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

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-sample = 50 (1%) of birds were sampled on a weekly basis once, but after infection was detected, N-sample = 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-sample = 50 of birds in the flock on a weekly or 2 weekly basis would be sufficient.