8
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Phylogeographic analysis of human influenza A and B viruses in Myanmar, 2010–2015

      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

          We investigated the circulation patterns of human influenza A and B viruses in Myanmar between 2010 and 2015 by analyzing full HA genes. Upper respiratory tract specimens were collected from patients with symptoms of influenza-like illness. A total of 2,860 respiratory samples were screened by influenza rapid diagnostic test, of which 1,577 (55.1%) and 810 (28.3%) were positive for influenza A and B, respectively. Of the 1,010 specimens that were positive for virus isolation, 370 (36.6%) were A(H1N1)pdm09, 327 (32.4%) were A(H3N2), 130 (12.9%) B(Victoria), and 183 (18.1%) were B(Yamagata) viruses. Our data showed that influenza epidemics mainly occurred during the rainy season in Myanmar. Our three study sites, Yangon, Pyinmana, and Pyin Oo Lwin had similar seasonality and circulating type and subtype of influenza in a given year. Moreover, viruses circulating in Myanmar during the study period were closely related genetically to those detected in Thailand, India, and China. Phylogeographic analysis showed that A(H1N1)pdm09 viruses in Myanmar originated from Europe and migrated to other countries via Japan. Similarly, A(H3N2) viruses in Myanmar originated from Europe, and disseminated to the various countries via Australia. In addition, Myanmar plays a key role in reseeding of influenza B viruses to Southeast Asia and East Asia as well as Europe and Africa. Thus, we concluded that influenza virus in Myanmar has a strong link to neighboring Asian countries, Europe and Oceania.

          Related collections

          Most cited references19

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

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

            SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

            Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Influenza seasonality and vaccination timing in tropical and subtropical areas of southern and south-eastern Asia

              Objective To characterize influenza seasonality and identify the best time of the year for vaccination against influenza in tropical and subtropical countries of southern and south-eastern Asia that lie north of the equator. Methods Weekly influenza surveillance data for 2006 to 2011 were obtained from Bangladesh, Cambodia, India, Indonesia, the Lao People's Democratic Republic, Malaysia, the Philippines, Singapore, Thailand and Viet Nam. Weekly rates of influenza activity were based on the percentage of all nasopharyngeal samples collected during the year that tested positive for influenza virus or viral nucleic acid on any given week. Monthly positivity rates were then calculated to define annual peaks of influenza activity in each country and across countries. Findings Influenza activity peaked between June/July and October in seven countries, three of which showed a second peak in December to February. Countries closer to the equator had year-round circulation without discrete peaks. Viral types and subtypes varied from year to year but not across countries in a given year. The cumulative proportion of specimens that tested positive from June to November was > 60% in Bangladesh, Cambodia, India, the Lao People's Democratic Republic, the Philippines, Thailand and Viet Nam. Thus, these tropical and subtropical countries exhibited earlier influenza activity peaks than temperate climate countries north of the equator. Conclusion Most southern and south-eastern Asian countries lying north of the equator should consider vaccinating against influenza from April to June; countries near the equator without a distinct peak in influenza activity can base vaccination timing on local factors.
                Bookmark

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: ConceptualizationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Software
                Role: Data curationRole: Project administration
                Role: Data curationRole: Project administration
                Role: Data curationRole: Project administrationRole: Software
                Role: Data curationRole: Formal analysisRole: Project administration
                Role: Data curationRole: Formal analysisRole: Project administration
                Role: MethodologyRole: Project administration
                Role: Project administrationRole: Resources
                Role: InvestigationRole: Project administrationRole: ResourcesRole: Supervision
                Role: InvestigationRole: Project administrationRole: Resources
                Role: InvestigationRole: ResourcesRole: Supervision
                Role: ConceptualizationRole: InvestigationRole: Project administrationRole: ResourcesRole: Supervision
                Role: Project administrationRole: Resources
                Role: InvestigationRole: Project administrationRole: Resources
                Role: Data curationRole: InvestigationRole: Project administrationRole: Resources
                Role: Project administration
                Role: ValidationRole: Writing – review & editing
                Role: Project administration
                Role: Methodology
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 January 2019
                2019
                : 14
                : 1
                : e0210550
                Affiliations
                [1 ] Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachi-dori, Chuo-ku, Niigata, Niigata, Japan
                [2 ] Department of Virology, Graduate School of Medicine, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
                [3 ] Influenza and Prion Disease Research Center, National Agriculture and Food Research Organization, NARO, 3-1-1 Kannondai, Tsukuba, Ibaraki, Japan
                [4 ] Niigata Prefectural Institute of Public Health and Environmental Sciences, 314–1 Sowa, Nishi-ku, Niigata, Niigata, Japan
                [5 ] Infectious Diseases Research Center of Niigata University in Myanmar, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, Japan
                [6 ] Respiratory Medicine Department, Thingangyun Sanpya Hospital, Yangon, Yangon Division, Myanmar
                [7 ] Clinical Laboratory, Microbiology Section, Pyinmana Township Hospital, Pyinmana Township, Nay Pyi Taw, Myanmar
                [8 ] Yangon General Hospital, Lanmadaw, Yangon, Yangon Division, Myanmar
                [9 ] National Health Laboratory, Ministry of Health and Sports, Dagon, Yangon, Yangon Division, Myanmar
                [10 ] Pathology department, Niigata Medical Center Hospital, Nishi-ku, Niigata, Niigata, Japan
                [11 ] Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
                [12 ] Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
                [13 ] School of Nursing and Psychology, Niigata Seiryo University, Suido-cho Chuo-ku, Niigata, Niigata, Japan
                [14 ] Graduate School of Science and Technology, Niigata University, Nishi-ku, Niigata, Niigata, Japan
                University of Alberta Department of Resource Economics and Environmental Sociology, CANADA
                Author notes

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

                Author information
                http://orcid.org/0000-0001-8048-1745
                http://orcid.org/0000-0002-7616-4680
                http://orcid.org/0000-0001-8198-0992
                Article
                PONE-D-18-23591
                10.1371/journal.pone.0210550
                6328249
                30629691
                b4b646d6-b3e5-4cb0-ad12-8666371174bc
                © 2019 Htwe 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
                : 16 August 2018
                : 27 December 2018
                Page count
                Figures: 8, Tables: 1, Pages: 21
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100009619, Japan Agency for Medical Research and Development;
                Award ID: 15fm0108009h0001
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: JSPS Core-to-core Program B
                Award Recipient :
                This work was supported by the International Development Strategy Program for Infectious Diseases Research (J-GRID) of AMED (Japan Medical Research and Development Organization) (15fm0108009h0001 to RS), JSPS Core-to-core Program, B to RS. Asia-Africa Science Platforms, and Kakenhi (Grants-in-Aid for Scientific Research), sourced from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), and Health and Labor Sciences Research Grant, Ministry of Health, Labor and Welfare, Japan.
                Categories
                Research Article
                Medicine and Health Sciences
                Infectious Diseases
                Viral Diseases
                Influenza
                People and Places
                Geographical Locations
                Asia
                People and Places
                Geographical Locations
                Asia
                Myanmar
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Orthomyxoviruses
                Influenza Viruses
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Viral Pathogens
                Orthomyxoviruses
                Influenza Viruses
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Viral Pathogens
                Orthomyxoviruses
                Influenza Viruses
                Biology and Life Sciences
                Organisms
                Viruses
                Viral Pathogens
                Orthomyxoviruses
                Influenza Viruses
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Orthomyxoviruses
                Influenza viruses
                Influenza B virus
                Biology and life sciences
                Microbiology
                Medical microbiology
                Microbial pathogens
                Viral pathogens
                Orthomyxoviruses
                Influenza viruses
                Influenza B virus
                Medicine and health sciences
                Pathology and laboratory medicine
                Pathogens
                Microbial pathogens
                Viral pathogens
                Orthomyxoviruses
                Influenza viruses
                Influenza B virus
                Biology and life sciences
                Organisms
                Viruses
                Viral pathogens
                Orthomyxoviruses
                Influenza viruses
                Influenza B virus
                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
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Orthomyxoviruses
                Influenza viruses
                Influenza A virus
                Biology and life sciences
                Microbiology
                Medical microbiology
                Microbial pathogens
                Viral pathogens
                Orthomyxoviruses
                Influenza viruses
                Influenza A virus
                Medicine and health sciences
                Pathology and laboratory medicine
                Pathogens
                Microbial pathogens
                Viral pathogens
                Orthomyxoviruses
                Influenza viruses
                Influenza A virus
                Biology and life sciences
                Organisms
                Viruses
                Viral pathogens
                Orthomyxoviruses
                Influenza viruses
                Influenza A virus
                Custom metadata
                All nucleotide sequences have already registered to GISAID. The accession numbers are EPI1002260 to EPI1002693 for the HA genes of the A(H1N1)pdm09 isolates, EPI1002701 to EPI1002743 for the A(H3N2) isolates, and EPI1002745 to EPI568165 for the influenza B viruses.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article