First molecular detection of porcine rotavirus B (RVB) in Poland - case study and genome analysis

In view of its massive financial impact related to increased preweaning mortality and poor growth performance, neonatal diarrhoea in piglets is widely regarded as one of the most common issues in modern swine production. Currently, the diarrhoea of undetermined aetiology arises as a complex diagnostic problem in several pig-rearing countries; therefore, the role of agents with not completely established clinical importance, such as non-group A rotaviruses (RVs), should be taken into consideration in a differential diagnosis procedure. The aim of this study was to report the detection of RVB acting as a potential causative agent of porcine diarrhoea.

The investigation was conducted in a Polish commercial, high-performing farm with 3,300 sows weaning piglets in weekly batches. For the scope of this research, five 3-day-old dead diarrhoeic piglets were collected. All the animals originated from different litters displaying clinical signs regarded as typical of rotaviral enteritis. Prior to the NGS investigation, all the piglets sampled in our current investigation were tested negative for diarrhoea-associated viruses (RVA, RVC, TGEV, PEDV) using commercially available PCR setups. The NGS data for the faecal sample resulted in 510,843 reads after adapter trimming. 981 reads were assigned at species level to RVB (strain GCZ04) during read classification. The genotype constellation of the strain was found to be typical for swine viruses and the nucleotide identities of the segments of the strain were within the cut off values established for different genotypes. The remaining viral reads were annotated to porcine kobuvirus (PKV) (23 reads). Furthermore, the analysis revealed presence of the following taxa: Qubevirus faecium (334 reads), and Gaprivervirus (1 read).

Our study reports the first molecular detection of porcine RVB in faecal samples collected from pigs reared on a commercial swine farm in Poland. Since the material was obtained from clinically affected animals and RVB was proven dominant among viral reads obtained during the NGS investigation, the virus may be considered as a potential causative agent of diarrhoeal disease in suckling piglets. Moreover, our research provides the tenth porcine RVB genome in Europe. The identities and phylogenetic clustering of different segment sequences to those from North America, Asia or Europe may suggest a complex evolutionary history of the Polish strain.