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Comparative analysis of methods for detecting Avian Paramyxovirus type 1
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
2013 (English)Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
Abstract [en]

Avian paramyxovirus type 1 (APMV-1) is a species of closely related viruses in the genus Avulavirus that can infect most bird species across the globe. The virus, due to its endemic nature and pathogenic potential, posits a threat to the poultry industry worldwide. Surveillance programs to monitor the prevalence of the virus in wild and domesticated birds are therefore important. However, the high mutation rate of this virus poses a challenge when developing methods for virus detection.

 

Virus detection methods include real-time reverse transcription PCR methods that amplify and detect highly conserved regions of the APMV-1 genome. The matrix (M) gene, is targeted in the detection method (M-qPCR) presently used in the laboratory, and the more recently established protocol (L-qPCR) targets the RNA-dependent RNA polymerase (L) gene. In this project, the sensitivity and specificity of these methods were evaluated by comparing the screening results, preformed previously with the M-qPCR, with the results from the L-qPCR screening performed in this project.

 

Comparing the result from L-qPCR screening with those obtained previously with the   method revealed no significant difference in detection frequency between methods. Thus, among the 940 samples screened, 40 (4.3%) were positive in the L-qPCR screening, while 41 (4.4%) were positive in the previous screening using the M-qPCR method. However, although there were no significant difference in detection frequency, there was a difference in the detection pattern. The L-qPCR method detected 11 new positive samples but was, at the same time, not able to detect virus in 12 other samples that previously had been identified as positive with the M-qPCR method. In order to enable molecular characterization of virus detected with the M- and the L-qPCR methods, 33 samples, including those detected with only one of the detection methods, were inoculated in embryonated chicken eggs. Eight virus strains were obtained by egg isolation. Viral fusion gene sequences of these strains were determined and their phylogenetic relatedness analysed. These analyses showed that these viral strains were phylogenetically most closely related to genotype I viruses within the class II clade of APMV-1. This result is in agreement with previous studies on samples from waterfowl on Öland, Sweden.

Place, publisher, year, edition, pages
2013. , 15 p.
Keyword [en]
Virus detection, APMV-1, NDV, phylogenetic analysis, M-qPCR, L-qPCR, avian virus infection, Mallards.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:lnu:diva-27932OAI: oai:DiVA.org:lnu-27932DiVA: diva2:639411
Subject / course
Biology
Educational program
Biology Programme, 180 credits
Supervisors
Examiners
Available from: 2013-08-12 Created: 2013-08-07 Last updated: 2013-08-12Bibliographically approved

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CiteExportLink to record
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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
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