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      Isolation and complete genome analysis of neurotropic dengue virus serotype 3 from the cerebrospinal fluid of an encephalitis patient

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          Abstract

          Although neurological manifestations associated with dengue viruses (DENV) infection have been reported, there is very limited information on the genetic characteristics of neurotropic DENV. Here we describe the isolation and complete genome analysis of DENV serotype 3 (DENV-3) from cerebrospinal fluid of an encephalitis paediatric patient in Jakarta, Indonesia. Next-generation sequencing was employed to deduce the complete genome of the neurotropic DENV-3 isolate. Based on complete genome analysis, two unique and nine uncommon amino acid changes in the protein coding region were observed in the virus. A phylogenetic tree and molecular clock analysis revealed that the neurotropic virus was a member of Sumatran-Javan clade of DENV-3 genotype I and shared a common ancestor with other isolates from Jakarta around 1998. This is the first report of neurotropic DENV-3 complete genome analysis, providing detailed information on the genetic characteristics of this virus.

          Author summary

          Dengue viruses (DENV) are viruses that can cause asymptomatic infection to life-threatening haemorrhagic fever disease. Although DENV are not classically known to infect and invade central nervous system (CNS) in human, numerous cases of DENV infection in the CNS have been reported with limited information about the characteristics of the infecting virus. Here, we report the isolation and first complete genome analysis of DENV serotype 3 (DENV-3) from cerebrospinal fluid of a patient diagnosed with dengue encephalitis in Jakarta, Indonesia. By using next-generation sequencing strategy, we recovered the complete genome of the virus isolate and identified unique amino acid changes not found in any other recovered DENV-3 strains. The virus was determined to be closely related to isolates from Jakarta, Indonesia, which have been circulating for almost four decades.

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          Most cited references33

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          Dengue virus pathogenesis: an integrated view.

          Much remains to be learned about the pathogenesis of the different manifestations of dengue virus (DENV) infections in humans. They may range from subclinical infection to dengue fever, dengue hemorrhagic fever (DHF), and eventually dengue shock syndrome (DSS). As both cell tropism and tissue tropism of DENV are considered major determinants in the pathogenesis of dengue, there is a critical need for adequate tropism assays, animal models, and human autopsy data. More than 50 years of research on dengue has resulted in a host of literature, which strongly suggests that the pathogenesis of DHF and DSS involves viral virulence factors and detrimental host responses, collectively resulting in abnormal hemostasis and increased vascular permeability. Differential targeting of specific vascular beds is likely to trigger the localized vascular hyperpermeability underlying DSS. A personalized approach to the study of pathogenesis will elucidate the basis of individual risk for development of DHF and DSS as well as identify the genetic and environmental bases for differences in risk for development of severe disease.
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            Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.

            Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the demographic history of a population. Because researchers are rarely able to choose a priori a deterministic model describing effective population size dynamics for data at hand, nonparametric curve-fitting methods based on multiple change-point (MCP) models have been developed. We propose an alternative to change-point modeling that exploits Gaussian Markov random fields to achieve temporal smoothing of the effective population size in a Bayesian framework. The main advantage of our approach is that, in contrast to MCP models, the explicit temporal smoothing does not require strong prior decisions. To approximate the posterior distribution of the population dynamics, we use efficient, fast mixing Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. In a simulation study, we demonstrate that the proposed temporal smoothing method, named Bayesian skyride, successfully recovers "true" population size trajectories in all simulation scenarios and competes well with the MCP approaches without evoking strong prior assumptions. We apply our Bayesian skyride method to 2 real data sets. We analyze sequences of hepatitis C virus contemporaneously sampled in Egypt, reproducing all key known aspects of the viral population dynamics. Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons.
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              Neurological manifestations of dengue infection.

              Severe forms of dengue, the most important arboviral infection of man, are associated with haemorrhagic disease and a generalised vascular leak syndrome. The importance of dengue as a cause of neurological disease is uncertain. During 1995, all patients with suspected CNS infections admitted to a referral hospital in southern Vietnam were investigated by culture, PCR, and antibody measurement in serum and CSF for dengue and other viruses. Of 378 patients, 16 (4.2%) were infected with dengue viruses, compared with four (1.4%) of 286 hospital controls (odds ratio [95% CI] 3.1 [1.7-5.8]). Five additional dengue positive patients with CNS abnormalities were studied subsequently. No other cause of CNS infection was identified. Seven infections were primary dengue, 13 secondary, and one was not classified. Ten patients had dengue viruses isolated or detected by PCR, and three had dengue antibody in the CSF. 12 of the 21 had no characteristic features of dengue on admission. The most frequent neurological manifestations were reduced consciousness and convulsions. Nine patients had encephalitis. No patient died, but six had neurological sequelae at discharge. Phylogenetic analysis of the four DEN-2 strains isolated mapped them with a DEN-2 strain isolated from a patient with dengue haemorrhagic fever, and with other strains previously isolated in southern Vietnam. In dengue endemic areas patients with encephalitis and encephalopathy should be investigated for this infection, whether or not they have other features of the disease.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: Project administrationRole: Resources
                Role: InvestigationRole: Resources
                Role: Investigation
                Role: InvestigationRole: Project administration
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Formal analysisRole: Investigation
                Role: Formal analysisRole: Investigation
                Role: Resources
                Role: Investigation
                Role: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Project administrationRole: SupervisionRole: Writing – original draft
                Role: ConceptualizationRole: Project administrationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                plosntds
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                12 January 2018
                January 2018
                : 12
                : 1
                : e0006198
                Affiliations
                [1 ] Eijkman Institute for Molecular Biology, Jakarta, Indonesia
                [2 ] Department of Paediatrics, Dr. Cipto Mangunkusumo National Central Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
                [3 ] Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
                CDC, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-2087-7331
                Article
                PNTD-D-17-01155
                10.1371/journal.pntd.0006198
                5809095
                29329287
                0f3de47a-9779-4ec5-8f03-b8618d089eea

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 20 July 2017
                : 28 December 2017
                Page count
                Figures: 3, Tables: 1, Pages: 14
                Funding
                This work was funded by the Ministry of Research, Technology, and Higher Education of the Republic of Indonesia and the US Centers for Disease Control and Prevention. The funders participated in the preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Anatomy
                Body Fluids
                Cerebrospinal Fluid
                Medicine and Health Sciences
                Anatomy
                Body Fluids
                Cerebrospinal Fluid
                Biology and Life Sciences
                Physiology
                Body Fluids
                Cerebrospinal Fluid
                Medicine and Health Sciences
                Physiology
                Body Fluids
                Cerebrospinal Fluid
                Biology and Life Sciences
                Anatomy
                Nervous System
                Cerebrospinal Fluid
                Medicine and Health Sciences
                Anatomy
                Nervous System
                Cerebrospinal Fluid
                Medicine and Health Sciences
                Infectious Diseases
                Infectious Diseases of the Nervous System
                Encephalitis
                Medicine and Health Sciences
                Neurology
                Infectious Diseases of the Nervous System
                Encephalitis
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                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
                Microbial Pathogens
                Viral Pathogens
                Flaviviruses
                Dengue Virus
                Biology and Life Sciences
                Organisms
                Viruses
                Viral Pathogens
                Flaviviruses
                Dengue Virus
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Animal Genomics
                Mammalian Genomics
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Protein Sequencing
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Protein Sequencing
                Custom metadata
                vor-update-to-uncorrected-proof
                2018-02-12
                All data are available in the manuscript and supporting information files, and deposited in the GenBank repository with accession number KY863456.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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