Recombinant PRRS Involved in High Morbidity and Mortality Outbreaks, By Doug MacDougald South West Ontario Veterinary Services

Porcine reproductive and respiratory syndrome virus (PRRSV) is generally accepted to be our number 1 problem in swine health in Ontario. Susutained control of the virus has been elusive in large part due to the continuing genetic evolution of the virus. South Korea recently experienced an increase in severe cases of PRRS. These South Korean researchers wanted to examine the genetic background of  two novel Korean lineage 1 PRRSV Type 2 (North American ) strains. KNU-1901 and KNU-1902, were isolated from vaccinated pig farms experiencing unusually high morbidity and mortality.

The researchers found the following:

  • Both isolates contained notable discontinuous 423-nucleotide deletions (DELs) within the genes encoding nonstructural protein 2 (nsp2) and GP3 when compared with the prototype strain VR-2332. The nucleotides provide the coding that guides the manufacture of structural proteins that in large part allow the body to recognize a particular strain of virus.
  • These nsp2 DEL viruses had unique discontinuous “deletion signatures” in 4 areas (111-1-19-9 deletion) in nsp2. This is an expansion from the 3 area (111-1-19 deletion)  previously identified in lineage 1 PRRSV-2 strains with enhanced or virulent disease causing ability.
  • The standard phylogenetic analysis (family tree) based on ORF 5  initially indicated that both novel nsp2 DEL viruses belong to the Korean clade (KOR C) of lineage 1 isolates.
  • But ….. whole genome sequencing had these viruses clustered with lineage KOR A strains based on the nsp2.
  • Recombination detection analysis suggested that both novel isolates are recombinants and may have evolved via natural inter-lineage recombination between circulating KOR A and KOR C strains.

Take Home Messages:

  • PRRS KNU-1901 and KNU-1902 appear to be recently evolved recombinant variants of the virulent lineage 1 family that caused the regional severe PRRS outbreaks in South Korea .
  • PRRS gene sequence comparisons based on ORF 5 can tell us a lot about the genetic evolution and spread of PRRS virus within a regional control program but unfortunately the ORF 5 genetic comparison does not always reveal the entire story.
  • When given a window of opportunity with two different PRRS viruses circulating within the same pig population viral recombination can sometimes produce genetically new and virulent PRRS viruses that can evade the pig’s immune system.

Submitted by Dr. Doug MacDougald

Ref: Jonghyun Park, Subin Choi , Ji Hyun Jeon , Kyung-Won Lee , Changhee Lee    Novel lineage 1 recombinants of porcine reproductive and respiratory syndrome virus isolated from vaccinated herds: genome sequences and cytokine production profilesArch Virol. 2020 Jul 22. doi: 10.1007/s00705-020-04743-y. Online ahead of print.