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 j14 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 %; P50.01). 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.

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

“…Enteroviruses have been more generally linked to neurological disorders in pigs, although they are commonly found in feces as well 11,12,[32][33][34] . In a study from Vietnam, no significant correlation was found between diarrhea status and presence of enterovirus G in feces 35 . The involvement of both astro-and enteroviruses in the pathogenesis of enteric disorders might be questioned here, but cannot be completely ruled out.…”

“…However, the prevalence of kobuvirus has been widely described in pigs from several European countries (The Netherlands (16.7%), Slovakia (63.4%), Hungary (81.0%), Czech Republic (87.3%), Austria (46.2%), Italy (52.4%), Germany (54.5%) and Sweden (45.0%)), American countries (The United States (21.9%) and Brazil (53.0%)), African countries (Kenya (14.9%) and Uganda (15.5%)) and Asian countries (Thailand (99%), South Korea (52.1%) and Vietnam (29.3%)) [44][45][46][48][49][50][51][52][53] . In a small proportion of these studies, statistically significant associations between prevalence of kobuvirus and diarrhea in pigs were demonstrated, such as in Hungary (54.5% prevalence in healthy pigs vs 92.3% prevalence in diarrheic pigs), Spain (47.5% healthy vs 74.4% diarrheic), Brazil (41% vs 78.4%), Thailand (19.3% vs 84.5%) and Vietnam (27.6% to 40.9%) 35,45,46,52 . Indeed, it is difficult to make correlations between prevalence of the virus and diarrhea, as the pathogenicity of the virus could be largely influenced by other factors such as co-infections with other enteric viruses, microbiota and management factors.…”

A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease

“…In 2016, the prevalence of EV-G infections in Vietnam was up to 90 % in piglets and 40 % in pigs over 1 year of age [8,9], and the prevalence among Spanish swine herds at six farms ranged from 2 to 82 % [10]. A recent analysis found no difference in the prevalence of EV-G infection in pigs from Vietnam, with or without diarrhoea [8].…”

“…The 14 currently available EV-G complete genomes from GenBank (with VP1-based genotypes: 1-6, 8-10) were identified from swine in the UK, Belgium, China, Hungary, Vietnam, South Korea and the USA [9,13,[27][28][29][30][31][32][33]. Currently, EV-G genotypes are classified solely by the VP1.…”

Molecular Identification of Enteroviruses from Cattle and Goat Feces and Environment in Thailand

“…EV-Gs are detected mainly in domestic pigs (EV-G1 to -4, -6, -8 to -15, and -17 to -19) (http://www.picornaviridae.com/enterovirus/ev-g/ev_g_seq.htm). Recent reports have shown that the virus can also be isolated from wild boars (EV-G4 and -16), small ruminants such as sheep (EV-G5 and -7), goats (EV-G20), and Sichuan takins from several countries in Europe, Asia, and the Americas (19,20,(27)(28)(29). In animals naturally infected with EV-G, neurological disorders, fertility disorders, diarrhea, and dermal lesions have been reported, although the mechanism of their pathogenesis remains unclear (30)(31)(32).…”