Implementing a user-friendly format to analyze PRRSV next-generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

Trevisan, Giovani
Zeller, Michael
Li, Ganwu
Zhang, Jianqiang
Gauger, Phillip
Linhares, Daniel
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Veterinary Diagnostic and Production Animal Medicine
The ORF5 represents approximately 4% of the PRRSV-2 genome (whole-PRRSV) and is often determined by the Sanger technique, which rarely detects > 1 PRRSV strain if present in the sample. Next-generation sequencing (NGS) may provide a more appropriate method of detecting multiple PRRSV strains in one sample. This work assessed the effect of PRRSV genetic variability and recombination events, using NGS, on the time-to-low prevalence (TTLP) and total losses in breeding herds (n 20) that detected a PRRSV outbreak and adopted measures to eliminate PRRSV. Serum, lung, or live virus inoculation material collected within 3-weeks of outbreak, and subsequently, processing fluids (PF) were tested for PRRSV by RT-qPCR and NGS. Recovered whole-PRRSV or partial sequences were used to characterize within and between herd PRRSV genetic variability. Whole-PRRSV was recovered in 5/6 (83.3%) lung, 16/22 (72.73%) serum, and in 5/95 (5.26%) PF. Whole-PRRSV recovered from serum or lung were used as farm referent strains in 16/20 (80%) farms. In 4 farms, only partial genome sequences were recovered and used as farm referent strains. At least two wild-type PRRSV strains (wt-PRRSV) were circulating simultaneously in 18/20 (90%) and at least one vaccine-like strain co-circulating in 8/20 (40%) farms. PRRSV recombination events were detected in 12 farms (59%), been 10/12 between wt-PRRSV and 2/12 between wt-PRRSV and vaccine-like strains. Farms having ≥3 strains had a 12-week increase TTLP vs. herds ≤2 strains detected. Farms with ≤2 strains (n 10) had 1,837, and farms with no recombination events detected (n 8) had 1,827 fewer piglet losses per 1,000 sows vs. farms with ≥3 PRRSV strains (n 8) or detected recombination (n 10), respectively. NGS outcomes and novel visualization methods provided more thorough insight into PRRSV dynamics, genetic variability, detection of multiple strains co-circulating in breeding herds and helped establish practical guidelines for using PRRSV NGS outputs.
This is the peer-reviewed version of the following article: Trevisan, Giovani, Michael Zeller, Ganwu Li, Jianqiang Zhang, Phillip Gauger, and Daniel CL Linhares. "Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events." Transboundary and Emerging Diseases (2022), which has been published in final form at DOI: 10.1111/tbed.14560. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. Copyright 2022 Wiley. Posted with permission.