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Appl Environ Microbiol. 2015 Dec 11. pii: AEM.03283-15. [Epub ahead of print]
How does sampling methodology influence molecular detection and isolation success in influenza A virus field studies?
Latorre-Margalef N1, Avril A2, Tolf C2, Olsen B3, Waldenstr?m J2.
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Abstract
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.
Copyright ? 2015, American Society for Microbiology. All Rights Reserved.
PMID: 26655759 [PubMed - as supplied by publisher]
How does sampling methodology influence molecular detection and isolation success in influenza A virus field studies?
Latorre-Margalef N1, Avril A2, Tolf C2, Olsen B3, Waldenstr?m J2.
Author information
Abstract
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.
Copyright ? 2015, American Society for Microbiology. All Rights Reserved.
PMID: 26655759 [PubMed - as supplied by publisher]