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      Phylogeography of Dengue Virus Serotype 4, Brazil, 2010–2011

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          Abstract

          Multiple origins indicate this serotype was introduced in several episodes.

          Abstract

          Dengue virus serotype 4 (DENV-4) reemerged in Roraima State, Brazil, 28 years after it was last detected in the country in 1982. To study the origin and evolution of this reemergence, full-length sequences were obtained for 16 DENV-4 isolates from northern (Roraima, Amazonas, Pará States) and northeastern (Bahia State) Brazil during the 2010 and 2011 dengue virus seasons and for an isolate from the 1982 epidemic in Roraima. Spatiotemporal dynamics of DENV-4 introductions in Brazil were applied to envelope genes and full genomes by using Bayesian phylogeographic analyses. An introduction of genotype I into Brazil from Southeast Asia was confirmed, and full genome phylogeographic analyses revealed multiple introductions of DENV-4 genotype II in Brazil, providing evidence for >3 introductions of this genotype within the last decade: 2 from Venezuela to Roraima and 1 from Colombia to Amazonas. The phylogeographic analysis of full genome data has demonstrated the origins of DENV-4 throughout Brazil.

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          SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

          Filip Bielejec, Andrew Rambaut, Marc Suchard … (2011)
          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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            Counting labeled transitions in continuous-time Markov models of evolution.

            Marc Suchard, Vladimir N. Minin (2008)
            Counting processes that keep track of labeled changes to discrete evolutionary traits play critical roles in evolutionary hypothesis testing. If we assume that trait evolution can be described by a continuous-time Markov chain, then it suffices to study the process that counts labeled transitions of the chain. For a binary trait, we demonstrate that it is possible to obtain closed-form analytic solutions for the probability mass and probability generating functions of this evolutionary counting process. In the general, multi-state case we show how to compute moments of the counting process using an eigen decomposition of the infinitesimal generator, provided the latter is a diagonalizable matrix. We conclude with two examples that demonstrate the utility of our results.
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              Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

              Ceiridwen J. Edwards, Marc A. Suchard, Philippe Lemey … (2011)
              Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change. We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene. The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration. Copyright © 2011 Elsevier Ltd. All rights reserved.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Emerg Infect Dis
                Journal ID (iso-abbrev): Emerging Infect. Dis
                Journal ID (publisher-id): EID
                Title: Emerging Infectious Diseases
                Publisher: Centers for Disease Control and Prevention
                ISSN (Print): 1080-6040
                ISSN (Electronic): 1080-6059
                Publication date (Print): November 2012
                Volume: 18
                Issue: 11
                Pages: 1858-1864
                Affiliations
                [1]Instituto Evandro Chagas, Ananindeua, Brazil (M.R.T. Nunes, H. Baldez Vasconcelos, D. Barbosa de Almeida Medeiros, C. Pereira Silva de Lima, V. Lima Carvalho, E. Vieira Pinto da Silva, J. Ferreira Cardoso, E. Costa Sousa Jr, K.N. Barbosa Nunes, S.G. Rodrigues, P.F. da Costa Vasconcelos);
                [2]KU Leuven, Leuven, Belgium (N. Rodrigues Faria, P. Lemey); Universidade Nova de Lisboa, Lisbon, Portugal (A. Barroso Abecasis);
                [3]University of California, Los Angeles, California, USA (M.A. Suchard);
                [4]and Universidade do Estado do Pará, Belém, Brazil (P.F. da Costa Vasconcelos)
                Author notes
                Address for correspondence: Pedro Fernando da Costa Vasconcelos, Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, Rodovia BR-316 km-7, CEP: 67030-000, Ananindeua, Brazil; email: pedrovasconcelos@ 123456iec.pa.gov.br
                Article
                Publisher ID: 12-0217
                DOI: 10.3201/eid1811.120217
                PMC ID: 3559147
                PubMed ID: 23092706
                SO-VID: 5749d56c-eb47-42d7-af08-27b4c247214b
                History
                Categories
                Subject: Research
                Subject: Research

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: spatiotemporal patterns,phylogeography,reemergence,genetic characterization,molecular epidemiology,dengue virus,serotype 4,brazil,viruses
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: spatiotemporal patterns, phylogeography, reemergence, genetic characterization, molecular epidemiology, dengue virus, serotype 4, brazil, viruses

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