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      • Record: found
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      Evolutionary phylogeography and transmission pattern of echovirus 14: an exploration of spatiotemporal dynamics based on the 26-year acute flaccid paralysis surveillance in Shandong, China

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          Abstract

          Background

          Echovirus 14 (E-14) causes various clinical recognized syndromes, mostly with gastrointestinal syndrome and paralysis. The current study summarized the Shandong E-14 strains isolated from a 26-year acute flaccid paralysis (AFP) surveillance, and elucidated the characterization of phylogenetic and phylogeographic relationships of E-14 worldwide.

          Results

          As a predominant serotype circulating in AFP surveillance, phylogenetic analysis showed that E-14 exhibited both time and geographic subdivision worldwide. In order to know the evolutionary history and spatial temporal dynamics of E-14, evolutionary phylogeography was reconstructed using BEAST and SPREAD software based on the VP1 sequences. The time of the most recent common ancestor of E-14 was estimated around 85 years and evolved with 9.17 × 10 −3 substitutions/site/year. Phylogeographic analysis suggested that two regional transmissions of E-14 were mainly detected, with one located between Europe and Africa countries and the other was in the Asia-Pacific region.

          Conclusions

          Our study investigates the molecular evolution and phylogeographic of E-14, and brings new insight to the dispersal of E-14 worldwide. Regional transmission was mainly detected and Australia may be responsible for the spread of E-14 in recent years.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-016-3418-3) contains supplementary material, which is available to authorized users.

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          Most cited references39

          • Record: found
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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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            Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification.

            M. Oberste, K Maher, D Kilpatrick … (1999)
            Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.
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              Consequences of recombination on traditional phylogenetic analysis.

              Selina J. Hein, Mikkel H. Schierup (2000)
              We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.
              Article 0 comments Cited 145 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Peng Chen: chenpeng2403@163.com
                Yan Li: liyan7516@163.com
                Zexin Tao: zexin.tao@163.com
                Haiyan Wang: whyan732002@163.com
                Xiaojuan Lin: linxiaojuan@aliyun.com
                Yao Liu: sdepi@163.com
                Suting Wang: bendan0617@163.com
                Nan Zhou: sduzhounan@163.com
                Pei Wang: wang_pei@yeah.net
                Aiqiang Xu: +86 531 82679606 , aqxuepi@163.com
                Journal
                Journal ID (nlm-ta): BMC Genomics
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC Genomics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2164
                Publication date (Electronic): 7 January 2017
                Publication date PMC-release: 7 January 2017
                Publication date Collection: 2017
                Volume: 18
                Electronic Location Identifier: 48
                Affiliations
                [1 ]Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012 People’s Republic of China
                [2 ]Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014 People’s Republic of China
                Article
                Publisher ID: 3418
                DOI: 10.1186/s12864-016-3418-3
                PMC ID: 5219651
                PubMed ID: 28061751
                SO-VID: 604f8f57-2d60-43c3-ba75-6c5e46292cdf
                Copyright © © The Author(s). 2017
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 16 September 2016
                Date accepted : 13 December 2016
                Funding
                Funded by: Taishan Scholar Program of Shandong Province
                Award ID: ts.201511105
                Award Recipient :
                Funded by: the National Natural Science Foundation of China
                Award ID: 81302481
                Award Recipient :
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Genetics
                Keywords: echovirus 14,acute flaccid paralysis,phylogeny,phylogeography
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: echovirus 14, acute flaccid paralysis, phylogeny, phylogeography

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