Avian influenza: Mixed infections and missing viruses

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

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


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
Pages (from-to)1964-1977
Number of pages14
Issue number8
StatePublished - 5 Aug 2013
Externally publishedYes


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


Dive into the research topics of 'Avian influenza: Mixed infections and missing viruses'. Together they form a unique fingerprint.

Cite this