: 11/08/2023]
Abstract
Dengue fever is expanding as a global public health threat including countries within Africa. For the past few decades, Cameroon has experienced sporadic cases of arboviral infections including dengue fever. Here, we conducted genomic analyses to investigate the origin and phylogenetic profile of Cameroon DENV-1 outbreak strains and predict the impact of emerging therapeutics on these strains. Bayesian and maximum-likelihood phylogenetic inference approaches were employed in virus evolutionary analyses. An in silico analysis was performed to assess the divergence in immunotherapeutic and vaccine targets in the new genomes. Six complete DENV-1 genomes were generated from 50 samples that met a clinical definition for DENV infection. Phylogenetic analyses revealed that the strains from the current study belong to a sub-lineage of DENV-1 genotype V and form a monophyletic taxon with a 2012 strain from Gabon. The most recent common ancestor (TMRCA) of the Cameroon and Gabon strains was estimated to have existed around 2008. Comparing our sequences to the vaccine strains, 19 and 15 amino acid (aa) substitutions were observed in the immuno-protective prM-E protein segments of the Dengvaxia® and TetraVax-DV-TV003 vaccines, respectively. Epitope mapping revealed mismatches in aa residues at positions E155 and E161 located in the epitope of the human anti-DENV-1 monoclonal antibody HMAb 1F4. The new DENV strains constitute a conserved genomic pool of viruses endemic to the Central African region that needs prospective monitoring to track local viral evolution. Further work is needed to ascertain the performance of emerging therapeutics in DENV strains from the African region.
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Affiliation(s)
- Bright Agbodzi
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | | | | | | | - Clara Yeboah
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | | | | | - Heather G. Coatsworth
- Department of Infectious Diseases & Immunology and Emerging Pathogens Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Naiki Attram
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | | | - Anne T. Fox
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | - Joseph H. K. Bonney
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - William Ampofo
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Rhoel R. Dinglasan
- Department of Infectious Diseases & Immunology and Emerging Pathogens Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Terrel Sanders
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | - Michael R. Wiley
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
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4
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Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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5
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Frutos R, Pliez O, Gavotte L, Devaux CA. There is no "origin" to SARS-CoV-2. ENVIRONMENTAL RESEARCH 2022; 207:112173. [PMID: 34626592 PMCID: PMC8493644 DOI: 10.1016/j.envres.2021.112173] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 05/04/2023]
Abstract
Since the beginning of the COVID-19 pandemic in 2020 caused by SARS-CoV-2, the question of the origin of this virus has been a highly debated issue. Debates have been, and are still, very disputed and often violent between the two main hypotheses: a natural origin through the "spillover" model or a laboratory-leak origin. Tenants of these two options are building arguments often based on the discrepancies of the other theory. The main problem is that it is the initial question of the origin itself which is biased. Charles Darwin demonstrated in 1859 that all species are appearing through a process of evolution, adaptation and selection. There is no determined origin to any animal or plant species, simply an evolutionary and selective process in which chance and environment play a key role. The very same is true for viruses. There is no determined origin to viruses, simply also an evolutionary and selective process in which chance and environment play a key role. However, in the case of viruses the process is slightly more complex because the "environment" is another living organism. Pandemic viruses already circulate in humans prior to the emergence of a disease. They are simply not capable of triggering an epidemic yet. They must evolve in-host, i.e. in-humans, for that. The evolutionary process which gave rise to SARS-CoV-2 is still ongoing with regular emergence of novel variants more adapted than the previous ones. The real relevant question is how these viruses can emerge as pandemic viruses and what the society can do to prevent the future emergence of pandemic viruses.
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Affiliation(s)
| | | | | | - Christian A Devaux
- MEPHI, Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, Marseille, France; CNRS, Marseille, France
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6
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Katzelnick LC, Escoto AC, Huang AT, Garcia-Carreras B, Chowdhury N, Berry IM, Chavez C, Buchy P, Duong V, Dussart P, Gromowski G, Macareo L, Thaisomboonsuk B, Fernandez S, Smith DJ, Jarman R, Whitehead SS, Salje H, Cummings DA. Antigenic evolution of dengue viruses over 20 years. Science 2021; 374:999-1004. [PMID: 34793238 PMCID: PMC8693836 DOI: 10.1126/science.abk0058] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Infection with one of dengue viruses 1 to 4 (DENV1-4) induces protective antibodies against homotypic infection. However, a notable feature of dengue viruses is the ability to use preexisting heterotypic antibodies to infect Fcγ receptor–bearing immune cells, leading to higher viral load and immunopathological events that augment disease. We tracked the antigenic dynamics of each DENV serotype by using 1944 sequenced isolates from Bangkok, Thailand, between 1994 and 2014 (348 strains), in comparison with regional and global DENV antigenic diversity (64 strains). Over the course of 20 years, the Thailand DENV serotypes gradually evolved away from one another. However, for brief periods, the serotypes increased in similarity, with corresponding changes in epidemic magnitude. Antigenic evolution within a genotype involved a trade-off between two types of antigenic change (within-serotype and between-serotype), whereas genotype replacement resulted in antigenic change away from all serotypes. These findings provide insights into theorized dynamics in antigenic evolution.
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Affiliation(s)
- Leah C. Katzelnick
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Ana Coello Escoto
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Angkana T. Huang
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Bernardo Garcia-Carreras
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Nayeem Chowdhury
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Chris Chavez
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Philippe Buchy
- GlaxoSmithKline (GSK) Vaccines, 637421 Singapore, Singapore
| | - Veasna Duong
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh 12201, Cambodia
| | - Philippe Dussart
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh 12201, Cambodia
| | - Gregory Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Louis Macareo
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Stephen S. Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Henrik Salje
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Derek A.T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
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7
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Calvez E, Bounmany P, Balière C, Somlor S, Viengphouthong S, Xaybounsou T, Keosenhom S, Fangkham K, Brey PT, Caro V, Lacoste V, Grandadam M. Using Background Sequencing Data to Anticipate DENV-1 Circulation in the Lao PDR. Microorganisms 2021; 9:microorganisms9112263. [PMID: 34835389 PMCID: PMC8617722 DOI: 10.3390/microorganisms9112263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Since its first detection in 1979, dengue fever has been considered a major public health issue in the Lao People’s Democratic Republic (PDR). Dengue virus (DENV) serotype 1 was the cause of an epidemic in 2010–2011. Between 2012 and 2020, major outbreaks due successively to DENV-3, DENV-4 and recently DENV-2 have been recorded. However, DENV-1 still co-circulated in the country over this period. Here, we summarize epidemiological and molecular data of DENV-1 between 2016 and 2020 in the Lao PDR. Our data highlight the continuous circulation of DENV-1 in the country at levels ranging from 16% to 22% among serotyping tests. In addition, the phylogenetic analysis has revealed the circulation of DENV-1 genotype I at least since 2008 with a co-circulation of different clusters. Sequence data support independent DENV-1 introductions in the Lao PDR correlated with an active circulation of this serotype at the regional level in Southeast Asia. The maintenance of DENV-1 circulation over the last ten years supports a low level of immunity against this serotype within the Lao population. Thereby, the risk of a DENV-1 epidemic cannot be ruled out in the future, and this emphasizes the importance of maintaining an integrated surveillance approach to prevent major outbreaks.
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Affiliation(s)
- Elodie Calvez
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
- Correspondence:
| | - Phaithong Bounmany
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Charlotte Balière
- Environment and Infectious Risks Unit, Institut Pasteur, 75015 Paris, France; (C.B.); (V.C.)
| | - Somphavanh Somlor
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Souksakhone Viengphouthong
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Thonglakhone Xaybounsou
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Sitsana Keosenhom
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Kitphithak Fangkham
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
- Lao Army Institute for Preventive Medicine, Vientiane 01030, Laos
| | - Paul T. Brey
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane 01030, Laos;
| | - Valérie Caro
- Environment and Infectious Risks Unit, Institut Pasteur, 75015 Paris, France; (C.B.); (V.C.)
| | - Vincent Lacoste
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Marc Grandadam
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
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8
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O'Connor O, Ou TP, Aubry F, Dabo S, Russet S, Girault D, In S, Minier M, Lequime S, Hoem T, Boyer S, Dussart P, Pocquet N, Burtet-Sarramegna V, Lambrechts L, Duong V, Dupont-Rouzeyrol M. Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings. Emerg Microbes Infect 2021; 10:1346-1357. [PMID: 34139961 PMCID: PMC8259877 DOI: 10.1080/22221751.2021.1944789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dengue virus (DENV) evolutionary dynamics are characterized by frequent DENV genotype/lineage replacements, potentially associated with changes in disease severity and human immunity. New Caledonia (NC) and Cambodia, two contrasted epidemiological settings, respectively experienced a DENV-1 genotype IV to I replacement in 2012 and a DENV-1 genotype I lineage 3–4 replacement in 2005–2007, both followed by a massive dengue outbreak. However, their underlying evolutionary drivers have not been elucidated. Here, we tested the hypothesis that these genotype/lineage switches reflected a higher transmission fitness of the replacing DENV genotype/lineage in the mosquito vector using in vivo competition experiments. For this purpose, field-derived Aedes aegypti from NC and Cambodia were orally challenged with epidemiologically relevant pairs of four DENV-1 genotype I and IV strains from NC or four DENV-1 genotype I lineage 3 and 4 strains from Cambodia, respectively. The relative transmission fitness of each DENV-1 genotype/lineage was measured by quantitative RT–PCR for infection, dissemination, and transmission rates. Results showed a clear transmission fitness advantage of the replacing DENV-1 genotype I from NC within the vector. A similar but more subtle pattern was observed for the DENV-1 lineage 4 replacement in Cambodia. Our results support the hypothesis that vector-driven selection contributed to the DENV-1 genotype/lineage replacements in these two contrasted epidemiological settings, and reinforce the idea that natural selection taking place within the mosquito vector plays an important role in DENV short-term evolutionary dynamics.
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Affiliation(s)
- Olivia O'Connor
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Tey Putita Ou
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sylvie Russet
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Dominique Girault
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Saraden In
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Marine Minier
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Sebastian Lequime
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Thavry Hoem
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Sébastien Boyer
- Medical Entomology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Nicolas Pocquet
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Valérie Burtet-Sarramegna
- Institute For Exact and Applied Sciences, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Veasna Duong
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Myrielle Dupont-Rouzeyrol
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
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9
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Ma M, Wu S, He Z, Yuan L, Bai Z, Jiang L, Marshall J, Lu J, Yang Z, Jing Q. New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China. Parasit Vectors 2021; 14:126. [PMID: 33639996 PMCID: PMC7910771 DOI: 10.1186/s13071-021-04631-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/06/2021] [Indexed: 11/26/2022] Open
Abstract
Background Dengue fever is a mosquito-borne infectious disease that has caused major health problems. Variations in dengue virus (DENV) genes are important features of epidemic outbreaks. However, the associations of DENV genes with epidemic potential have not been extensively examined. Here, we assessed new genotype invasion of DENV-1 isolated from Guangzhou in China to evaluate associations with epidemic outbreaks. Methodology/principal findings We used DENV-1 strains isolated from sera of dengue cases from 2002 to 2016 in Guangzhou for complete genome sequencing. A neighbor-joining phylogenetic tree was constructed to elucidate the genotype characteristics and determine if new genotype invasion was correlated with major outbreaks. In our study, a new genotype invasion event was observed during each significant outbreak period in 2002–2003, 2006–2007, and 2013–2014. Genotype II was the main epidemic genotype in 2003 and before. Invasion of genotype I in 2006 caused an unusual outbreak with 765 cases (relative risk [RR] = 16.24, 95% confidence interval [CI] 12.41–21.25). At the middle and late stages of the 2013 outbreak, genotype III was introduced to Guangzhou as a new genotype invasion responsible for 37,340 cases with RR 541.73 (95% CI 417.78–702.45), after which genotypes I and III began co-circulating. Base mutations occurred after new genotype invasion, and the gene sequence of NS3 protein had the lowest average similarity ratio (99.82%), followed by the gene sequence of E protein (99.86%), as compared to the 2013 strain. Conclusions/significance Genotype replacement and co-circulation of multiple DENV-1 genotypes were observed. New genotype invasion was highly correlated with local unusual outbreaks. In addition to DENV-1 genotype I in the unprecedented outbreak in 2014, new genotype invasion by DENV-1 genotype III occurred in Guangzhou.![]()
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Affiliation(s)
- Mengmeng Ma
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - Sean Wu
- Department of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Zhenjian He
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Lihong Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, People's Republic of China
| | - Zhijun Bai
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - Liyun Jiang
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - John Marshall
- Department of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Jiahai Lu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Zhicong Yang
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - Qinlong Jing
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China.
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10
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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11
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Genomic analysis of dengue virus serotype 1 (DENV-1) genotypes from Surabaya, Indonesia. Virus Genes 2018; 54:461-465. [PMID: 29616396 DOI: 10.1007/s11262-018-1558-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Dengue has caused a significant public health impact globally. With the diverse genetic of the causative viruses, analysis of dengue virus (DENV) genomes is important to supplement epidemiological data with information that can be used to reconstruct the history of epidemics in time and space. We have reported the clinical and virological characteristics of dengue in Surabaya, Indonesia and revealed the presence of all four DENV serotypes and the predominance of DENV-1. The further classification of Surabaya DENV-1 into two different genotypes warrants in-depth genomic analysis to study the dynamics of both genotypes and their contribution to virus evolution, virus transmission, and disease. We performed full-length genome sequencing to nine isolates' representatives from DENV-1 Genotype I and Genotype IV. Phylogenetic and evolutionary analyses suggested the more recent introduction of Genotype I viruses compared to the more endemic Genotype IV. Comparative analysis of Surabaya DENV-1 genomes and other sequences available publicly revealed that the majority of the DENV-1 codons were under strong purifying selection, while seven codon sites identified to be under positive selection. We highlight a unique codon site under the positive pressure in the NS1 gene of DENV-1. Our results provide additional genomic data of DENV from Indonesia that may contribute to the better understanding of dengue disease dynamics.
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12
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Mulyatno KC, Kotaki T, Yotopranoto S, Rohmah EA, Churotin S, Sucipto TH, Amarullah IH, Wardhani P, Soegijanto S, Kameoka M. Detection and Serotyping of Dengue Viruses in Aedes aegypti and Aedes albopictus (Diptera: Culicidae) Collected in Surabaya, Indonesia from 2008 to 2015. Jpn J Infect Dis 2017; 71:58-61. [PMID: 29093315 DOI: 10.7883/yoken.jjid.2017.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aedes aegypti and Aedes albopictus are the primary and secondary vectors, respectively, of dengue, the most important arboviral disease in the world. The aim of this study was to detect and serotype dengue viruses (DENV) in the vectors Ae. aegypti and Ae. albopictus in Surabaya, Indonesia. Between 2008 and 2015, 16,605 Aedes mosquitoes were collected in 15 sub-districts of Surabaya. Ae. aegypti was dominant (90.9%), whereas few Ae. albopictus were collected (9.1%). A total of 330 pools of adult Aedes mosquitoes were subjected to the serotyping of DENV by RT-PCR. DENV-1 (52.3%) was the most frequently detected serotype, followed by DENV-2 (40.3%), DENV-4 (4.6%), and DENV-3 (2.8%). The average minimum infection rate for Ae. aegypti in various sub-districts of Surabaya was 7.2 per 1,000 mosquitoes, while that for Ae. albopictus was 0.7 per 1,000 mosquitoes. The results showed that the predominantly circulating DENV serotype in mosquitoes continuously shifted from DENV-2 (2008) to DENV-1 (2009-2012), to DENV-2 again (2013-2014), and then back to DENV-1 (2015). The circulating DENV serotypes in mosquitoes were generally consistent with those in humans. Therefore, the surveillance of infected mosquitoes with DENV might provide an early warning sign for the risk of future dengue outbreaks.
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Affiliation(s)
- Kris Cahyo Mulyatno
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University.,Institute of Tropical Disease, Airlangga University
| | - Tomohiro Kotaki
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University.,Center of Infectious Diseases, Kobe University Graduate School of Medicine.,Department of International Health, Kobe University Graduate School of Health Sciences
| | - Subagyo Yotopranoto
- Institute of Tropical Disease, Airlangga University.,Faculty of Medicine, Airlangga University
| | | | - Siti Churotin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University.,Institute of Tropical Disease, Airlangga University
| | - Teguh Hari Sucipto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University.,Institute of Tropical Disease, Airlangga University
| | | | - Puspa Wardhani
- Institute of Tropical Disease, Airlangga University.,Faculty of Medicine, Airlangga University
| | - Soegeng Soegijanto
- Institute of Tropical Disease, Airlangga University.,Faculty of Medicine, Airlangga University
| | - Masanori Kameoka
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University.,Center of Infectious Diseases, Kobe University Graduate School of Medicine.,Department of International Health, Kobe University Graduate School of Health Sciences
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13
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Andrade CC, Young KI, Johnson WL, Villa ME, Buraczyk CA, Messer WB, Hanley KA. Rise and fall of vector infectivity during sequential strain displacements by mosquito-borne dengue virus. J Evol Biol 2016; 29:2205-2218. [PMID: 27500505 DOI: 10.1111/jeb.12939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/31/2022]
Abstract
Each of the four serotypes of mosquito-borne dengue virus (DENV-1-4) comprises multiple, genetically distinct strains. Competitive displacement between strains within a serotype is a common feature of DENV epidemiology and can trigger outbreaks of dengue disease. We investigated the mechanisms underlying two sequential displacements by DENV-3 strains in Sri Lanka that each coincided with abrupt increases in dengue haemorrhagic fever (DHF) incidence. First, the post-DHF strain displaced the pre-DHF strain in the 1980s. We have previously shown that post-DHF is more infectious than pre-DHF for the major DENV vector, Aedes aegypti. Then, the ultra-DHF strain evolved in situ from post-DHF and displaced its ancestor in the 2000s. We predicted that ultra-DHF would be more infectious for Ae. aegypti than post-DHF but found that ultra-DHF infected a significantly lower percentage of mosquitoes than post-DHF. We therefore hypothesized that ultra-DHF had effected displacement by disseminating in Ae. aegypti more rapidly than post-DHF, but this was not borne out by a time course of mosquito infection. To elucidate the mechanisms that shape these virus-vector interactions, we tested the impact of RNA interference (RNAi), the principal mosquito defence against DENV, on replication of each of the three DENV strains. Replication of all strains was similar in mosquito cells with dysfunctional RNAi, but in cells with functional RNAi, replication of pre-DHF was significantly suppressed relative to the other two strains. Thus, differences in susceptibility to RNAi may account for the differences in mosquito infectivity between pre-DHF and post-DHF, but other mechanisms underlie the difference between post-DHF and ultra-DHF.
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Affiliation(s)
- C C Andrade
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - K I Young
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - W L Johnson
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - M E Villa
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - C A Buraczyk
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - W B Messer
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, OR, USA.,Division of Infectious Diseases, Department of Medicine, Oregon Health and Sciences University, Portland, OR, USA
| | - K A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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14
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Vazeille M, Gaborit P, Mousson L, Girod R, Failloux AB. Competitive advantage of a dengue 4 virus when co-infecting the mosquito Aedes aegypti with a dengue 1 virus. BMC Infect Dis 2016; 16:318. [PMID: 27390932 PMCID: PMC4939008 DOI: 10.1186/s12879-016-1666-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/14/2016] [Indexed: 01/30/2023] Open
Abstract
Background Dengue viruses (DENV) are comprised in four related serotypes (DENV-1 to 4) and are critically important arboviral pathogens affecting human populations in the tropics. South American countries have seen the reemergence of DENV since the 1970’s associated with the progressive re-infestation by the mosquito vector, Aedes aegypti. In French Guiana, DENV is now endemic with the co-circulation of different serotypes resulting in viral epidemics. Between 2009 and 2010, a predominant serotype change occurred from DENV-1 to DENV-4 suggesting a competitive displacement. The aim of the present study was to evaluate the potential role of the mosquito in the selection of the new epidemic serotype. Methods To test this hypothesis of competitive displacement of one serotype by another in the mosquito vector, we performed mono- and co-infections of local Ae. aegypti collected during the inter-epidemic period with both viral autochthonous epidemic serotypes and compared infection, dissemination and transmission rates. We performed oral artificial infections of F1 populations in BSL-3 conditions and analyzed infection, dissemination and transmission rates. Results When two populations of Ae. aegypti from French Guiana were infected with either serotype, no significant differences in dissemination and transmission were observed between DENV-1 and DENV-4. However, in co-infection experiments, a strong competitive advantage for DENV-4 was seen at the midgut level leading to a much higher dissemination of this serotype. Furthermore only DENV-4 was present in Ae. aegypti saliva and therefore able to be transmitted. Conclusions In an endemic context, mosquito vectors may be infected by several DENV serotypes. Our results suggest a possible competition between serotypes at the midgut level in co-infected mosquitoes leading to a drastically different transmission potential and, in this case, favoring the competitive displacement of DENV-1 by DENV-4. This phenomenon was observed despite a similar replicative fitness in mono-infections conditions.
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Affiliation(s)
- Marie Vazeille
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Pascal Gaborit
- Medical Entomology Unit, Institut Pasteur of French Guiana, Cayenne, French Guiana
| | - Laurence Mousson
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur of French Guiana, Cayenne, French Guiana
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France.
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15
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Kim Lien PT, Briant L, Tang TB, Trang BM, Gavotte L, Cornillot E, Duoc VT, Duong TN, Frutos R, Nga PT. Surveillance of dengue and chikungunya infection in Dong Thap, Vietnam: A 13-month study. ASIAN PAC J TROP MED 2015; 9:39-43. [PMID: 26851784 DOI: 10.1016/j.apjtm.2015.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/20/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE To establish a surveillance in Dong Thap, at the border with Cambodia by assessing the presence of DENV serotypes and CHIKV among patients hospitalized at Dong Thap general hospital. METHODS Cross-sectional descriptive analysis was conducted on a cohort of 131 patients hospitalized with acute fever and symptoms compatible with dengue or chikungunya. The study was conducted from January 2012 to February 2013. The full clinical picture was established as well as serological and molecular detection. Serological analysis was sequentially performed on blood samples collected on admission and an average of seven days after admission. The detection of IgM antibody to DENV was performed by IgM capture ELISA and the detection of DENV and CHIKV RNA was done by reverse-transcription multiplex PCR. RESULTS 101 patients out of 131 (77%) were confirmed with dengue. All four dengue serotypes were detected with a predominance of DENV2 and DENV4. No chikungunya infection was detected although reported in neighboring Cambodia. A differential efficiency of serological dengue detection was observed. Efficiency was 29% upon admission and 53% after seven days on the same patients. 30 patients out of 131 (23%) were negative with both DENV and CHIKV. CONCLUSIONS Dengue is at risk of being underestimated and chikungunya is not systematically detected. Changes in detection and surveillance procedures are therefore discussed to increase efficiency of dengue detection and continue the monitoring the emergence of CHIKV in Dong Thap province and in Vietnam.
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Affiliation(s)
- Pham Thi Kim Lien
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam; University of Montpellier, CEMIPAI-CPBS, UMR 5236, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Laurence Briant
- University of Montpellier, CEMIPAI-CPBS, UMR 5236, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Truong Ba Tang
- Department of Biology, Dong Thap General Hospital, 144, Mai Van Khai, My Xuan, 870000 Cao Lanh, Dong Thap, Viet Nam
| | - Bui Minh Trang
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam
| | - Laurent Gavotte
- University of Montpellier, ISEM, CC063, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Emmanuel Cornillot
- University of Montpellier, CEMIPAI-CPBS, UMR 5236, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Vu Trong Duoc
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam
| | - Roger Frutos
- University of Montpellier, CEMIPAI-CPBS, UMR 5236, 1919, route de Mende, 34293 Montpellier Cedex 5, France; Cirad, TA-A17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
| | - Phan Thi Nga
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam.
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16
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Naughtin M, Sareth R, Sentilhes AC, Vong S, Joffret ML, Cornillot E, Deubel V, Delpeyroux F, Frutos R, Buchy P. Genetic diversity of human rhinoviruses in Cambodia during a three-year period reveals novel genetic types. INFECTION GENETICS AND EVOLUTION 2015; 35:42-9. [PMID: 26231720 PMCID: PMC7105975 DOI: 10.1016/j.meegid.2015.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/06/2022]
Abstract
Five novel genotypes are identified based on VP1 sequences. Co-infections with other viruses is demonstrated. The genome of rhinoviruses is saturated. A novel classification system considering amino acid sequences should be developed.
Acute respiratory viral infections are a major cause of morbidity during early childhood in developing countries. Human rhinoviruses are the most frequent cause of upper respiratory tract infections in humans, which can range in severity from asymptomatic to clinically severe disease. In this study we collected 4170 nasopharyngeal swabs from patients hospitalised with influenza-like illness in two Cambodian provincial hospitals between 2007 and 2010. Samples were screened for 18 respiratory viruses using 5 multiplex PCRs. A total of 11.2% of samples tested positive for human rhinoviruses (HRV). VP4/2 and VP1 regions were amplified and sequenced to study the distribution of rhinoviruses genotypes and species in Cambodia during this three-year period. Five novel genotypes, 2 species A, 2 species B and 1 species C were identified based on VP1 sequences. Co-infections with other viruses were demonstrated.
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Affiliation(s)
- Monica Naughtin
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | - Rith Sareth
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | | | - Sirenda Vong
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | - Marie-Line Joffret
- Institut Pasteur, Biologie des Virus Entériques, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM U994, Institut National de Santé et de La Recherche Médicale, Paris, France
| | - Emmanuel Cornillot
- CEMIPAI, CPBS, UMR 5236, CNRS-UM1-UM2, 1919 route de Mende, 34293 Montpellier Cedex 5, France
| | - Vincent Deubel
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | - Francis Delpeyroux
- Institut Pasteur, Biologie des Virus Entériques, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM U994, Institut National de Santé et de La Recherche Médicale, Paris, France
| | - Roger Frutos
- CEMIPAI, CPBS, UMR 5236, CNRS-UM1-UM2, 1919 route de Mende, 34293 Montpellier Cedex 5, France; Cirad, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
| | - Philippe Buchy
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia.
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de Bruycker-Nogueira F, Nogueira RMR, Faria NRDC, Simões JBS, Nunes PCG, de Filippis AMB, dos Santos FB. Insights of the genetic diversity of DENV-1 detected in Brazil in 25 years: Analysis of the envelope domain III allows lineages characterization. INFECTION GENETICS AND EVOLUTION 2015; 34:126-36. [PMID: 26160541 DOI: 10.1016/j.meegid.2015.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 01/03/2023]
Abstract
Dengue virus type 1 (DENV-1) was first isolated in Brazil in 1986 in the state of Rio de Janeiro (RJ) and during 25years, this serotype emerged and re-emerged causing explosive epidemics in the country. Here, we aimed to present the phylogeny and molecular characterization based on the envelope gene (E) of DENV-1 (n=48) isolated during epidemics occurred from 1986 to 2011. Six full coding region genomes of DENV-1 were fully sequenced and possible genomic recombination events were analyzed. The results showed that the Brazilian DENV-1 isolates analyzed belong to genotype V (Americas/Africa), but grouping into distinct clades. Three groups were identified, one dating from 1986 to 2002 (lineage 1a), a second group isolated from 2009 to 2011 and a representative strain isolated in 2002 (lineage 2), and a group of strains isolated from 2010 to 2011 (lineage 1b). The lineages 1a and 1b were more closely related to the American strains, while lineage 2 to the Asian strains. Amino acids (aa) substitutions were observed in the domains I and III of the E protein and were associated to the lineages segregation. A substitution on E297 differentiated the lineage 1a from the lineages 1b and 2. Substitutions on E338, E394 (domain III), E428 and E436 (stem region) differentiated lineages 1a, 1b and 2. With the exception of the C gene, all the others genes analyzed allowed the DENV-1 classification into the distinct genotypes. Interestingly, the E gene's domain III and stem regions alone were able to characterize the distinct lineages, as observed by the analysis of the entire E gene and the complete coding region. No recombinant events were detected, but a strain belonging to lineage 1a was closely related to a known recombinant strain (AF513110/BR/2001).
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Affiliation(s)
| | - Rita Maria Ribeiro Nogueira
- Laboratory of Flavivirus, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
| | | | | | | | - Ana Maria Bispo de Filippis
- Laboratory of Flavivirus, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
| | - Flávia Barreto dos Santos
- Laboratory of Flavivirus, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil.
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18
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Pereira GV, Freitas VA, Oliveira HS, Oliveira LCA, Belchior JC. A photocatalytic process for the eradication of dengue through ˙OH generation in the presence of sunlight and iron oxide. RSC Adv 2014. [DOI: 10.1039/c4ra13435d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Dash PK, Sharma S, Soni M, Agarwal A, Sahni AK, Parida M. Complete genome sequencing and evolutionary phylogeography analysis of Indian isolates of Dengue virus type 1. Virus Res 2014; 195:124-34. [PMID: 25197040 DOI: 10.1016/j.virusres.2014.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022]
Abstract
Dengue is now hyper-endemic in most parts of south and southeast Asia including India. The northern India particularly national capital New Delhi witnessed major Dengue outbreaks with Dengue virus type 1 (DENV-1) as the dominant serotype since last five years. This study was initiated to decipher the complete genome information of recently circulating DENV-1 (2009-2011) along with the prototype Indian DENV-1, isolated in 1956. Further extensive ML phylogenetic and Bayesian phylogeography analysis was carried out to investigate the evolution of this virus and understand its spatiotemporal diffusion across the globe. The complete genome analysis revealed deletion of a unique 21-nucleotide stretch in the 3' un-translated region of recent Indian DENV-1. The north Indian DENV-1 revealed up to 5.2% nucleotide sequence difference compared to recent isolates from southern India. Selection pressure analysis revealed positive selection in few amino acid sites of both structural and non-structural proteins. The molecular phylogeny classified the Indian DENV-1 into genotype III, which is also known as cosmopolitan genotype. The northern and southern Indian DENV-1 were grouped into distinct clades. The molecular clock analysis estimated a mean evolutionary rate of 7.08×10(-4) substitutions/site/year for cosmopolitan genotype. The phylogeography analysis revealed that the cosmopolitan genotype DENV-1 originated ∼1938 in India and subsequently spread globally. The diffusion of virus from India to Caribbean and South America was confirmed through SPREAD analysis. This study also confirmed the temporal displacement of different clades of DENV-1 in India over last five decades.
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Affiliation(s)
- Paban Kumar Dash
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India.
| | - Shashi Sharma
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Manisha Soni
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Ankita Agarwal
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Ajay Kumar Sahni
- Department of Microbiology & Pathology, Army Research & Referral (R&R) Hospital, Delhi Cantt, Delhi, India
| | - Manmohan Parida
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
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Satoto TBT, Umniyati SR, Astuti FD, Wijayanti N, Gavotte L, Devaux C, Frutos R. Assessment of vertical dengue virus transmission in Aedes aegypti and serotype prevalence in Bantul, Indonesia. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014. [DOI: 10.1016/s2222-1808(14)60677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Villabona-Arenas CJ, Zanotto PMDA. Worldwide spread of Dengue virus type 1. PLoS One 2013; 8:e62649. [PMID: 23675416 PMCID: PMC3652851 DOI: 10.1371/journal.pone.0062649] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/24/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND DENV-1 is one of the four viral serotypes that causes Dengue, the most common mosquito-borne viral disease of humans. The prevalence of these viruses has grown in recent decades and is now present in more than 100 countries. Limited studies document the spread of DENV-1 over the world despite its importance for human health. METHODOLOGY/PRINCIPAL FINDINGS We used representative DENV-1 envelope gene sequences to unravel the dynamics of viral diffusion under a Bayesian phylogeographic approach. Data included strains from 45 distinct geographic locations isolated from 1944 to 2009. The estimated mean rate of nucleotide substitution was 6.56 × 10⁻⁴ substitutions/site/year. The larger genotypes (I, IV and V) had a distinctive phylogenetic structure and since 1990 they experienced effective population size oscillations. Thailand and Indonesia represented the main sources of strains for neighboring countries. Besides, Asia broadcast lineages into the Americas and the Pacific region that diverged in isolation. Also, a transmission network analysis revealed the pivotal role of Indochina in the global diffusion of DENV-1 and of the Caribbean in the diffusion over the Americas. CONCLUSIONS/SIGNIFICANCE The study summarizes the spatiotemporal DENV-1 worldwide spread that may help disease control.
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Affiliation(s)
- Christian Julián Villabona-Arenas
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
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OhAinle M, Balmaseda A, Macalalad AR, Tellez Y, Zody MC, Saborío S, Nuñez A, Lennon NJ, Birren BW, Gordon A, Henn MR, Harris E. Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity. Sci Transl Med 2012; 3:114ra128. [PMID: 22190239 DOI: 10.1126/scitranslmed.3003084] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The rapid spread of dengue is a worldwide public health problem. In two clinical studies of dengue in Managua, Nicaragua, we observed an abrupt increase in disease severity across several epidemic seasons of dengue virus serotype 2 (DENV-2) transmission. Waning DENV-1 immunity appeared to increase the risk of severe disease in subsequent DENV-2 infections after a period of cross-protection. The increase in severity coincided with replacement of the Asian/American DENV-2 NI-1 clade with a new virus clade, NI-2B. In vitro analyses of viral isolates from the two clades and analysis of viremia in patient blood samples support the emergence of a fitter virus in later, relative to earlier, epidemic seasons. In addition, the NI-1 clade of viruses was more virulent specifically in children who were immune to DENV-1, whereas DENV-3 immunity was associated with more severe disease among NI-2B infections. Our data demonstrate that the complex interaction between viral genetics and population dynamics of serotype-specific immunity contributes to the risk of severe dengue disease. Furthermore, this work provides insights into viral evolution and the interaction between viral and immunological determinants of viral fitness and virulence.
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Affiliation(s)
- Molly OhAinle
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-7354, USA
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Dengue-1 virus clade replacement in Thailand associated with enhanced mosquito transmission. J Virol 2011; 86:1853-61. [PMID: 22130539 DOI: 10.1128/jvi.06458-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dengue viruses (DENV) are characterized by extensive genetic diversity and can be organized in multiple, genetically distinct lineages that arise and die out on a regular basis in regions where dengue is endemic. A fundamental question for understanding DENV evolution is the relative extent to which stochastic processes (genetic drift) and natural selection acting on fitness differences among lineages contribute to lineage diversity and turnover. Here, we used a set of recently collected and archived low-passage DENV-1 isolates from Thailand to examine the role of mosquito vector-virus interactions in DENV evolution. By comparing the ability of 23 viruses isolated on different dates between 1985 and 2009 to be transmitted by a present-day Aedes aegypti population from Thailand, we found that a major clade replacement event in the mid-1990s was associated with virus isolates exhibiting increased titers in the vector's hemocoel, which is predicted to result in a higher probability of transmission. This finding is consistent with the hypothesis that selection for enhanced transmission by mosquitoes is a possible mechanism underlying major DENV clade replacement events. There was significant variation in transmission potential among isolates within each clade, indicating that in addition to vector-driven selection, other evolutionary forces act to maintain viral genetic diversity. We conclude that occasional adaptive processes involving the mosquito vector can drive major DENV lineage replacement events.
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