Get whole-genome insights in your PRRSV strain with PathoSense DeepDive
by Sebastiaan Theuns
Sample type
Rectal swab (yes, we were also starstruck)… Pool of 5 nursery pigs.
Case discussion
Diarrhea and finding PRRSV in Spain… This combination got us starstruck as PRRSV is found typically in a respiratory or reproductive context. Not surprisingly, this Spanish farm showed mortality linked to a PRRSV outbreak. Furthermore, the nursery piglets were also showing severe watery diarrhea. The veterinarians took a sample of the gut content. A strong load of rotavirus A was present, besides kobuvirus, and enteric bacteria such as Lawsonia intracellularis, Escherichia coli and Chlamydia suis. Due to excessive polyserositis and fibrin formation in the abdomen, systemic infections were likely picked up as well. This explains this finding of Mycoplasma hyorhinis. Although it is often a non-pathogenic inhabitant of the airways, it can also cause polyserositis in pigs. Moreover, PRRSV was detected at a high load as well.
PRRSV is a primary respiratory pathogen and important as a driver for co-infections. Using the PathoSense DeepDive feature, it was possible to perform a further phylogenetic analysis of the strain. This indicated that this strain was a wild-type strain and variant of the ‘Rosalia’ strains that were circulating at the time in Spain. Interestingly, if the analysis would have been made only for ORF5, the conclusion would have been that a vaccine strain was present. Indeed, recombination analysis showed that this strain was a recombinant between a vaccine strain and the Rosalia strain, demonstrating that whole genome sequencing is a crucial tool in following the evolution of PRRSV on farms.
When and how to request a DeepDive analysis
When sufficient high-quality data is available from your PathoSense analysis for certain viral strains or viruses, a DeepDive phylogenetic analysis can be requested. This is indicated on your PathoSense report.
To request a DeepDive analysis, contact your lab directly following the instructions that are available on the report.
For Influenza A (e.g. H1avN2) and Rotavirus A (e.g. G5P7), you don't need to request a DeepDive. The genotyping information is always included in the standard PathoSense diagnostic report at no extra cost, provided the required genes are detected during analysis.
PathoSense DeepDive is currently available for the following viral pathogens:
- Pig: PRRSV, PCV2, Porcine parvovirus 1
- Cattle: BRSV, bovine coronavirus, BVDV
- Poultry: reovirus, IBDV (Gumboro)
- Feline/canine: feline/canine parvovirus, feline calicivirus
Pathogens in the Spotlight 11: Prof. Guillermo Ramis & dr. Gabriel Moyano on Swine Diagnostics in Spain
Podcast
The impact of the highly virulent 'Rosalia' PRRS strain and how the industry is recovering through better monitoring is discussed. Prof. Ramis introduces his diagnostic philosophy, "Dime qué tengo" ("Tell me what I have"), arguing against the traditional method of just 'ticking boxes' on a form. The conversation dives deep into the value of full genome sequencing, sharing a fascinating case where a necrotoxigenic E. coli was unexpectedly found in the lungs, distinguished only by specific virulence factors that traditional PCRs would miss.