Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study

Abstract

Describing PRRSV whole-genome viral diversity data over time within the host and withinfarm 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 wildtype 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.