Genetic diversity in envelope genes of contemporary U.S. porcine reproductive and respiratory syndrome virus strains influences viral antigenicity

The mRNA vaccine expressing fused structural protein of PRRSV protects piglets against PRRSV challenge

The swine industry experiences substantial economic losses annually due to the porcine reproductive and respiratory syndrome virus (PRRSV). The limited protective efficacy of existing commercial vaccines against epidemic PRRSV underscores the urgent need for innovative solutions. The mRNA vaccines, which elicit robust immune responses, have emerged as a promising avenue in vaccine development. In this study, two distinct mRNA vaccines were engineered: one encoding the full-length GP5 and M proteins (GP5-M), and the other encoding the full-length N protein along with epitope peptide segments of the M and E proteins (NMEpep). Our findings indicate that, compared with NMEpep, piglets immunized with the GP5-M mRNA vaccine produced specific antibodies, exhibited elevated levels of PRRSV-specific IFN-γ, and demonstrated effective activation of CD4+ and CD8+ T cells as well as CD21+ B cells. Furthermore, the GP5-M vaccine conferred protective efficacy against HP-PRRSV challenge, evidenced by the mitigation of clinical symptoms, reduction in viral loads, and alleviation of tissue damage. In conclusion, this study presents a promising candidate vaccine for addressing epidemic PRRSV and establishes the GP5-M mRNA vaccine as a viable platform for the development of next-generation PRRSV vaccines.

Repeat offenders: PRRSV-2 clinical re-breaks from a whole genome perspective

Clinical re-breaks of PRRSV on sow farms are a frustrating reality for producers and practitioners. The underlying mechanisms allowing for a single viral variant to persist and cause repeated clinical outbreaks within a herd that should have strong immunity, through recent exposure to a highly similar genetic variant (≥%97 homology), are poorly understood. This study systematically identified clinical re-breaks on sow farms and performed whole genome sequencing on viral isolates available from each outbreak event to evaluate the hypothesis that such re-breaks may be associated with evolution on glycoprotein ectodomains. Pairwise comparisons between re-break isolates revealed multiple amino acid sites in structural proteins that frequently differed between re-break pairs. For sites identified on GP5, several sites were found to be changed in a higher proportion of re-breaks than expected from background variability. Intriguingly, 4 of 13 re-break events had no changes on GP5 but numerous changes in other structural protein ectodomains; GP2, E, GP3, and GP4 all contained several sites that were substituted in a high proportion of rebreak pairs, highlighting the multigenic nature of immune evasion. Across all structural proteins, most sites were located on ectodomains (15/22; 68 %). Several GP5 sites (6/8; 75 %) have been associated with escape from antibody neutralization in in vivo and in vitro experiments. To conclude, identification of suspected immune escape events from production and surveillance data resulted in detection of crucial amino acid positions on structural proteins that potentially underly antigenic diversity. Such micro-evolutionary change could result in escape from antibody neutralization, complicating interventions such as herd closures and leading to persistence of clinical outbreaks on sow farms.

Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hypothesized that whole-genome sequencing (WGS) of the PRRSV genome would allow better epidemiological monitoring than ORF5 gene sequencing. PRRSV PCR-positive serum, oral fluid, and tissue clinical samples submitted to the diagnostic laboratory for routine surveillance or diagnosis of PRRSV infection in Québec, Canada, swine herds were used. The PRRSV reverse transcription-quantitative PCR Cq values of the processed samples varied between 11.5 and 34.34. PRRSV strain genomes were isolated using a poly (A)-tail method and were sequenced with a MiSeq Illumina sequencer. Ninety-two full-length PRRSV genomes were obtained from 88 clinical samples out of 132 tested samples, resulting in a PRRSV WGS success rate of 66.67%. Three important deletions in ORF1a were found in most wild-type (i.e., not vaccine-like) strains. The importance of these deletions remains undetermined. Two different full-length PRRSV genomes were found in four different samples (three serum samples and one pool of tissues), suggesting a 4.55% PRRSV strain coinfection prevalence in swine. Moreover, six PRRSV whole genomes (6.52% of PRRSV strains) were found to cluster differently than they did under the ORF5 classification method. Overall, WGS of PRRSV enables better strain classification and/or interpretation of results in 9.10% of clinical samples than ORF5 sequencing, as well as allowing interesting research avenues.

Porcine reproductive and respiratory syndrome virus whole-genome sequencing efficacy with field clinical samples using a poly(A)-tail viral genome purification method

The genomic surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) is based on sequencing of the ORF5 gene of the virus, which covers only 4% of the entire viral genome. It is expected that PRRSV whole-genome sequencing (WGS) will improve PRRSV genomic data and allow better understanding of clinical discrepancies observed in the field when using ORF5 sequencing. Our main objective was to implement an efficient method for WGS of PRRSV from clinical samples. The viral genome was purified using a poly(A)-tail viral genome purification method and sequenced using Illumina technology. We tested 149 PRRSV-positive samples: 80 sera, 33 lungs, 33 pools of tissues, 2 oral fluids, and 1 processing fluid (i.e., castration liquid). Overall, WGS of 67.1% of PRRSV-positive cases was successful. The viral load, in particular for tissues, had a major impact on the PRRSV WGS success rate. Serum was the most efficient type of sample to conduct PRRSV WGS poly(A)-tail assays, with a success rate of 76.3%, and this result can be explained by improved sequencing reads dispersion matching throughout the entire viral genome. WGS was unsuccessful for all pools of tissue and lung samples with Cq values > 26.5, whereas it could still be successful with sera at Cq ≤ 34.1. Evaluation of results of highly qualified personnel confirmed that laboratory skills could affect PRRSV WGS efficiency. Oral fluid samples seem very promising and merit further investigation because, with only 2 samples of low viral load (Cq = 28.8, 32.8), PRRSV WGS was successful.

Virus Metagenomics in Farm Animals: A Systematic Review

A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.