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      Emergence of genotype Cosmopolitan of dengue virus type 2 and genotype III of dengue virus type 3 in Thailand

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          Abstract

          Dengue is a mosquito-borne disease that has spread to over 100 countries. Dengue fever is caused by dengue virus (DENV), which belongs to the Flavivirus genus of the family Flaviviridae. DENV comprises 4 serotypes (DENV-1 to DENV-4), and each serotype is divided into distinct genotypes. Thailand is an endemic area where all 4 serotypes of DENV co-circulate. To understand the current genotype distribution of DENVs in Thailand, we enrolled 100 cases of fever with dengue-like symptoms at the Bamrasnaradura Infectious Diseases Institute during 2016–2017. Among them, 37 cases were shown to be dengue-positive by real-time PCR. We were able to isolate DENVs from 21 cases, including 1 DENV-1, 8 DENV-2, 4 DENV-3, and 8 DENV-4. To investigate the divergence of the viruses, RNA was extracted from isolated DENVs and viral near-whole genome sequences were determined. Phylogenetic analysis of the obtained viral sequences revealed that DENV-2 genotype Cosmopolitan was co-circulating with DENV-2 genotype Asian-I, the previously predominating genotype in Thailand. Furthermore, DENV-3 genotype III was found instead of DENV-3 genotype II. The DENV-2 Cosmopolitan and DENV-3 genotype III found in Thailand were closely related to the respective strains found in nearby countries. These results indicated that DENVs in Thailand have increased in genotypic diversity, and suggested that the DENV genotypic shift observed in other Asian countries also might be taking place in Thailand.

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          Most cited references51

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          Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.

          Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.
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            SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

            Summary: SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial–temporal diffusion. The software maps phylogenies annotated with both discrete and continuous spatial information and can export high-dimensional posterior summaries to keyhole markup language (KML) for animation of the spatial diffusion through time in virtual globe software. In addition, SPREAD implements Bayes factor calculation to evaluate the support for hypotheses of historical diffusion among pairs of discrete locations based on Bayesian stochastic search variable selection estimates. SPREAD takes advantage of multicore architectures to process large joint posterior distributions of phylogenies and their spatial diffusion and produces visualizations as compelling and interpretable statistical summaries for the different spatial projections. Availability: SPREAD is licensed under the GNU Lesser GPL and its source code is freely available as a GitHub repository: https://github.com/phylogeography/SPREAD Contact: filip.bielejec@rega.kuleuven.be
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              Emergence and Global Spread of a Dengue Serotype 3, Subtype III Virus

              Over the past two decades, dengue virus serotype 3 (DENV-3) has caused unexpected epidemics of dengue hemorrhagic fever (DHF) in Sri Lanka, East Africa, and Latin America. We used a phylogenetic approach to evaluate the roles of virus evolution and transport in the emergence of these outbreaks. Isolates from these geographically distant epidemics are closely related and belong to DENV-3, subtype III, which originated in the Indian subcontinent. The emergence of DHF in Sri Lanka in 1989 correlated with the appearance there of a new DENV-3, subtype III variant. This variant likely spread from the Indian subcontinent into Africa in the 1980s and from Africa into Latin America in the mid-1990s. DENV-3, subtype III isolates from mild and severe disease outbreaks formed genetically distinct groups, which suggests a role for viral genetics in DHF.
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                Author and article information

                Contributors
                Role: InvestigationRole: Writing – original draft
                Role: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Supervision
                Role: Supervision
                Role: Funding acquisitionRole: Writing – review & editing
                Role: Project administration
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                12 November 2018
                2018
                : 13
                : 11
                : e0207220
                Affiliations
                [1 ] Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
                [2 ] Department of Medical Research, Mackay Memorial Hospital, New Taipei, Taiwan
                [3 ] Research Institute for Microbial Diseases, Osaka University, Suita, Japan
                [4 ] Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand
                Faculty of Science, Ain Shams University (ASU), EGYPT
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-6739-0144
                http://orcid.org/0000-0002-3439-8331
                Article
                PONE-D-18-21503
                10.1371/journal.pone.0207220
                6231660
                30419004
                2a9180ee-d455-48e4-b7a9-d13268a9a9e2
                © 2018 Phadungsombat et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 20 July 2018
                : 26 October 2018
                Page count
                Figures: 8, Tables: 1, Pages: 26
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100009619, Japan Agency for Medical Research and Development;
                Award ID: JP18fm0108003
                Award Recipient :
                This work was supported by funder Japan Agency for Medical Research and Development (AMED), https://www.amed.go.jp/; Program: Japan Initiative for Global Research Network on Infectious Diseases (J-GRID) JP18fm0108003 to Tatsuo Shioda.
                Categories
                Research Article
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
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                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
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                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
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                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Flaviviruses
                Dengue Virus
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Viral Pathogens
                Flaviviruses
                Dengue Virus
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
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                Biology and Life Sciences
                Organisms
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                People and Places
                Geographical Locations
                Asia
                Thailand
                Research and Analysis Methods
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                People and Places
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                Research and analysis methods
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                Sequence analysis
                DNA sequence analysis
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Nucleotide Sequencing
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Nucleotide Sequencing
                Custom metadata
                All relevant data are within the paper and its Supporting Information files. Additionally, the nucleotide sequencing data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers LC410183-LC410203.

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