title: Inferring patterns of influenza transmission in swine from multiple streams of surveillance data.
abstract: Swine populations are known to be an important source of new human strains of influenza A, including those responsible for global pandemics. Yet our knowledge of the epidemiology of influenza in swine is dismayingly poor, as highlighted by the emergence of the 2009 pandemic strain and the paucity of data describing its origins. Here, we analyse a unique dataset arising from surveillance of swine influenza at a Hong Kong abattoir from 1998 to 2010. We introduce a state-space model that estimates disease exposure histories by joint inference from multiple modes of surveillance, integrating both virological and serological data. We find that an observed decrease in virus isolation rates is not due to a reduction in the regional prevalence of influenza. Instead, a more likely explanation is increased infection of swine in production farms, creating greater immunity to disease early in life. Consistent with this, we find that the weekly risk of exposure on farms equals or exceeds the exposure risk during transport to slaughter. We discuss potential causes for these patterns, including competition between influenza strains and shifts in the Chinese pork industry, and suggest opportunities to improve knowledge and reduce prevalence of influenza in the region.
authors: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.
authors: Christopher C
authors: CC
authors: Strelioff
authors: Dhanasekaran
authors: D
authors: Vijaykrishna
authors: Steven
authors: S
authors: Riley
authors: Yi
authors: Y
authors: Guan
authors: J S Malik
authors: JS
authors: Peiris
authors: James O
authors: JO
authors: Lloyd-Smith
mesh_terms: D000003:Abattoirs; D000822:Animal Husbandry; D000818:Animals; D001499:Bayes Theorem; D062665:Epidemiological Monitoring / Q000662:veterinary*; D006723:Hong Kong / Q000453:epidemiology; D053118:Influenza A Virus, H1N1 Subtype / Q000502:physiology*; D008954:Models, Biological; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000635:transmission / Q000662:veterinary* / Q000821:virology; D012307:Risk Factors; D012621:Seasons; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000635:transmission* / Q000821:virology; D013997:Time Factors; D014186:Transportation
keywords: disease ecology; infectious disease surveillance; influenza; state–space model; swine; zoonosis
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