title: Sampling guidelines for oral fluid-based surveys of group-housed animals.
abstract: Formulas and software for calculating sample size for surveys based on individual animal samples are readily available. However, sample size formulas are not available for oral fluids and other aggregate samples that are increasingly used in production settings. Therefore, the objective of this study was to develop sampling guidelines for oral fluid-based porcine reproductive and respiratory syndrome virus (PRRSV) surveys in commercial swine farms. Oral fluid samples were collected in 9 weekly samplings from all pens in 3 barns on one production site beginning shortly after placement of weaned pigs. Samples (n=972) were tested by real-time reverse-transcription PCR (RT-rtPCR) and the binary results analyzed using a piecewise exponential survival model for interval-censored, time-to-event data with misclassification. Thereafter, simulation studies were used to study the barn-level probability of PRRSV detection as a function of sample size, sample allocation (simple random sampling vs fixed spatial sampling), assay diagnostic sensitivity and specificity, and pen-level prevalence. These studies provided estimates of the probability of detection by sample size and within-barn prevalence. Detection using fixed spatial sampling was as good as, or better than, simple random sampling. Sampling multiple barns on a site increased the probability of detection with the number of barns sampled. These results are relevant to PRRSV control or elimination projects at the herd, regional, or national levels, but the results are also broadly applicable to contagious pathogens of swine for which oral fluid tests of equivalent performance are available.
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA. Electronic address: mrotolo@iastate.edu.
authors.forename: Marisa L
authors.initials: ML
authors.lastname: Rotolo
authors.affiliation: Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA.
authors.forename: Yaxuan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA.
authors.forename: Chong
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Luis
authors.initials: L
authors.lastname: Giménez-Lirola
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Baum
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Phillip C
authors.initials: PC
authors.lastname: Gauger
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Karen M
authors.initials: KM
authors.lastname: Harmon
authors.affiliation: Smithfield Foods, Algona, IA, USA.
authors.forename: Marlin
authors.initials: M
authors.lastname: Hoogland
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Rodger
authors.initials: R
authors.lastname: Main
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Zimmerman
mesh_terms: D000818:Animals; D019937:Diagnostic Techniques and Procedures / Q000592:standards / Q000662:veterinary; D017408:Guidelines as Topic; D006799:Housing, Animal; D008954:Models, Biological; D011159:Population Surveillance; D019318:Porcine Reproductive and Respiratory Syndrome / Q000175:diagnosis* / Q000517:prevention & control / Q000635:transmission; D019316:Porcine respiratory and reproductive syndrome virus / Q000235:genetics; D012107:Research Design / Q000592:standards*; D012463:Saliva / Q000821:virology*; D013552:Swine
keywords: Modeling; Monitoring; Oral fluid; PRRSV; Probability of detection; Sample size; Sampling; Surveillance