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

Abstract

Background Worldwide, Porcine Reproductive and Respiratory Syndrome (PRRS) is among the diseases that cause the highest economic impact in modern pig production. PRRS was first detected in Costa Rica in 1996 and has since then severely affected the local swine industry. Studies of the molecular characterization of circulating strains, correlation with clinical records, and associations with pathogens associated with Porcine Respiratory Disease Complex (PRDC) have not been done in Costa Rica. Results Sequencing and phylogenetic analysis of ORF5 proved that PRRSV-2 was the only species detected in all locations analyzed. These sequences were grouped into three clusters. When comparing samples from San Jose, Alejuela, and Puntarenas to historical isolates of the previously described lineages (1 to 9), it has been shown that these were closely related to each other and belonged to Lineage 5, along with the samples from Heredia. Intriguingly, samples from Cartago clustered in a separate clade, phylogenetically related to Lineage 1. Epitope analysis conducted on the GP5 sequence of field isolates from Costa Rica revealed seven peptides with at least 80% amino acid sequence identity with previously described and experimentally validated immunogenic regions. Previously described epitopes A, B, and C, were detected in the Santa Barbara-Heredia isolate. Conclusions Our data suggest that the virus has three distinct origins or introductions to the country. Future studies will elucidate how recently introduced vaccines will shape the evolutionary change of circulating field strains.

Porcine Reproductive and Respiratory Syndrome Surveillance in breeding Herds and Nurseries Using Tongue Tips from Dead Animals

“…Each 25 µL-reaction contained 7 µL of RNA and 18 µL of Mix PRRS European (EU) and North American (NA) strains (EU/NA) from the kit. The RT-PCR reactions were carried out on a 7500 Fast Real-Time PCR System, laptop, QST (Life Technologies, Thermo Fisher Scientific Inc., Waltham, MA, USA) in a 96-well format according to the manufacturer's recommendations ( Moreover, the open reading frame 5 region (ORF5) of all positive serum samples were sequenced using Sanger technology as previously described [21] and some sequences coming from tongue exudate (from farms 4, 50, 36, 6, 9, and 52) were also sequenced for this study.…”

“…A sample was considered positive if the RT-PCR PRRSV Ct value was equal to or below 35. Moreover, the open reading frame 5 region (ORF5) of all positive serum samples were sequenced using Sanger technology as previously described[21] and some sequences coming from tongue exudate (from farms 4, 50, 36, 6, 9, and 52) were also sequenced for this study.…”

A descriptive study on spatial and temporal distributions of genetic clusters of porcine reproductive and respiratory syndrome virus infecting pig sites in Quebec, Canada, between 2010 and 2019

“…Unlike other studies which focused on a single or on few clusters [ 13 ] or subgroups or lineages [ 14 , 22 , 34 ] or limited to a few farms [ 8 ] our study covered all wild-type clusters found over a 10 year-period at the provincial level. Furthermore, each cluster was described based on its detection in at least one of pig site within a year instead of the number of detections, in order to prevent the influence of repeated sampling of the same strain within a herd during the same year.…”

Characterization and Pathogenicity of Two Novel PRRSVs Recombined by NADC30-like and NADC34-like Strains in China

“…GP5 is also proposed to be the primary target for neutralization, of which importance is supported by the identification of a neutralizing epitope and the discovery of neutralization-resistant mutants in GP5 [ 12 , 26 , 30 , 31 ]. Therefore, the genetic analysis, including the nucleotide acid mutations and fragments recombination of ORF5, portends a potential evolutionary direction of PRRSV [ 6 , 32 ]. The two novel strains GD-H1 and GD-F1 in our study both have recombinant fragments derived from NADC30 and NADC34-like strains, suggesting that it may lead to the immune escape of the PRRSV and bring more difficulties to the prevention and control of PRRS.…”