Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain

Abstract

Background The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotavirus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically characterized. Results PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 different viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained a total of 24 ARN viral genomes (> 90% genome sequence), characterizing for first time the full genome of circulating strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing countries. Conclusions Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion into routine diagnostic panels for diarrhoea in swine should be considered.

Differential transcriptome response following infection of porcine ileal enteroids with species A and C rotaviruses

“…In this study, we identified 9 DEGs (Galnt 1–5, 7, 10–12) following RVA and RVC infection. Among them, expression of six [ 3 – 5 , 7 , 11 , 12 ] genes was significantly modulated. The most prominent effect (downregulation) on the expression of these enzymes was observed for GALNT5 in PIEs infected with RVC and G9P[13].…”

“…However, there is growing evidence that species C RV (RVC) is a significant cause of infectious diarrhea in humans and animals [ 4 – 7 ]. While RVAs mostly affect piglets or young children after weaning [ 8 , 9 ], RVC diarrhea is highly prevalent among nursing, 1–10-day-old piglets, causing significant economic losses to farmers and the pork industry [ 4 , 10 , 11 ]. Recent data suggest that reassortant RVC strains circulate in northeast Asia in both the human and swine populations [ 12 ].…”

Development of a multiplex reverse transcription-quantitative PCR (qPCR) method for detecting common causative agents of swine viral diarrhea in China

“…As leading causes of swine diarrhea, PEDV, RVA, PDCoV and/or TGEV are frequently characterized on worldwide pig farms [ 15 , 16 ]. It is of clinical significance to develop rapid and accurate multiplex methods to differentiate these four agents from diarrheal causes as the symptoms induced by them are similar [ 11 ].…”

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

“…In a separate investigation, Sachsenröder and colleagues demonstrated that the proportion of porcine viruses in the intestinal virome decreased with increasing pig age, whereas the opposite was observed for phages [ 14 ]. This suggests a potential correlation between the porcine enteric virome and age [ 15 , 16 ]. Nonetheless, there is still a gap in the research on the intestinal virome of weaned Tibetan pigs.…”