Avian influenza: Mixed infections and missing viruses

LeAnn L. Lindsay, Terra R. Kelly, Magdalena Plancarte, Seth Schobel, Xudong Lin, Vivien G. Dugan, David E. Wentworth, Walter M Boyce

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

A high prevalence and diversity of avian influenza (AI) viruses were detected in a population of wild mallards sampled during summer 2011 in California, providing an opportunity to compare results obtained before and after virus culture. We tested cloacal swab samples prior to culture by matrix real-time PCR, and by amplifying and sequencing a 640bp portion of the hemagglutinin (HA) gene. Each sample was also inoculated into embryonated chicken eggs, and full genome sequences were determined for cultured viruses. While low matrix Ct values were a good predictor of virus isolation from eggs, samples with high or undetectable Ct values also yielded isolates. Furthermore, a single passage in eggs altered the occurrence and detection of viral strains, and mixed infections (different HA subtypes) were detected less frequently after culture. There is no gold standard or perfect reference comparison for surveillance of unknown viruses, and true negatives are difficult to distinguish from false negatives. This study showed that sequencing samples prior to culture increases the detection of mixed infections and enhances the identification of viral strains and sequences that may have changed or even disappeared during culture.

Original languageEnglish (US)
Pages (from-to)1964-1977
Number of pages14
JournalViruses
Volume5
Issue number8
DOIs
StatePublished - Aug 5 2013

Keywords

  • Avian influenza
  • Embryonated chicken egg
  • Genome
  • Hemagglutinin
  • Sequencing
  • Surveillance
  • Virus isolation

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

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  • Cite this

    Lindsay, L. L., Kelly, T. R., Plancarte, M., Schobel, S., Lin, X., Dugan, V. G., Wentworth, D. E., & Boyce, W. M. (2013). Avian influenza: Mixed infections and missing viruses. Viruses, 5(8), 1964-1977. https://doi.org/10.3390/v5081964