title: High turnover drives prolonged persistence of influenza in managed pig herds.
abstract: Pigs have long been hypothesized to play a central role in the emergence of novel human influenza A virus (IAV) strains, by serving as mixing vessels for mammalian and avian variants. However, the key issue of viral persistence in swine populations at different scales is ill understood. We address this gap using epidemiological models calibrated against seroprevalence data from Dutch finishing pigs to estimate the 'critical herd size' (CHS) for IAV persistence. We then examine the viral phylogenetic evidence for persistence by comparing human and swine IAV. Models suggest a CHS of approximately 3000 pigs above which influenza was likely to persist, i.e. orders of magnitude lower than persistence thresholds for IAV and other acute viruses in humans. At national and regional scales, we found much stronger empirical signatures of prolonged persistence of IAV in swine compared with human populations. These striking levels of persistence in small populations are driven by the high recruitment rate of susceptible piglets, and have significant implications for management of swine and for overall patterns of genetic diversity of IAV.
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06520, USA Fogarty International Center, National Institutes of Health, Bethesda, MD 20850, USA virginia.pitzer@yale.edu.
authors.forename: Virginia E
authors.identifier: 0000-0003-1015-2289
authors.initials: VE
authors.lastname: Pitzer
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London SW7 2AZ, UK.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Aguas
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London SW7 2AZ, UK.
authors.forename: Steven
authors.initials: S
authors.lastname: Riley
authors.affiliation: Department of Virology, Central Veterinary Institute, part of Wageningen UR, Lelystad 8200AB, The Netherlands.
authors.forename: Willie L A
authors.initials: WL
authors.lastname: Loeffen
authors.affiliation: Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
authors.forename: James L N
authors.initials: JL
authors.lastname: Wood
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD 20850, USA Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Bryan T
authors.initials: BT
authors.lastname: Grenfell
mesh_terms: D000818:Animals; D009980:Influenza A virus; D008954:Models, Biological; D009976:Orthomyxoviridae Infections / Q000453:epidemiology* / Q000635:transmission*; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000635:transmission*
keywords: influenza; mathematical modelling; surveillance; swine; transmission dynamics