Porcine Reproductive and Respiratory Syndrome Viral Diversity within a Farrow-to-Wean Farm Cohort

Today we are sharing a recent publication from the MSHMP team in collaboration with the VanderWaal and Schroeder’s labs. The objective of the study was to assess the diversity of PRRS genomes within a cohort of naïve pigs undergoing a PRRS outbreak. The full paper is available online in open access.


  • 2,500 farrow-to-wean farm undergoing a PRRS outbreak
  • Live-virus inoculation of a PRRS strain with RFLP pattern 1-3-4 and lineage 1E
  • 127 piglets were sampled at 3-5 days of age and again at 17-19 days of age
  • Samples tested by RT-PCR and whole-genome sequencing


  • All samples tested positive for PRRS in piglets 3-5 DOA (median Ct= 14.7)
  • Female piglets had significantly higher Ct-values than males at 3-5DOA.
  • About 53% of piglets died before reaching 17-19 DOA. These piglets had significantly lower Ct value than the surviving ones.
  • All surviving piglets were PCR positive at 17-19 DOA (median Ct=18.3)
  • Comparing all ORFs 2-7, the minimum percent nucleotide identity was 99.84% at 3-5DOA and 99.57% at 17-19DOA.
  • The minimum within pig identity was 99.65%.
  • Within a littler and at the same timepoint, the lowest nucleotide identity was 95.81%, found in ORF4 at 17–19 DOA. Next was ORF5a at 3-5DOA with 97.74%.
  • 10 regions displayed an increased genetic variation throughout ORFs 2a/2b, 4, 5a/5, 6, and 7 (see figure below)
Within-farm nucleotide of porcine reproductive and respiratory syndrome within a 31-nucleotide sliding window; increased diversity regions highlighted in grey 


Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3–5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17–19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal–Wallis p < 0.001) at 3–5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17–19 DOA decreased with every one unit increase in Ct values at 3–5 DOA (OR = 0.76, 95% CI 0.61–0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3–5 DOA and 17–19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3–5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7.

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