3
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Rapid genotyping protocol to improve dengue virus serotype 2 survey in Lao PDR

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Dengue fever is one of the major public health problems in Lao PDR. Over the last decade, dengue virus (DENV) epidemics were characterized by a novel predominant serotype accompanied by at least two other serotypes. Since 2008, DENV-2 circulated at a low level in Lao PDR but its epidemiologic profile changed at the end of 2018. Indeed, the number of confirmed DENV-2 cases suddenly increased in October 2018 and DENV-2 became predominant at the country level in early 2019. We developed a Genotype Screening Protocol (GSP) to determine the origin(s) of the Lao DENV-2 and study their genetic polymorphism. With a good correlation with full envelope gene sequencing data, this molecular epidemiology tool evidence the co-circulation of two highly polymorphic DENV-2 genotypes, i.e. Asian I and Cosmopolitan genotypes, over the last five years, suggesting multiple introductions of DENV-2 in the country. GSP approach provides relevant first line information that may help countries with limited laboratory resources to reinforce their capabilities to DENV-2 and to follow the epidemics progresses and assess situations at the regional level.

          Related collections

          Most cited references50

          • Record: found
          • Abstract: found
          • Article: not found

          Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas.

          The recent emergence and spread of dengue hemorrhagic fever in the Americas have been a major source of concern. Efforts to control this disease are dependent on understanding the pathogenicity of dengue viruses and their transmission dynamics. Pathogenicity studies have been hampered by the lack of in vitro or in vivo models of severe dengue disease. Alternatively, molecular epidemiologic studies which associate certain dengue virus genetic types with severe dengue outbreaks may point to strains with increased pathogenicity. The comparison of nucleotide sequences (240 bp) from the E/NS1 gene region of the dengue virus genome has been shown to reflect evolutionary relationships and geographic origins of dengue virus strains. This approach was used to demonstrate an association between the introduction of two distinct genotypes of dengue type 2 virus and the appearance of dengue hemorrhagic fever in the Americas. Phylogenetic analyses suggest that these genotypes originated in Southeast Asia and that they displaced the native, American genotype in at least four countries. Vaccination and other control efforts should therefore be directed at decreasing the transmission of these "virulent" genotypes.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            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.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Dengue virus structural differences that correlate with pathogenesis.

              The understanding of dengue virus pathogenesis has been hampered by the lack of in vitro and in vivo models of disease. The study of viral factors involved in the production of severe dengue, dengue hemorrhagic fever (DHF), versus the more common dengue fever (DF), have been limited to indirect clinical and epidemiologic associations. In an effort to identify viral determinants of DHF, we have developed a method for comparing dengue type 2 genomes (reverse transcriptase PCR in six fragments) directly from patient plasma. Samples for comparison were selected from two previously described dengue type 2 genotypes which had been shown to be the cause of DF or DHF. When full genome sequences of 11 dengue viruses were analyzed, several structural differences were seen consistently between those associated with DF only and those with the potential to cause DHF: a total of six encoded amino acid charge differences were seen in the prM, E, NS4b, and NS5 genes, while sequence differences observed within the 5' nontranslated region (NTR) and 3' NTR were predicted to change RNA secondary structures. We hypothesize that the primary determinants of DHF reside in (i) amino acid 390 of the E protein, which purportedly alters virion binding to host cells; (ii) in the downstream loop (nucleotides 68 to 80) of the 5' NTR, which may be involved in translation initiation; and (iii) in the upstream 300 nucleotides of the 3' NTR, which may regulate viral replication via the formation of replicative intermediates. The significance of four amino acid differences in the nonstructural proteins NS4b and NS5, a presumed transport protein and the viral RNA polymerase, respectively, remains unknown. This new approach to the study of dengue virus genome differences should better reflect the true composition of viral RNA populations in the natural host and permit their association with pathogenesis.
                Bookmark

                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Resources
                Role: Formal analysisRole: InvestigationRole: Resources
                Role: InvestigationRole: Methodology
                Role: Resources
                Role: Resources
                Role: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 August 2020
                2020
                : 15
                : 8
                : e0237384
                Affiliations
                [1 ] Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
                [2 ] Institut Pasteur, Paris, France
                [3 ] Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
                CEA, FRANCE
                Author notes

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

                Author information
                http://orcid.org/0000-0002-5772-8161
                Article
                PONE-D-20-05656
                10.1371/journal.pone.0237384
                7413503
                32764809
                2f74c220-2b5e-4dc3-a5d3-e52000d165e6
                © 2020 Calvez 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
                : 27 February 2020
                : 24 July 2020
                Page count
                Figures: 3, Tables: 2, Pages: 14
                Funding
                Funded by: Agence Française de Développement
                Award ID: n° CZZ 2146 01 (Ecomore2 project)
                Award Recipient :
                MG received funding from the Agence Française de Développement grant n° CZZ 2146 01 (Ecomore2 project). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Proteins
                Plasma Proteins
                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
                Molecular biology
                Molecular biology techniques
                Sequencing techniques
                DNA sequencing
                Gene Sequencing
                Research and analysis methods
                Molecular biology techniques
                Sequencing techniques
                DNA sequencing
                Gene Sequencing
                Medicine and Health Sciences
                Medical Conditions
                Tropical Diseases
                Neglected Tropical Diseases
                Dengue Fever
                Medicine and Health Sciences
                Medical Conditions
                Infectious Diseases
                Viral Diseases
                Dengue Fever
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Reverse Transcriptase-Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Reverse Transcriptase-Polymerase Chain Reaction
                Biology and Life Sciences
                Genetics
                Gene Identification and Analysis
                Genetic Screens
                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
                People and Places
                Population Groupings
                Ethnicities
                Asian People
                Lao People
                Custom metadata
                All sequence files are available from the genBank database (accession numbers MN444556-MN444622).

                Uncategorized
                Uncategorized

                Comments

                Comment on this article