Molecular characterization of type 1 porcine reproductive and respiratory syndrome viruses (PRRSV) isolated in the Netherlands from 2014 to 2016

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of a devastating pig disease present all over the world. The remarkable genetic variation of PRRSV, makes epidemiological and molecular analysis of circulating viruses highly important to review current diagnostic tools and vaccine efficacy. Monitoring PRRS viruses supports modern herd management by explaining the source of found viruses, either internally or externally from the herd. No epidemiological or molecular study has been published on circulating PRRS-viruses in the Netherlands, since the early nineties. Therefore, the objective of this study is to investigate circulating PRRS-viruses in the Netherlands in 2014, 2015 and 2016 on a molecular level by sequencing ORF2, ORF3, ORF4, ORF5, ORF6 and ORF7. The results demonstrate that the 74 PRRSV strains belong to PRRSV-1, but the diversity among strains is high, based on nucleotide identity, individual ORF length and phylogenetic trees of individual ORFs. Furthermore, the data presented here show that the phylogenetic topology of some viruses is ORF dependent and suggests recombination. The identity of the strain of interest might be misinterpreted and wrong conclusions may be drawn in a diagnostic and epidemiological perspective, when only ORF5 is analyzed, as performed in many routine sequencing procedures.

A recombination between two Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV‐1) vaccine strains has caused severe outbreaks in Danish pigs

“…Recombination between PRRSV field strains has been extensively described for PRRSV-2 (Dong et al, 2017;Li et al, 2009;Wenhui et al, 2012;Zhao et al, 2017) and less frequently for PRRSV-1 (Dortmans, Buter, Dijkman, Houben, & Duinhof, 2019;Martin-Valls et al, 2014). More rarely, recombination between PRRSV-1 field strains and strains of PRRSV-1 MLV vaccine strains has been reported (Chen et al, 2017;Frossard et al, 2013;Marton et al, 2019).…”

Challenge of Naïve and Vaccinated Pigs with a Vaccine-Derived Recombinant Porcine Reproductive and Respiratory Syndrome Virus 1 Strain (Horsens Strain)

“…Recombination between PRRSV field strains has been extensively described for PRRSV-2 [ 19 , 20 ] and less frequently for PRRSV-1 [ 21 , 22 ]. More rarely, recombination between PRRSV-1 field strains and PRRSV-1 MLV vaccine strains has been reported [ 23 , 24 ].…”

Analysis of ORF5 sequences of Porcine Reproductive and Respiratory Syndrome virus (PRRSV) circulating within swine farms in Costa Rica

“…Currently, PRRSV genotyping is still performed mostly based on ORF5 and/or ORF7 sequence analysis and ORF-dependent clustering in phylogenetic trees has been observed, possibly associated with recombination [ 37 ]. However, there are more ORF5 sequences available on public databases which help to improve the resolution of the phylogenetic relationships.…”

“…ORF5 has about 600 nucleotides, shows great genetic diversity, and has a mutation rate of approximately 0.5-1% per year. Although whole-genome sequencing of the PRRSV may give a more complete picture in support of the molecular epidemiology, sequencing ORF5 provides sufficient information to conduct phylogenetic inferences [ 37 , 41 ].…”