Genome Characterization of a Pathogenic Porcine Rotavirus B Strain Identified in Buryat Republic, Russia in 2015

Abstract

An outbreak of enteric disease of unknown etiology with 60% morbidity and 8% mortality in weaning piglets occurred in November 2015 on a farm in Buryat Republic, Russia. Metagenomic sequencing revealed the presence of rotavirus B in feces from diseased piglets while no other pathogens were identified. Clinical disease was reproduced in experimentally infected piglets, yielding the 11 RVB gene segments for strain Buryat15, with an RVB genotype constellation of G12-P[4]-I13-R4-C4-M4-A8-N10-T4-E4-H7. This genotype constellation has also been identified in the United States. While the Buryat15 VP7 protein lacked unique amino acid differences in the predicted neutralizing epitopes compared to the previously published swine RVB G12 strains, this report of RVB in Russian swine increases our epidemiological knowledge on the global prevalence and genetic diversity of RVB.

Porcine rotavirus B as primary causative agent of diarrhea outbreaks in newborn piglets

“…Kuga et al 16 and Marthaler et al 11 observed the highest frequencies of RVB in animals > 55 days of age or fattening pigs, implying that RVB detection in clinical samples appears to increase with age. On the other hand, Alekseev et al 22 detected RVB causing a diarrhoea outbreak in suckling piglets with 3 to 5 days of age in Russia, corroborating our results. The diarrhoea outbreaks described in our study affected only piglets < 20 days of age, mostly newborn piglets, suggesting that RVB can be highly detected in all age groups.…”

Prevalence of enteric pathogens in diarrheic and non-diarrheic samples from pig farms with neonatal diarrhea in the North East of Spain

“…In a study conducted in the United States, the authors reported similar rotaviruses prevalence with 62% RVA, followed by 53% RVC and 33% RVB (Marthaler et al, 2014). Rotavirus B has also been detected in several Asian countries, South Africa, and Brazil (Alekseev et al, 2015). In Europe, limited reports of RVB have been described in Germany (Otto et al, 2015) and the Czech Republic (Smitalova et al, 2009) so far, with prevalence of 1.6% and 0.6% respectively.…”

Novel Mammalian orthorubulavirus 5 Discovered as Accidental Cell Culture Contaminant

“…In November 2015, an outbreak of enteric disease occurred in three-day-old piglets on a farm residing in the Republic of Buryatia, Russia (Supplemental Materials and Methods) [9]. Fecal sample supernatants were passaged on Vero cells in the hope of isolating RVB [9]. Concurrently, the scientist passaging the cell cultures exhibited mild respiratory symptoms including tussis and rhinorrhea.…”

“…Cytopathic effect (syncytia formation) was observed on the fourth passage of the cells (Figure 1). The nucleic acid from the 15th passage was extracted, and NGS was performed to identify the CPE causative pathogen using an Illumina HiSeq2000 (Illumina, San Diego, CA, USA) [9]. NGS generated 9,280,254 paired reads while 8,949,411 reads resulted after trimming [9].…”

“…The nucleic acid from the 15th passage was extracted, and NGS was performed to identify the CPE causative pathogen using an Illumina HiSeq2000 (Illumina, San Diego, CA, USA) [9]. NGS generated 9,280,254 paired reads while 8,949,411 reads resulted after trimming [9]. Kraken identified ~85% (7,602,876) paired reads as Eukaryotic and ~9% (818,499) as viral.…”