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How does sampling methodology influence molecular detection and isolation success in influenza A virus field studies?
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
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2016 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 82, no 4, 1147-1153 p.Article in journal (Refereed) Published
Abstract [en]

Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source to spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways initiated several programs in Europe, North America and Africa to monitor circulation of HPAI and low-pathogenic precursor viruses (LPAI). Given the costs for maintaining such programs it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation for LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal and cloacal) collected from wild mallards were screened by real-time PCR and positives subjected to isolation in embryonated chicken eggs. LPAI detection rate was influenced by sample type, where cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value compared to oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the amount of RNA copies in the sample. Interestingly, for a given Ct-value, the isolation success was lower in samples from adult birds than from juveniles. Comparing the results from specific RRT-PCRs and from isolation it was clear that co-infections were common in the investigated birds. The effect of sample type and detection methods warrants some caution for interpretation of results of surveillance data.

Place, publisher, year, edition, pages
2016. Vol. 82, no 4, 1147-1153 p.
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
URN: urn:nbn:se:uu:diva-271076DOI: 10.1128/AEM.03283-15ISI: 000369375900017PubMedID: 26655759OAI: oai:DiVA.org:uu-271076DiVA: diva2:891119
Swedish Environmental Protection Agency, V-124-01Swedish Environmental Protection Agency, V-98-04Swedish Research Council, 2008-58Swedish Research Council, 2010-3067Swedish Research Council, 2011-48Swedish Research Council Formas, 2007-297Swedish Research Council Formas, 2009-1220EU, European Research Council
Available from: 2016-01-05 Created: 2016-01-05 Last updated: 2016-03-02Bibliographically approved

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Olsen, Björn
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