Molecular detection of  Porcine circovirus type 2  in swine herds of Eastern Cape Province South Africa

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Abstract

Background

Porcine circovirus type 2 (PCV2) remains the main causative viral pathogen of porcine circovirus-associated diseases (PCVAD) of great economic importance in pig industry globally. This present study aims at determining the occurrence of the viral pathogen in swine herds of the Province.

Results

The data obtained revealed that 15.93% of the screened samples (54/339) from the swine herds of the studied areas were positive for PCV2; while the severity of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6 to 60% in the studied farms. The majority (15 out of 17 = 88%) of the analyzed sequences were found clustering with other PCV2b strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genogroup, which is presently another fast-spreading genotype with observable higher virulence in global swine herds.

Conclusion

This is the first report of PCV2 in swine herds of the Province and the first detection of PCV2b and PCV2d in South African swine herds. It follows the first reported case of PCV2a in an outbreak of porcine multisystemic wasting syndrome (PMWS) in Gauteng Province, South Africa more than one decade ago. This finding confirmed the presence of this all-important viral pathogen in pigs of the region; which could result in a serious outbreak of PCVAD and huge economic loss at the instances of triggering factors if no appropriate measures are taken to effectively curb its spread.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1121-4) contains supplementary material, which is available to authorized users.

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Most cited references 36

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)

We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.

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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Matthew Kearse, Richard Moir, Amy Wilson … (2012)

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com

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Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2.

Cadhla Firth, Siobain Duffy, Michael Charleston … (2009)

Porcine circovirus 2 (PCV2) is the primary etiological agent of postweaning multisystemic wasting syndrome (PMWS), one of the most economically important emerging swine diseases worldwide. Virulent PCV2 was first identified following nearly simultaneous outbreaks of PMWS in North America and Europe in the 1990s and has since achieved global distribution. However, the processes responsible for the emergence and spread of PCV2 remain poorly understood. Here, phylogenetic and cophylogenetic inferences were utilized to address key questions on the time scale, processes, and geographic diffusion of emerging PCV2. The results of these analyses suggest that the two genotypes of PCV2 (PCV2a and PCV2b) are likely to have emerged from a common ancestor approximately 100 years ago and have been on independent evolutionary trajectories since that time, despite cocirculating in the same host species and geographic regions. The patterns of geographic movement of PCV2 that we recovered appear to mimic those of the global pig trade and suggest that the movement of asymptomatic animals is likely to have facilitated the rapid spread of virulent PCV2 around the globe. We further estimated the rate of nucleotide substitution for PCV2 to be on the order of 1.2 x 10(-3) substitutions/site/year, the highest yet recorded for a single-stranded DNA virus. This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide.

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Author and article information

Contributors

Kayode Olayinka Afolabi: kayodeolayinkaafolabi@gmail.com , 201512532@ufh.ac.za

Benson Chuks Iweriebor: biweriebor@ufh.ac.za

Larry Chikwelu Obi: lobi@ufh.ac.za

Anthony Ifeanyi Okoh: aokoh@ufh.ac.za

Journal

Journal ID (nlm-ta): BMC Microbiol

Journal ID (iso-abbrev): BMC Microbiol

Title: BMC Microbiology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2180

Publication date (Electronic): 2 November 2017

Publication date PMC-release: 2 November 2017

Publication date Collection: 2017

Volume: 17

Electronic Location Identifier: 212

Affiliations

[1 ]ISNI 0000 0001 2152 8048, GRID grid.413110.6, Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, , University of Fort Hare, ; Private Bag X1314, Alice, Eastern Cape Province 5700 South Africa

[2 ]ISNI 0000 0001 2152 8048, GRID grid.413110.6, SAMRC Microbial Water Quality Monitoring Centre, , University of Fort Hare, ; Private Bag X1314, Alice, Eastern Cape Province 5700 South Africa

[3 ]ISNI 0000 0001 2152 8048, GRID grid.413110.6, Academic and Research Division, , University of Fort Hare, ; Private Bag X1314, Alice, Eastern Cape Province South Africa

Article

Publisher ID: 1121

DOI: 10.1186/s12866-017-1121-4

PMC ID: 5669008

PubMed ID: 29096613

SO-VID: 1a89beac-4429-4116-ab96-fa4d345ef59e

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 : 11 June 2017

Date accepted : 23 October 2017

Funding

Funded by: South African Medical Research Council (ZA)

Award ID: SAMRC/UFH/P790

Award Recipient : Anthony Ifeanyi Okoh

Funded by: FundRef http://dx.doi.org/10.13039/501100001321, National Research Foundation;

Award ID: 109622

Award Recipient : Larry Chikwelu Obi

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ScienceOpen disciplines: Microbiology & Virology

Keywords: porcine circovirus type 2,eastern cape province,south africa

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ScienceOpen disciplines: Microbiology & Virology

Keywords: porcine circovirus type 2, eastern cape province, south africa

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Molecular detection of Porcine circovirus type 2 in swine herds of Eastern Cape Province South Africa

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Most cited references 36

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2.

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