PMID- 35416426 OWN - NLM STAT- MEDLINE DCOM- 20220929 LR - 20221229 IS - 1865-1682 (Electronic) IS - 1865-1674 (Print) IS - 1865-1674 (Linking) VI - 69 IP - 5 DP - 2022 Sep TI - 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. PG - e2214-e2229 LID - 10.1111/tbed.14560 [doi] AB - The open reading frames (ORF)5 represents approximately 4% of the porcine reproductive and respiratory syndrome virus (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 (PFs) 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 five out of six (83.3%) lung, 16 out of 22 (72.73%) serum and in five out of 95 (5.26%) PF. Whole-PRRSV recovered from serum or lung were used as farm referent strains in 16 out of 20 (80%) farms. In four 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 out of 20 (90%) and at least one vaccine-like strain co-circulating in eight out of 20 (40%) farms. PRRSV recombination events were detected in 12 farms (59%), been 10 out of 12 between wt-PRRSV and two out of 12 between wt-PRRSV and vaccine-like strains. Farms having >/=3 strains had a 12-week increase TTLP versus herds /=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. CI - (c) 2022 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH. FAU - Trevisan, Giovani AU - Trevisan G AUID- ORCID: 0000-0002-4980-526X AD - Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA. FAU - Zeller, Michael AU - Zeller M AD - Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA. AD - Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. FAU - Li, Ganwu AU - Li G AUID- ORCID: 0000-0002-6370-9573 AD - Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA. FAU - Zhang, Jianqiang AU - Zhang J AUID- ORCID: 0000-0001-7228-6202 AD - Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA. FAU - Gauger, Phillip AU - Gauger P AD - Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA. FAU - Linhares, Daniel C L AU - Linhares DCL AD - Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA. LA - eng GR - #19-178/National Pork Board/ GR - #20-109/Iowa Pork Producers Association/ PT - Journal Article DEP - 20220428 PL - Germany TA - Transbound Emerg Dis JT - Transboundary and emerging diseases JID - 101319538 RN - 0 (Viral Vaccines) SB - IM MH - Animals MH - Female MH - High-Throughput Nucleotide Sequencing/veterinary MH - Open Reading Frames MH - *Porcine Reproductive and Respiratory Syndrome/epidemiology/prevention & control MH - *Porcine respiratory and reproductive syndrome virus/genetics MH - Swine MH - *Swine Diseases MH - *Viral Vaccines PMC - PMC9790532 OTO - NOTNLM OT - NGS OT - PRRSV OT - production outcomes OT - recombination COIS- The authors declare no conflict of interest. EDAT- 2022/04/14 06:00 MHDA- 2022/09/30 06:00 PMCR- 2022/12/25 CRDT- 2022/04/13 08:43 PHST- 2022/03/27 00:00 [revised] PHST- 2022/02/04 00:00 [received] PHST- 2022/04/11 00:00 [accepted] PHST- 2022/04/14 06:00 [pubmed] PHST- 2022/09/30 06:00 [medline] PHST- 2022/04/13 08:43 [entrez] PHST- 2022/12/25 00:00 [pmc-release] AID - TBED14560 [pii] AID - 10.1111/tbed.14560 [doi] PST - ppublish SO - Transbound Emerg Dis. 2022 Sep;69(5):e2214-e2229. doi: 10.1111/tbed.14560. Epub 2022 Apr 28.