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Background  Both high and low pathogenic subtype A avian influenza remain ongoing threats to the commercial poultry industry globally. The emergence of a novel low pathogenic H7N9 lineage in China presents itself as a new concern to both human and animal health and may necessitate additional surveillance in commercial poultry operations in affected regions.    Methods  Sampling data was simulated using a mechanistic model of H7N9 influenza transmission within commercial poultry barns together with a stochastic observation process. Parameters were estimated using maximum likelihood. We assessed the probability of detecting an outbreak at time of slaughter using both real-time polymerase chain reaction (rt-PCR) and a hemagglutinin inhibition assay (HI assay) before considering more intense sampling prior to slaughter. The day of virus introduction and  R  0  were estimated jointly from weekly flock sampling data. For scenarios where  R  0  was known, we estimated the day of virus introduction into a barn under different sampling frequencies.    Results  If birds were tested at time of slaughter, there was a higher probability of detecting evidence of an outbreak using an HI assay compared to rt-PCR, except when the virus was introduced <2 weeks before time of slaughter. Prior to the initial detection of infection  N   s  a  m  p  l  e   = 50 (1%) of birds were sampled on a weekly basis once, but after infection was detected,  N   s  a  m  p  l  e   = 2000 birds (40%) were sampled to estimate both parameters. We accurately estimated the day of virus introduction in isolation with weekly and 2-weekly sampling.    Conclusions  A strong sampling effort would be required to infer both the day of virus introduction and  R  0 . Such a sampling effort would not be required to estimate the day of virus introduction alone once  R  0  was known, and sampling  N   s  a  m  p  l  e   = 50 of birds in the flock on a weekly or 2 weekly basis would be sufficient.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2334-14-427) contains supplementary material, which is available to authorized users.

bmc infectious diseases

Surveillance of low pathogenic novel H7N9 avian influenza in commercial poultry barns: detection of outbreaks and estimation of virus introduction time