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      New insight into dolphin morbillivirus phylogeny and epidemiology in the northeast Atlantic: opportunistic study in cetaceans stranded along the Portuguese and Galician coasts

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          Abstract

          Background

          Screening Atlantic cetacean populations for Cetacean Morbillivirus (CeMV) is essential to understand the epidemiology of the disease. In Europe, Portugal and Spain have the highest cetacean stranding rates, mostly due to the vast extension of coastline. Morbillivirus infection has been associated with high morbidity and mortality in cetaceans, especially in outbreaks reported in the Mediterranean Sea. However, scarce information is available regarding this disease in cetaceans from the North-East Atlantic populations. The presence of CeMV genomic RNA was investigated by reverse transcription-quantitative PCR in samples from 279 specimens stranded along the Portuguese and Galician coastlines collected between 2004 and 2015.

          Results

          A total of sixteen animals ( n = 16/279, 5.7 %) were positive. The highest prevalence of DMV was registered in striped dolphins ( Stenella coeruleoalba) ( n = 14/69; 20.3 %), slightly higher in those collected in Galicia ( n = 8/33; 24.2 %) than in Portugal ( n = 6/36; 16.7 %).

          Conclusions

          Phylogenetic analysis revealed that, despite the low genetic distances between samples, the high posterior probability (PP) values obtained strongly support the separation of the Portuguese and Galician sequences in an independent branch, separately from samples from the Mediterranean and the Canary Islands. Furthermore, evidence suggests an endemic rather than an epidemic situation in the striped dolphin populations from Portugal and Galicia, since no outbreaks have been detected and positive samples have been detected annually since 2007, indicating that this virus is actively circulating in these populations and reaching prevalence values as high as 24 % among the Galician samples tested.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12917-016-0795-4) contains supplementary material, which is available to authorized users.

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          Most cited references 34

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          CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

          The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
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            MrBayes 3: Bayesian phylogenetic inference under mixed models.

            MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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              Jalview Version 2—a multiple sequence alignment editor and analysis workbench

              Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org Contact: g.j.barton@dundee.ac.uk
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                Author and article information

                Contributors
                (+351) 21 365 2800 , mcarolinabento@fmv.ulisboa.pt
                catarina.eira@ua.pt
                jvv@bio.uminho.pt
                amarcalo@gmail.com
                mctferreira@socpvs.org
                cemma@arrakis.es
                ltavares@fmv.ulisboa.pt
                anaduarte@fmv.ulisboa.pt
                Journal
                BMC Vet Res
                BMC Vet. Res
                BMC Veterinary Research
                BioMed Central (London )
                1746-6148
                26 August 2016
                26 August 2016
                2016
                : 12
                : 1
                Affiliations
                [1 ]Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
                [2 ]Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
                [3 ]Portuguese Wildlife Society, Department of Biology, Minho University, 4710-057 Braga, Portugal
                [4 ]Department of Biology and CESAM, Minho University, 4710-057 Braga, Portugal
                [5 ]Department of Biology and CBMA, Minho University, 4710-057 Braga, Portugal
                [6 ]Coordinadora para o Estudo dos Mamíferos Mariños, 36380 Gondomar, Pontevedra Spain
                Article
                795
                10.1186/s12917-016-0795-4
                5002201
                27566667
                © The Author(s). 2016

                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.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001871, Fundação para a Ciência e a Tecnologia;
                Award ID: CetSenti RECI/AAG-GLO/0470/2012
                Award ID: UID/AMB/50017/2013
                Award ID: SFRH/BD/30240/2006
                Award ID: SFRH/BPD/82407/2011
                Award ID: SFRH/BPD/64889/2009
                Award Recipient :
                Funded by: Life+ Marpro
                Award ID: Life09 NAT/PT/000038
                Funded by: FundRef http://dx.doi.org/10.13039/501100007048, EEA Grants;
                Award ID: PT0039
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2016

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