title: Surveillance of low pathogenic novel H7N9 avian influenza in commercial poultry barns: detection of outbreaks and estimation of virus introduction time.
abstract: 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 R0 were estimated jointly from weekly flock sampling data. For scenarios where R0 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 R0. Such a sampling effort would not be required to estimate the day of virus introduction alone once R0 was known, and sampling N sample = 50 of birds in the flock on a weekly or 2 weekly basis would be sufficient.
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, UK. amy.pinsent07@imperial.ac.uk.
authors.forename: Amy
authors.initials: A
authors.lastname: Pinsent
authors.forename: Isobel M
authors.initials: IM
authors.lastname: Blake
authors.forename: Michael T
authors.initials: MT
authors.lastname: White
authors.forename: Steven
authors.initials: S
authors.lastname: Riley
mesh_terms: D000822:Animal Husbandry / Q000295:instrumentation* / Q000706:statistics & numerical data; D000818:Animals; D002681:China / Q000453:epidemiology; D004196:Disease Outbreaks / Q000662:veterinary; D064766:Influenza A Virus, H7N9 Subtype / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D008962:Models, Theoretical; D011159:Population Surveillance; D011200:Poultry; D011201:Poultry Diseases / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors
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