title: Farm-level prevalence and risk factors for detection of hepatitis E virus, porcine enteric calicivirus, and rotavirus in Canadian finisher pigs.
abstract: Hepatitis E virus (HEV), norovirus (NoV), and rotavirus (RV) are all hypothesized to infect humans zoonotically via exposure through swine and pork. Our study objectives were to estimate Canadian farm-level prevalence of HEV, NoV [specifically porcine enteric calicivirus (PEC)], and RV in finisher pigs, and to study risk factors for farm level viral detection. Farms were recruited using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) and FoodNet Canada on-farm sampling platforms. Six pooled groups of fecal samples were collected from participating farms, and a questionnaire capturing farm management and biosecurity practices was completed. Samples were assayed using validated real-time polymerase chain reaction (RT-PCR). We modeled predictors for farm level viral RNA detection using logistic and exact logistic regression. Seventy-two herds were sampled: 51 CIPARS herds (15 sampled twice) and 21 FoodNet Canada herds (one sampled twice). Hepatitis E virus was detected in 30/88 farms [34.1% (95% CI 25.0%, 44.5%)]; PEC in 18 [20.5% (95% CI: 13.4%, 30.0%)], and RV in 6 farms [6.8% (95% CI: 3.2%, 14.1%)]. Farm-level prevalence of viruses varied with province and sampling platform. Requiring shower-in and providing boots for visitors were significant predictors (P < 0.05) in single fixed effect mixed logistic regression analysis for detection of HEV and PEC, respectively. In contrast, all RV positive farms provided boots and coveralls, and 5 of 6 farms required shower-in. We hypothesized that these biosecurity measures delayed the mean age of RV infection, resulting in an association with RV detection in finishers. Obtaining feeder pigs from multiple sources was consistently associated with greater odds of detecting each virus.
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Barbara
authors.initials: B
authors.lastname: Wilhelm
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Danielle
authors.initials: D
authors.lastname: Leblanc
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: David
authors.initials: D
authors.lastname: Leger
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Sheryl
authors.initials: S
authors.lastname: Gow
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Anne
authors.initials: A
authors.lastname: Deckert
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: David L
authors.initials: DL
authors.lastname: Pearl
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Robert
authors.initials: R
authors.lastname: Friendship
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Andrijana
authors.initials: A
authors.lastname: Rajić
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Alain
authors.initials: A
authors.lastname: Houde
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario N1G 2W1 (Wilhelm, Pearl, Friendship, Rajić, McEwen); Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, St-Hyacinthe, Quebec J2S 8E3 (Leblanc, Houde); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario N1G 5B2 (Leger, Deckert); Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Western College of Veterinary Medicine, 52 Campus Drive, Saskatoon, Saskatchewan S7K 3J8 (Gow).
authors.forename: Scott
authors.initials: S
authors.lastname: McEwen
mesh_terms: D000822:Animal Husbandry; D000818:Animals; D002139:Caliciviridae / Q000145:classification / Q000302:isolation & purification*; D017250:Caliciviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D002170:Canada / Q000453:epidemiology; D005243:Feces / Q000821:virology; D016751:Hepatitis E / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D016752:Hepatitis E virus / Q000302:isolation & purification*; D015995:Prevalence; D012307:Risk Factors; D012401:Rotavirus / Q000302:isolation & purification*; D012400:Rotavirus Infections / Q000453:epidemiology / Q000662:veterinary / Q000821:virology; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*