Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam

Abstract

Picornaviruses infecting pigs, described for many years as 'porcine enteroviruses', have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 59 untranslated region (59 UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90 % in recently weaned pigs but declining to 40 % in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74 % (n570) compared with 72 % (n5128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among these, VP1 sequence comparisons identified six type 1 and seven type 6 variants, while four further VP1 sequences failed to group with any previously identified EV-G types. These have now been formally assigned as EV-G types 8-11 by the Picornavirus Study Group. Comparison of VP1, VP4/VP2, 3D pol and 59 UTRs of study samples and those available on public databases showed frequent, bootstrap-supported differences in their phylogenies indicative of extensive within-species recombination between genome regions. In summary, we identified extremely high frequencies of infection with EV-G in pigs in Vietnam, substantial genetic diversity and recombination within the species, and evidence for a much larger number of circulating EV-G types than currently described.

A Naturally Occurring Recombinant Enterovirus Expresses a Torovirus Deubiquitinase

“…Furthermore, the highly recombinogenic nature of PV was associated with the emergence of pathogenic vaccine-derived viruses during the global polio eradication campaign (10)(11)(12). Recombination within animal species of simian, swine, and bovine enteroviruses has also been documented (58)(59)(60). A typical example is the emergence of swine vesicular disease virus (SVDV), which is genetically closely linked to coxsackievirus B5 (CV-B5).…”

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].…”

“…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]. Indeed, EV-G has not been widely associated with pathogenic diseases in swine, except for single reports of skin lesions [11], flaccid paralysis [12] and the case (Porcine/USA/Texas1/2014, Porcine/USA/ Texas2/2014) of diarrhoeic pigs described in this study.…”

Poliovirus Polymerase Leu420 Facilitates RNA Recombination and Ribavirin Resistance

“…Enterovirus and rhinovirus species groups are dependent upon, and defined by, ongoing recombination among viruses within each species group (6)(7)(8)(9)(10)(11)(12). The capsid genes and nonstructural genes of viruses within each species group evolve separately due to the distinct functions and selective pressures associated with these gene cassettes (8).…”