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Luciani L, Combe P, Touret F, Gazin C, Klitting R, Pezzi L, Thirion L, Charrel R, Grard G, de Lamballerie X, Nougairède A. Broad-spectrum dengue virus detection using the commercial RealStar dengue RT-PCR kit 3.0 (Altona) and an in-house combined real-time RT-PCR assay. Heliyon 2024; 10:e31252. [PMID: 38803933 PMCID: PMC11128986 DOI: 10.1016/j.heliyon.2024.e31252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
In endemic areas, the genetic diversity among co-circulating dengue virus (DENV) strains is considerable and new, highly divergent strains are identified on a regular basis. It is thus critical to ensure that molecular diagnostic tools effectively detect virus genomes even in case of important genetic variation. Here, we tested both the pan-DENV detection capacity and the limit of detection of two real-time RT-PCR assays: (i) the commercial RealStar Altona 3.0 system and (ii) a laboratory developed test (LDT) combining two RT-PCR systems in a single reaction tube (DenAllDUO). We used a panel of DENV strains representative of the genetic diversity within DENV species, combined with three in vitro transcribed RNAs as surrogates for unavailable strains corresponding to recently discovered strains with substantial genetic divergence: DENV serotype 1 (DENV-1) Brun2014, DENV-2 QML22 and DENV-4 DKE121. Both systems (i) targeted the genome 3' untranslated region, (ii) displayed a broad detection spectrum, encompassing most of DENV species diversity, and (iii) detected the three aforementioned divergent strains. DenAllDUO detected all the strains tested, whereas the RealStar system failed to detect strains from DENV-4 genotype III. Altogether, our findings support the value of these two RT-PCR systems as part of the Dengue diagnostic arsenal.
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Affiliation(s)
- Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Pierre Combe
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Céline Gazin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Raphaëlle Klitting
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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2
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Dieng I, Sagne SN, Ndiaye M, Barry MA, Talla C, Mhamadi M, Balde D, Toure CT, Diop B, Sall AA, Fall G, Loucoubar C, Faye O, Faye O. Detection of a human case of dengue virus 2 belonging to the sylvatic genotype during routine surveillance of fever in Kolda, Senegal, in 2021. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1050880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dengue virus 2 (DENV-2) was detected in a febrile patient living in Saré Yoba in the Kolda region of southern Senegal. Phylogenetic analysis based on the full coding region revealed that the virus belongs to the DENV-2 sylvatic genotype and is closely related to a strain (JF260983/99.66% identity) detected in Spain in a tourist who traveled to Guinea-Bissau (which borders the Kolda region) in 2009. This highlights a potential recent under-reported circulation of sylvatic dengue in the southern part of Senegal and calls for reinforced integrated surveillance among humans, non-human primates, and arboreal mosquitoes through a one-health approach.
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3
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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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4
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Stica CJ, Barrero RA, Murray RZ, Devine GJ, Phillips MJ, Frentiu FD. Global Evolutionary History and Dynamics of Dengue Viruses Inferred from Whole Genome Sequences. Viruses 2022; 14:v14040703. [PMID: 35458433 PMCID: PMC9030598 DOI: 10.3390/v14040703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 12/20/2022] Open
Abstract
Dengue is an arboviral disease caused by dengue virus (DENV), leading to approximately 25,000 deaths/year and with over 40% of the world’s population at risk. Increased international travel and trade, poorly regulated urban expansion, and warming global temperatures have expanded the geographic range and incidence of the virus in recent decades. This study used phylogenetic and selection pressure analyses to investigate trends in DENV evolution, using whole genome coding sequences from publicly available databases alongside newly sequenced isolates collected between 1963–1997 from Southeast Asia and the Pacific. Results revealed very similar phylogenetic relationships when using the envelope gene and the whole genome coding sequences. Although DENV evolution is predominantly driven by negative selection, a number of amino acid sites undergoing positive selection were found across the genome, with the majority located in the envelope and NS5 genes. Some genotypes appear to be diversifying faster than others within each serotype. The results from this research improve our understanding of DENV evolution, with implications for disease control efforts such as Wolbachia-based biocontrol and vaccine design.
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Affiliation(s)
- Caleb J. Stica
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, 300 Herston Road, Herston, QLD 4006, Australia;
| | - Roberto A. Barrero
- eResearch Office, Division of Research and Innovation, Queensland University of Technology, P Block, 2 George Street, Brisbane, QLD 4000, Australia;
| | - Rachael Z. Murray
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, KG-Q Block, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4059, Australia;
| | - Gregor J. Devine
- Mosquito Control Lab, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia;
| | - Matthew J. Phillips
- School of Biology and Environmental Science, Queensland University of Technology, R Block, 2 George Street, Brisbane, QLD 4000, Australia;
| | - Francesca D. Frentiu
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, 300 Herston Road, Herston, QLD 4006, Australia;
- Correspondence:
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5
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Chen RE, Smith BK, Errico JM, Gordon DN, Winkler ES, VanBlargan LA, Desai C, Handley SA, Dowd KA, Amaro-Carambot E, Cardosa MJ, Sariol CA, Kallas EG, Sékaly RP, Vasilakis N, Fremont DH, Whitehead SS, Pierson TC, Diamond MS. Implications of a highly divergent dengue virus strain for cross-neutralization, protection, and vaccine immunity. Cell Host Microbe 2021; 29:1634-1648.e5. [PMID: 34610295 PMCID: PMC8595868 DOI: 10.1016/j.chom.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/15/2021] [Accepted: 09/10/2021] [Indexed: 01/29/2023]
Abstract
Although divergent dengue viruses (DENVs) have been isolated in insects, nonhuman primates, and humans, their relationships to the four canonical serotypes (DENV 1-4) are poorly understood. One virus isolated from a dengue patient, DKE-121, falls between genotype and serotype levels of sequence divergence to DENV-4. To examine its antigenic relationship to DENV-4, we assessed serum neutralizing and protective activity. Whereas DENV-4-immune mouse sera neutralize DKE-121 infection, DKE-121-immune sera inhibit DENV-4 less efficiently. Passive transfer of DENV-4 or DKE-121-immune sera protects mice against homologous, but not heterologous, DENV-4 or DKE-121 challenge. Antigenic cartography suggests that DENV-4 and DKE-121 are related but antigenically distinct. However, DENV-4 vaccination confers protection against DKE-121 in nonhuman primates, and serum from humans immunized with a tetravalent vaccine neutralize DENV-4 and DKE-121 infection equivalently. As divergent DENV strains, such as DKE-121, may meet criteria for serotype distinction, monitoring their capacity to impact dengue disease and vaccine efficacy appears warranted.
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Affiliation(s)
- Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Brittany K Smith
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - David N Gordon
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Chandni Desai
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Kimberly A Dowd
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Emerito Amaro-Carambot
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - M Jane Cardosa
- Institute of Health and Community Medicine, Universiti Sarawak Malaysia (UNIMAS), Kota Samarahan, Sarawak 94300, Malaysia; Integrated Research Associates, San Rafael, CA 94903, USA
| | - Carlos A Sariol
- Unit of Comparative Medicine, Caribbean Primate Research Center, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936-5067, USA
| | - Esper G Kallas
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Rafick-Pierre Sékaly
- Department of Microbiology and Immunology, Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; The Andrew M. Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Stephen S Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Theodore C Pierson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; The Andrew M. Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110-1010, USA.
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6
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Aliaga-Samanez A, Cobos-Mayo M, Real R, Segura M, Romero D, Fa JE, Olivero J. Worldwide dynamic biogeography of zoonotic and anthroponotic dengue. PLoS Negl Trop Dis 2021; 15:e0009496. [PMID: 34097704 PMCID: PMC8211191 DOI: 10.1371/journal.pntd.0009496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/17/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022] Open
Abstract
Dengue is a viral disease transmitted by mosquitoes. The rapid spread of dengue could lead to a global pandemic, and so the geographical extent of this spread needs to be assessed and predicted. There are also reasons to suggest that transmission of dengue from non-human primates in tropical forest cycles is being underestimated. We investigate the fine-scale geographic changes in transmission risk since the late 20th century, and take into account for the first time the potential role that primate biogeography and sylvatic vectors play in increasing the disease transmission risk. We apply a biogeographic framework to the most recent global dataset of dengue cases. Temporally stratified models describing favorable areas for vector presence and for disease transmission are combined. Our models were validated for predictive capacity, and point to a significant broadening of vector presence in tropical and non-tropical areas globally. We show that dengue transmission is likely to spread to affected areas in China, Papua New Guinea, Australia, USA, Colombia, Venezuela, Madagascar, as well as to cities in Europe and Japan. These models also suggest that dengue transmission is likely to spread to regions where there are presently no or very few reports of occurrence. According to our results, sylvatic dengue cycles account for a small percentage of the global extent of the human case record, but could be increasing in relevance in Asia, Africa, and South America. The spatial distribution of factors favoring transmission risk in different regions of the world allows for distinct management strategies to be prepared. The rate of disease emergence is increasing globally, and many long-existing diseases are extending their distribution ranges. This is the case for dengue, a global pandemic whose mosquito vectors are currently occupying ever-increasing numbers of regions worldwide. We updated the most complete global dataset of dengue cases available, and addressed the fine-scale analysis of the geographic changes experienced in dengue-transmission risk since the late 20th century. Our approach is the first to take into account the potential role of primates and sylvatic vectors in increasing the disease transmission risk in tropical forests. We built models that describe the favorable areas for vector presence and for disease occurrence, and combined them in order to obtain a novel model for predicting transmission risk. We show that dengue transmission is likely to spread to affected areas in Asia, Africa, North and South America, and Oceania, and to regions with presently no or very few cases, including cities in Europe and Japan. The global contribution of sylvatic dengue cycles is small but meaningful. Our methodological approach can differentiate the factors favoring risk in different world regions, thus allowing for management strategies to be prepared specifically for each of these regions.
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Affiliation(s)
- Alisa Aliaga-Samanez
- Grupo de Biogeografía, Diversidad y Conservación, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- * E-mail:
| | - Marina Cobos-Mayo
- Grupo de Biogeografía, Diversidad y Conservación, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Raimundo Real
- Grupo de Biogeografía, Diversidad y Conservación, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto IBYDA, Centro de Experimentación Grice-Hutchinson, Málaga, Spain
| | - Marina Segura
- Centro de Vacunación Internacional de Málaga, Ministerio de Sanidad, Consumo y Bienestar Social, Málaga, Spain
| | - David Romero
- Grupo de Biogeografía, Diversidad y Conservación, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Laboratorio de Desarrollo Sustentable y Gestión Ambiental del Territorio, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Julia E. Fa
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, United Kingdom
- Center for International Forestry Research (CIFOR), CIFOR Headquarters, Bogor, Indonesia
| | - Jesús Olivero
- Grupo de Biogeografía, Diversidad y Conservación, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto IBYDA, Centro de Experimentación Grice-Hutchinson, Málaga, Spain
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7
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Hall-Mendelin S, Pyke AT, Ramirez AL, Staunton KM, Burtonclay P, McMahon J, Barcelon J, van den Hurk AF. Infection, Dissemination, and Replication of Urban and Sylvatic Strains of Dengue Virus Type 2 (Flaviviridae: Flavivirus) in Australian Aedes aegypti (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1412-1418. [PMID: 33459781 DOI: 10.1093/jme/tjaa292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 06/12/2023]
Abstract
The dengue viruses (DENVs) occur throughout tropical and subtropical regions of the world where they infect 100s of millions of people annually. In Australia, the dengue receptive zone is confined to the northern state of Queensland where the principal vector Aedes aegypti (L.) is present. In the current study, two populations of Ae. aegypti from north Queensland were exposed to two urban outbreak strains and one sylvatic strain of dengue virus type 2 (DENV-2). The titer of virus required to infect 50% of mosquitoes was between 105 and 106 50% tissue culture infectious dose (TCID)50/ml and was influenced by the combination of the origin of Ae. aegypti population and virus strain. When exposed to infectious bloodmeal titers > 106 TCID50/ml, infection and dissemination rates were all > 50% and were significantly affected by the origin of the mosquito population but not by the strain of DENV-2. Replication of DENV-2 was also significantly affected by the mosquito population and the titer of the infectious bloodmeal that mosquitoes were exposed to. The results of this study are discussed in the context of DENV transmission dynamics in northern Australia and the relative fitness of the sylvatic virus strain in urban Ae. aegypti populations.
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Affiliation(s)
- Sonja Hall-Mendelin
- Public Health Virology, Forensic and Scientific Services, Department of Health, Brisbane, Queensland, Australia
| | - Alyssa T Pyke
- Public Health Virology, Forensic and Scientific Services, Department of Health, Brisbane, Queensland, Australia
| | - Ana L Ramirez
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, Queensland, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA
| | - Kyran M Staunton
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, Queensland, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Peter Burtonclay
- Public Health Virology, Forensic and Scientific Services, Department of Health, Brisbane, Queensland, Australia
| | - Jamie McMahon
- Public Health Virology, Forensic and Scientific Services, Department of Health, Brisbane, Queensland, Australia
| | - Jean Barcelon
- Public Health Virology, Forensic and Scientific Services, Department of Health, Brisbane, Queensland, Australia
| | - Andrew F van den Hurk
- Public Health Virology, Forensic and Scientific Services, Department of Health, Brisbane, Queensland, Australia
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8
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Young KI, Buenemann M, Vasilakis N, Perera D, Hanley KA. Shifts in mosquito diversity and abundance along a gradient from oil palm plantations to conterminous forests in Borneo. Ecosphere 2021; 12. [PMID: 33996190 DOI: 10.1002/ecs2.3463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Deforestation precipitates spillover of enzootic, vector-borne viruses into humans, but specific mechanisms for this effect have rarely been investigated. Expansion of oil palm cultivation is a major driver of deforestation. Here, we demonstrate that mosquito abundance decreased over ten stepwise distances from interior forest into conterminous palm plantations in Borneo. Diversity in interior plantation narrowed to one species, Aedes albopictus, a potential bridge vector for spillover of multiple viruses. A. albopictus was equally abundant across all distances in forests, forest-plantation edge, and plantations, while A. niveus, a known vector of sylvatic dengue virus, was found only in forests. A. albopictus collections were significantly female-biased in plantation but not in edge or forest. Our data reveal that the likelihood of encountering any mosquito is greater in interior forest and edge than plantation, while the likelihood of encountering A. albopictus is equivalent across the gradient sampled from interior plantation to interior forest.
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Affiliation(s)
- Katherine I Young
- Department of Biology, New Mexico State University, 1780 E University Ave, Las Cruces, New Mexico 88003 USA
| | - Michaela Buenemann
- Department of Geography, New Mexico State University, 1780 E University Ave, Las Cruces, New Mexico 88003 USA
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center of Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555 USA
| | - David Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Jalan Datuk Mohammad Musa, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, 1780 E University Ave, Las Cruces, New Mexico 88003 USA
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9
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Abstract
Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle - that underlying the Biological Species Concept (BSC) - to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
| | - Angela C O'Donnell
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
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10
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Cunha MDP, Duarte-Neto AN, Pour SZ, Hajjar LA, Frassetto FP, Dolhnikoff M, Saldiva PHDN, Zanotto PMDA. Systemic dengue infection associated with a new dengue virus type 2 introduction in Brazil - a case report. BMC Infect Dis 2021; 21:311. [PMID: 33794785 PMCID: PMC8015031 DOI: 10.1186/s12879-021-05959-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 03/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dengue infection is caused by an arbovirus with a wide range of presentations, varying from asymptomatic disease to unspecific febrile illness and haemorrhagic syndrome with shock, which can evolve to death. In Brazil, the virus circulates since the 1980s with many introductions of new serotypes, genotypes, and lineages since then. Here we report a fatal case of dengue associated with a Dengue virus (DENV) lineage not detected in the country until now. CASE PRESENTATION The patient, a 58-year-old man arrived at the hospital complaining of fever and severe abdominal pain due to intense gallbladder edema, mimicking acute abdomen. After 48 h of hospital admission, he evolved to refractory shock and death. DENV RNA was detected in all tissues collected (heart, lung, brain, kidney, spleen, pancreas, liver, and testis). Viral sequencing has shown that the virus belongs to serotype 2, American/Asian genotype, in a new clade, which has never been identified in Brazil before. The virus was phylogenetically related to isolates from central America [Puerto Rico (2005-2007), Martinique (2005), and Guadeloupe (2006)], most likely arriving in Brazil from Puerto Rico. CONCLUSION In summary, this was the first fatal documented case with systemic dengue infection associated with the new introduction of Dengue type 2 virus in Brazil during the 2019 outbreak.
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Affiliation(s)
- Marielton Dos Passos Cunha
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
| | | | - Shahab Zaki Pour
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Ludhmila Abrahão Hajjar
- Intensive Care Unit, Heart Institute (InCor), Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Marisa Dolhnikoff
- Pathology Department, Medical School, 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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11
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Fang Y, Tambo E, Xue JB, Zhang Y, Zhou XN, Khater EIM. Detection of DENV-2 and Insect-Specific Flaviviruses in Mosquitoes Collected From Jeddah, Saudi Arabia. Front Cell Infect Microbiol 2021; 11:626368. [PMID: 33718273 PMCID: PMC7947193 DOI: 10.3389/fcimb.2021.626368] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Mosquito-borne diseases are rapidly spreading due to increasing international travel and trade. Routine mosquito surveillance and screening for mosquito-borne pathogens can be early indicators for local disease transmission and outbreaks. However, arbovirus detection in mosquito vectors has rarely been reported in Saudi Arabia. Methods A total of 769,541 Aedes and Culex mosquitoes were collected by Black Hole traps during routine mosquito surveillance in the first half of 2016. Culex. quinquefasciatus and Ae. aegypti were the most prevalent species observed. Twenty-five and 24 randomly selected pools of Ae. aegypti and Cx. quinquefasciatus, respectively, were screened for arboviruses by RT-PCR. Results Dengue 2 (DENV-2) and four strains of insect-specific flaviviruses, including one of cell-fusing agent virus (CFAV) and three of Phlebotomus-associated flavivirus (PAFV) were detected in pools of Ae. aegypti. We also detected 10 strains of Culex flavivirus (CxFV) in pools of Cx. quinquefasciatus. Phylogenetic analysis using whole genome sequences placed the DENV strain into the cosmopolitan 1 sub-DENV-2 genotype, and the CxFVs into the African/Caribbean/Latin American genotype. These analyses also showed that the DENV-2 strain detected in the present study was closely related to strains detected in China in 2014 and in Japan in 2018, which suggests frequent movement of DENV-2 strains among these countries. Furthermore, the phylogenetic analysis suggested at least five introductions of DENV-2 into Saudi Arabia from 2014 through 2018, most probably from India. Conclusions To our knowledge, this study reports the first detection of four arboviruses DENV, CFAV, PAFV, and CxFV in mosquitoes in Saudi Arabia, which shows that they are co-circulating in Jeddah. Our findings show a need for widespread mosquito-based arbovirus surveillance programs in Saudi Arabia, which will improve our understanding of the transmission dynamics of the mosquito-borne arboviruses within the country and help early predict and mitigate the risk of human infections and outbreaks.
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Affiliation(s)
- Yuan Fang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Ernest Tambo
- Public Health Pests Laboratory, Municipality of Jeddah Governorate, Jeddah, Saudi Arabia
| | - Jing-Bo Xue
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention-Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Emad I M Khater
- Public Health Pests Laboratory, Municipality of Jeddah Governorate, Jeddah, Saudi Arabia.,Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
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12
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Pickering P, Hugo LE, Devine GJ, Aaskov JG, Liu W. Australian Aedes aegypti mosquitoes are susceptible to infection with a highly divergent and sylvatic strain of dengue virus type 2 but are unlikely to transmit it. Parasit Vectors 2020; 13:240. [PMID: 32393378 PMCID: PMC7212620 DOI: 10.1186/s13071-020-04091-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/17/2020] [Indexed: 11/10/2022] Open
Abstract
Background Humans are the primary hosts of dengue viruses (DENV). However, sylvatic cycles of transmission can occur among non-human primates and human encroachment into forested regions can be a source of emergence of new strains such as the highly divergent and sylvatic strain of DENV2, QML22, recovered from a dengue fever patient returning to Australia from Borneo. The objective of the present study was to evaluate the vector competence of Australian Aedes aegypti mosquitoes for this virus. Methods Four- to five-day-old mosquitoes from two strains of Ae. aegypti from Queensland, Australia, were fed a meal of sheep blood containing 108 50% cell culture infectious dose per ml (CCID50/ml) of either QML22 or an epidemic strain of DENV serotype 2 (QML16) isolated from a dengue fever patient in Australia in 2015. Mosquitoes were maintained at 28 °C, 75% relative humidity and sampled 7, 10 and 14 days post-infection (dpi). Live virions in mosquito bodies (abdomen/thorax), legs and wings and saliva expectorates from individual mosquitoes were quantified using a cell culture enzyme-linked immunosorbent assay (CCELISA) to determine infection, dissemination and transmission rates. Results The infection and dissemination rates of the sylvatic DENV2 strain, QML22, were significantly lower than that for QML16. While the titres of virus in the bodies of mosquitoes infected with either of these viruses were similar, titres in legs and wings were significantly lower in mosquitoes infected with QML22 at most time points although they reached similar levels by 14 dpi. QML16 was detected in 16% (n = 25) and 28% (n = 25) of saliva expectorates at 10 and 14 dpi, respectively. In contrast, no virus was detected in the saliva expectorates of QML22 infected mosquitoes. Conclusions Australia urban/peri-urban Ae. aegypti species are susceptible to infection by the sylvatic and highly divergent DENV 2 QML22 but replication of QML22 is attenuated relative to the contemporary strain, QML16. A salivary gland infection or escape barrier may be acting to prevent infection of saliva and would prevent onward transmission of this highly divergent virus in Australia.![]()
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Affiliation(s)
- Paul Pickering
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Leon E Hugo
- Queensland Institute of Medical Research-Berghofer Medical Research Institute, Brisbane, Australia
| | - Gregor J Devine
- Queensland Institute of Medical Research-Berghofer Medical Research Institute, Brisbane, Australia
| | - John G Aaskov
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia.,Queensland University of Technology, Brisbane, Australia
| | - Wenjun Liu
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia.
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13
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Incidence and epidemiological features of dengue in Sabah, Malaysia. PLoS Negl Trop Dis 2020; 14:e0007504. [PMID: 32392222 PMCID: PMC7241834 DOI: 10.1371/journal.pntd.0007504] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/21/2020] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
In South East Asia, dengue epidemics have increased in size and geographical distribution in recent years. We examined the spatiotemporal distribution and epidemiological characteristics of reported dengue cases in the predominantly rural state of Sabah, in Malaysian Borneo-an area where sylvatic and urban circulation of pathogens are known to intersect. Using a public health data set of routinely notified dengue cases in Sabah between 2010 and 2016, we described demographic and entomological risk factors, both before and after a 2014 change in the clinical case definition for the disease. Annual dengue incidence rates were spatially variable over the 7-year study period from 2010-2016 (state-wide mean annual incidence of 21 cases/100,000 people; range 5-42/100,000), but were highest in rural localities in the western districts of the state (Kuala Penyu, Nabawan, Tenom and Kota Marudu). Eastern districts exhibited lower overall dengue rates, although a high proportion of severe (haemorrhagic) dengue cases (44%) were focused in Sandakan and Tawau. Dengue incidence was highest for those aged between 10 and 29 years (24/100,000), and was slightly higher for males compared to females. Available vector surveillance data indicated that during large outbreaks in 2015 and 2016 the mosquito Aedes albopictus was more prevalent in both urban and rural households (House Index of 64%) than Ae. aegypti (15%). Demographic patterns remained unchanged both before and after the dengue case definition was changed; however, in the years following the change, reported case numbers increased substantially. Overall, these findings suggest that dengue outbreaks in Sabah are increasing in both urban and rural settings. Future studies to better understand the drivers of risk in specific age groups, genders and geographic locations, and to test the potential role of Ae. albopictus in transmission, may help target dengue prevention and control efforts.
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14
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Young KI, Medwid JT, Azar SR, Huff RM, Drumm H, Coffey LL, Pitts RJ, Buenemann M, Vasilakis N, Perera D, Hanley KA. Identification of Mosquito Bloodmeals Collected in Diverse Habitats in Malaysian Borneo Using COI Barcoding. Trop Med Infect Dis 2020; 5:tropicalmed5020051. [PMID: 32244739 PMCID: PMC7344668 DOI: 10.3390/tropicalmed5020051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022] Open
Abstract
Land cover and land use change (LCLUC) acts as a catalyst for spillover of arthropod-borne pathogens into novel hosts by shifting host and vector diversity, abundance, and distribution, ultimately reshaping host–vector interactions. Identification of bloodmeals from wild-caught mosquitoes provides insight into host utilization of particular species in particular land cover types, and hence their potential role in pathogen maintenance and spillover. Here, we collected 134 blood-engorged mosquitoes comprising 10 taxa across 9 land cover types in Sarawak, Malaysian Borneo, a region experiencing intense LCLUC and concomitant spillover of arthropod-borne pathogens. Host sources of blood were successfully identified for 116 (87%) mosquitoes using cytochrome oxidase subunit I (COI) barcoding. A diverse range of hosts were identified, including reptiles, amphibians, birds, and mammals. Sixteen engorged Aedes albopictus, a major vector of dengue virus, were collected from seven land cover types and found to feed exclusively on humans (73%) and boar (27%). Culex tritaeniohynchus (n = 2), Cx. gelidus (n = 3), and Cx. quiquefasciatus (n = 3), vectors of Japanese encephalitis virus, fed on humans and pigs in the rural built-up land cover, creating potential transmission networks between these species. Our data support the use of COI barcoding to characterize mosquito–host networks in a biodiversity hotspot.
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Affiliation(s)
- Katherine I. Young
- Department of Biology, New Mexico State University, Las Cruces NM 88003, USA; (J.T.M.); (K.A.H.)
- Correspondence:
| | - Joseph T. Medwid
- Department of Biology, New Mexico State University, Las Cruces NM 88003, USA; (J.T.M.); (K.A.H.)
| | - Sasha R. Azar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.R.A.); (N.V.)
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert M. Huff
- Department of Biology, Baylor University, Waco, TX 76706, USA; (R.M.H.); (R.J.P.)
| | - Hannah Drumm
- School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (H.D.); (L.L.C.)
| | - Lark L. Coffey
- School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (H.D.); (L.L.C.)
- Department of Pathology, Microbiology & Immunology, University of California Davis, Davis, CA 95616, USA
| | - R. Jason Pitts
- Department of Biology, Baylor University, Waco, TX 76706, USA; (R.M.H.); (R.J.P.)
| | - Michaela Buenemann
- Department of Geography, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.R.A.); (N.V.)
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - David Perera
- Institute of Health and Communiti Medicine, Universiti of Malaysia Sarawak, Sarawak 94300, Malaysia;
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces NM 88003, USA; (J.T.M.); (K.A.H.)
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15
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Abstract
Dengue fever is a disease with increasing incidence, now occurring in some regions which were not previously affected. Ribeirão Preto and São Paulo, municipalities in São Paulo state, Brazil, have been highlighted due to the high dengue incidences especially after 2009 and 2013. Therefore, the current study aims to analyse the temporal behaviour of dengue cases in the both municipalities and forecast the number of disease cases in the out-of-sample period, using time series models, especially SARIMA model. We fitted SARIMA models, which satisfactorily meet the dengue incidence data collected in the municipalities of Ribeirão Preto and São Paulo. However, the out-of-sample forecast confidence intervals are very wide and this fact is usually omitted in several papers. Despite the high variability, health services can use these models in order to anticipate disease scenarios, however, one should interpret with prudence since the magnitude of the epidemic may be underestimated.
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16
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Johari NA, Voon K, Toh SY, Sulaiman LH, Yap IKS, Lim PKC. Sylvatic dengue virus type 4 in Aedes aegypti and Aedes albopictus mosquitoes in an urban setting in Peninsular Malaysia. PLoS Negl Trop Dis 2019; 13:e0007889. [PMID: 31730672 PMCID: PMC6881067 DOI: 10.1371/journal.pntd.0007889] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/27/2019] [Accepted: 10/28/2019] [Indexed: 12/03/2022] Open
Abstract
Dengue fever is endemic in Malaysia, contributing to significant economic and health burden in the country. Aedes aegypti and Ae. albopictus are the main vectors of the dengue virus (DENV), which circulates in sylvatic and human transmission cycles and has been present in Malaysia for decades. The study investigated the presence and distribution of DENV in urban localities in the Klang Valley, Peninsular Malaysia. A total of 364 Ae. aegypti and 1,025 Ae. albopictus larvae, and 10 Ae. aegypti and 42 Ae. albopictus adult mosquitoes were screened for the presence of DENV. In total, 31 (2.2%) samples were positive, of which 2 Ae. albopictus larvae were co-infected with two serotypes, one with DENV-2 and DENV-3 and the other with DENV-3 and DENV-4. Phylogenetic analysis determined that the isolates belonged to DENV-1 genotype I (1 Ae. aegypti adult), DENV-2 (1 Ae. albopictus larva), DENV-3 genotype V (3 Ae. aegypti larvae and 10 Ae. albopictus larvae) and DENV-4 genotype IV (6 Ae. aegypti larvae and 12 Ae. albopictus larvae), a sylvatic strain of DENV-4 which was most closely related with sylvatic strains isolated from arboreal mosquitoes and sentinel monkeys in Peninsular Malaysia in the 1970s. All four DENV serotypes were co-circulating throughout the study period. The detection of a sylvatic strain of DENV-4 in Ae. aegypti and Ae. albopictus mosquitoes in urban areas in Peninsular Malaysia highlights the susceptibility of these vectors to infection with sylvatic DENV. The infectivity and vector competence of these urban mosquitoes to this strain of the virus needs further investigation, as well as the possibility of the emergence of sylvatic virus into the human transmission cycle.
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Affiliation(s)
- Nur Alia Johari
- Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia
| | - Kenny Voon
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Shen Yung Toh
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Lokman Hakim Sulaiman
- Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia
- Department of Community Medicine, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Ivan Kok Seng Yap
- Sarawak Research and Development Council, Ministry of Education, Science and Technological Research, Sarawak, Malaysia
| | - Patricia Kim Chooi Lim
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
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17
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Genome Sequences of Barmah Forest Virus Strains Isolated from Mosquitoes Trapped in Australian Defence Force Training Areas Reveal Multiple Nucleotide Insertions in the 3′ Untranslated Region. Microbiol Resour Announc 2019; 8:8/41/e00969-19. [PMID: 31601667 PMCID: PMC6787324 DOI: 10.1128/mra.00969-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequences of two Barmah Forest virus (BFV) strains isolated from mosquitoes trapped in the Australian Defence Force (ADF) training areas during 2017 and 2018 reveal multiple nucleotide insertions in the 3′ untranslated region (UTR) of ADF BFV strains compared with the BFV prototype strain whole-genome sequence in GenBank. The complete genome sequences of two Barmah Forest virus (BFV) strains isolated from mosquitoes trapped in the Australian Defence Force (ADF) training areas during 2017 and 2018 reveal multiple nucleotide insertions in the 3′ untranslated region (UTR) of ADF BFV strains compared with the BFV prototype strain whole-genome sequence in GenBank.
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18
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Turell MJ, Gozalo AS, Guevara C, Schoeler GB, Carbajal F, López-Sifuentes VM, Watts DM. Lack of Evidence of Sylvatic Transmission of Dengue Viruses in the Amazon Rainforest Near Iquitos, Peru. Vector Borne Zoonotic Dis 2019; 19:685-689. [PMID: 30964397 PMCID: PMC6716187 DOI: 10.1089/vbz.2018.2408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Dengue viruses (DENV) are currently responsible for more human morbidity and mortality than any other known arbovirus, and all four DENV are known to exist in sylvatic cycles that might allow these viruses to persist if the urban (Aedes aegypti) cycle could be controlled. To determine whether DENV were being maintained in a sylvatic cycle in a forested area about 14 km southwest of Iquitos, Peru, a city in which all 4 serotypes of DENV circulate, we placed 20 DENV seronegative Aotus monkeys in cages either in the canopy or near ground level for a total of 125.6 months. Despite capturing >66,000 mosquitoes in traps that collected some of the mosquitoes attracted to these monkeys, blood samples obtained once a month from each animal were tested and found to be negative by an enzyme-linked immunosorbent assay for IgM and IgG antibodies to dengue, yellow fever, Venezuelan equine encephalitis, Oropouche, and Mayaro viruses. Although all four DENV serotypes were endemic in nearby Iquitos, the findings of this study did not support a DENV sylvatic maintenance and transmission cycle in a selected area of the Amazon rainforest in northeastern Peru.
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Affiliation(s)
- Michael J. Turell
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, Maryland
| | - Alfonso S. Gozalo
- Department of Entomology, U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | - Carolina Guevara
- Department of Entomology, U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | - George B. Schoeler
- Department of Entomology, U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | - Faustino Carbajal
- Department of Entomology, U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | | | - Douglas M. Watts
- Department of Viral and Rickettsial Diseases, Naval Medical Research Center, Silver Spring, Maryland
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19
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Multiple introductions of dengue virus strains contribute to dengue outbreaks in East Kalimantan, Indonesia, in 2015-2016. Virol J 2019; 16:93. [PMID: 31345242 PMCID: PMC6659258 DOI: 10.1186/s12985-019-1202-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dengue fever is a febrile disease caused by dengue virus (DENV), which affects people throughout the tropical and subtropical regions of the world, including Indonesia. East Kalimantan (Borneo) province suffered a dramatic increase in dengue cases in 2015 and 2016, making it the province with the second highest incidence of dengue in Indonesia. Despite this, dengue in East Kalimantan is understudied; leaving transmission dynamics of the disease in the area are mostly unknown. In this study, we investigate the factors contributing to the outbreaks in East Kalimantan. METHODS Prospective clinical and molecular virology study was conducted in two main cities in the province, namely Samarinda and Balikpapan, in 2015-2016. Patients' clinical, hematological, and demographic data were recorded. Dengue detection and confirmation was performed using NS1-antigen and IgG/IgM antibody detection. RT-PCR was conducted to determine the serotypes of the virus. Phylogenetic analysis was performed based on envelope gene sequences. RESULTS Three hundred patients with suspected dengue were recruited. Among these, 132 (44%) were diagnosed with dengue by NS1 antigen and/or nucleic acid detection. The majority of the infections (60%) were primary, with dengue hemorrhagic fever (DHF) the predominant manifestation (71.9%). Serotyping detected all four DENV serotypes in 112 (37.3%) cases, with the majority of patients (58.9%) infected by DENV-3. Phylogenetic analysis based on envelope gene sequences revealed the genotypes of the viruses as DENV-1 Genotype I, DENV-2 Cosmopolitan, and DENV-3 Genotype I. Most virus strains were closely-related to strains from cities in Indonesia. CONCLUSIONS Our observations indicate that multiple introductions of endemic DENV from surrounding cities in Indonesia, coupled with relatively low herd immunity, were likely responsible for the outbreak of the dominant viruses. The study provides information on the clinical spectrum of the disease, together with serology, viral genetics, and demographic data, which will be useful for better understanding of dengue disease in Borneo.
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Complete Genomic Sequence of an Australian Sindbis Virus Isolated 44 Years Ago Reveals Unique Indels in the E2 and nsP3 Proteins. Microbiol Resour Announc 2019; 8:8/20/e00246-19. [PMID: 31097499 PMCID: PMC6522784 DOI: 10.1128/mra.00246-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The complete genome sequence of a Sindbis virus (SINV) strain (SINV_AUS_1975_18953) isolated in Australia in 1975 from Culex annulirostris mosquitoes revealed unique deletions in amino acid positions 182 to 184 and 201 to 228 of the E2 envelope protein and multiple indels in the nonstructural protein 3 (nsP3). The complete genome sequence of a Sindbis virus (SINV) strain (SINV_AUS_1975_18953) isolated in Australia in 1975 from Culex annulirostris mosquitoes revealed unique deletions in amino acid positions 182 to 184 and 201 to 228 of the E2 envelope protein and multiple indels in the nonstructural protein 3 (nsP3).
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21
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Genome Sequences of Three Ross River Virus Isolates Obtained from the Australian Defence Force. Microbiol Resour Announc 2019; 8:8/14/e00064-19. [PMID: 30948463 PMCID: PMC6449554 DOI: 10.1128/mra.00064-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequences of three Ross River virus (RRV) isolates from infected Australian Defence Force (ADF) personnel and from mosquitoes collected in ADF training areas were determined. Phylogenetic analysis in comparison with all available complete RRV nucleotide sequences from GenBank split these three RRV isolates into two distinct sublineages. The complete genome sequences of three Ross River virus (RRV) isolates from infected Australian Defence Force (ADF) personnel and from mosquitoes collected in ADF training areas were determined. Phylogenetic analysis in comparison with all available complete RRV nucleotide sequences from GenBank split these three RRV isolates into two distinct sublineages.
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22
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Klitting R, Fischer C, Drexler JF, Gould EA, Roiz D, Paupy C, de Lamballerie X. What Does the Future Hold for Yellow Fever Virus? (II). Genes (Basel) 2018; 9:E425. [PMID: 30134625 PMCID: PMC6162518 DOI: 10.3390/genes9090425] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023] Open
Abstract
As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas with low vaccination coverage but that are suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization's initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately viral dissemination, and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more yellow fever (YF) cases in the upcoming years. Hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of a two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
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Affiliation(s)
- Raphaëlle Klitting
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
| | - Carlo Fischer
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany.
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany.
| | - Jan F Drexler
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany.
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany.
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119991 Moscow, Russia.
| | - Ernest A Gould
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
| | - David Roiz
- UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Univ. Montpellier), 34394 Montpellier, France.
| | - Christophe Paupy
- UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Univ. Montpellier), 34394 Montpellier, France.
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
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23
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Dos Passos Cunha M, Ortiz-Baez AS, de Melo Freire CC, de Andrade Zanotto PM. Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2. INFECTION GENETICS AND EVOLUTION 2018; 64:207-211. [PMID: 29792991 PMCID: PMC7106335 DOI: 10.1016/j.meegid.2018.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 05/09/2018] [Accepted: 05/20/2018] [Indexed: 11/29/2022]
Abstract
Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for fine-tuning in viral codon usage, possibly due to viral adaptation to human transmission. We compared the codon adaptation of DENV serotype 2 (DENV-2) genotypes from urban and sylvatic habitats and tried to correlate the findings with key evolutionary determinants. We found that DENV-2 codons of urban and sylvatic genotypes had a higher CAI to humans than to Ae. aegypti. Remarkably, we found no significant differences in codon adaptation to human between urban American/Asian and sylvatic DENV-2 genotypes. Moreover, CAI values were significantly different, when comparing all genotypes to Ae. aegypti codon preferences, with lower values for sylvatic than urban genotypes. In summary, our findings suggest the presence of a molecular signature among the genotypes that circulate in sylvatic and urban environments, and may help explain the trafficking of DENV-2 strains to an urban cycle. DENV-2 codons of all genotypes had a higher CAI to humans than to Ae. Aegypti. CAI values for the sylvatic genotype were the lowest in humans and Ae. Aegypti. Similar CAI values were recovered for the American/Asian and the Sylvatic genotypes.
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Affiliation(s)
- Marielton Dos Passos Cunha
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Ayda Susana Ortiz-Baez
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil; Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | | | - 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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24
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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: 41] [Impact Index Per Article: 6.8] [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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25
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Young KI, Mundis S, Widen SG, Wood TG, Tesh RB, Cardosa J, Vasilakis N, Perera D, Hanley KA. Abundance and distribution of sylvatic dengue virus vectors in three different land cover types in Sarawak, Malaysian Borneo. Parasit Vectors 2017; 10:406. [PMID: 28859676 PMCID: PMC5580228 DOI: 10.1186/s13071-017-2341-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mosquito-borne dengue virus (DENV) is maintained in a sylvatic, enzootic cycle of transmission between canopy-dwelling non-human primates and Aedes mosquitoes in Borneo. Sylvatic DENV can spill over into humans living in proximity to forest foci of transmission, in some cases resulting in severe dengue disease. The most likely vectors of such spillover (bridge vectors) in Borneo are Ae. albopictus and Ae. niveus. Borneo is currently experiencing extensive forest clearance. To gauge the effect of this change in forest cover on the likelihood of sylvatic DENV spillover, it is first necessary to characterize the distribution of bridge vectors in different land cover types. In the current study, we hypothesized that Ae. niveus and Ae. albopictus would show significantly different distributions in different land cover types; specifically, we predicted that Ae. niveus would be most abundant in forests whereas Ae. albopictus would have a more even distribution in the landscape. RESULTS Mosquitoes were collected from a total of 15 sites using gravid traps and a backpack aspirator around Kampong Puruh Karu, Sarawak, Malaysian Borneo, where sylvatic DENV spillover has been documented. A total of 2447 mosquitoes comprising 10 genera and 4 species of Aedes, were collected over the three years, 2013, 2014 and 2016, in the three major land cover types in the area, homestead, agriculture and forest. Mosquitoes were identified morphologically, pooled by species and gender, homogenized, and subject to DNA barcoding of each Aedes species and to arbovirus screening. As predicted, Ae. niveus was found almost exclusively in forests whereas Ae. albopictus was collected in all land cover types. Aedes albopictus was significantly (P = 0.04) more abundant in agricultural fields than forests. Sylvatic DENV was not detected in any Aedes mosquito pools, however genomes of 14 viruses were detected using next generation sequencing. CONCLUSIONS Land cover type affects the abundance and distribution of the most likely bridge vectors of sylvatic DENV in Malaysia Borneo. Conversion of forests to agriculture will likely decrease the range and abundance of Ae. niveus but enhance the abundance of Ae. albopictus.
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Affiliation(s)
- Katherine I Young
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - Stephanie Mundis
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Robert B Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Disease, Center for Tropical Diseases; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Disease, Center for Tropical Diseases; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - David Perera
- Institute of Health & Community Medicine, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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26
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Complete Genome Sequence of a Highly Divergent Dengue Virus Type 2 Strain, Imported into Australia from Sabah, Malaysia. GENOME ANNOUNCEMENTS 2017; 5:5/29/e00546-17. [PMID: 28729258 PMCID: PMC5522925 DOI: 10.1128/genomea.00546-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 2015, a female patient returning to Australia from Sabah, Malaysia, was diagnosed with a suspected sylvatic dengue virus type 2 (DENV-2) infection, becoming the second case of imported highly divergent dengue virus infection recorded in Australia. We describe here the complete genome sequencing of the DENV-2 strain isolated from this patient.
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