title: Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in Vietnam.
abstract: A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types EV-G8-EV-G11). To better characterize the genetic diversity of EV-G and investigate the possible existence of further circulating types, we performed a larger-scale study on 484 pig and 45 farm-bred boar faecal samples collected in 2012 and 2014, respectively. All samples from the previous and current studies were also screened for kobuviruses. The overall EV infection frequency remained extremely high (395/484; 81.6%), but with comparable detection rates and viral loads between healthy and diarrhoeic pigs; this contrasted with less frequent detection of EV-G in boars (4/45; 8.9%). EV was most frequently detected in pigs ≤ 14 weeks old (∼ 95%) and declined in older pigs. Infections with EV-G1 and EV-G6 were most frequent, whilst less commonly detected types included EV-G3, EV-G4 and EV-G8-EV-G11, and five new types (EV-G12-EV-G16). In contrast, kobuvirus infection frequency was significantly higher in diarrhoeic pigs (40.9 versus 27.6%; P = 0.01). Kobuviruses also showed contrasting epizootiologies and age associations; a higher prevalence was found in boars (42%) compared with domestic pigs (29%), with the highest infection frequency amongst pigs >52 weeks old. Although genetically diverse, all kobuviruses identified belonged to the species Aichivirus C. In summary, this study confirms infection with EV-G was endemic in Vietnamese domestic pigs and exhibits high genetic diversity and extensive inter-type recombination.
authors.affiliation: Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.
authors.forename: Nguyen
authors.initials: N
authors.lastname: Van Dung
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: Pham Hong
authors.initials: PH
authors.lastname: Anh
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: Nguyen
authors.initials: N
authors.lastname: Van Cuong
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.|Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK.
authors.forename: Ngo Thi
authors.initials: NT
authors.lastname: Hoa
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: Juan
authors.initials: J
authors.lastname: Carrique-Mas
authors.affiliation: Subdepartment of Animal Health, Dong Thap Province, Vietnam.
authors.forename: Vo Be
authors.initials: VB
authors.lastname: Hien
authors.affiliation: Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.
authors.forename: C
authors.initials: C
authors.lastname: Sharp
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: M
authors.initials: M
authors.lastname: Rabaa
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: A
authors.initials: A
authors.lastname: Berto
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: James
authors.initials: J
authors.lastname: Campbell
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.|Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK.|London School of Hygiene and Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Farrar
authors.affiliation: Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Woolhouse
authors.affiliation: Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.|Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK.
authors.forename: Juliet E
authors.initials: JE
authors.lastname: Bryant
authors.affiliation: Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.|Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Simmonds
mesh_terms: D000818:Animals; D003967:Diarrhea / Q000453:epidemiology / Q000662:veterinary / Q000821:virology; D004770:Enterovirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004769:Enterovirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D005243:Feces / Q000821:virology*; D014644:Genetic Variation; D052699:Kobuvirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D008403:Mass Screening; D010850:Picornaviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D015995:Prevalence; D034421:Sus scrofa; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology*; D014744:Vietnam / Q000453:epidemiology; D019562:Viral Load