Porcine Reproductive and Respiratory Syndrome (PRRS) and CD163 Resistance Polymorphic Markers: What Is the Scenario in Naturally Infected Pig Livestock in Central Italy?

SIMPLE SUMMARY: Porcine Reproductive and Respiratory Syndrome (PRRS) is an infectious disease of viral etiology characteristic of the swine species. Although almost three decades have passed since its emergence, control of the disease still presents significant issues, representing a source of concern for veterinarians and breeders. In addition to management difficulties, the PRRS virus (PRRSV) causes severe economic losses in terms of abortions, a decrease in animal growth, increased mortality, and the massive use of drugs. Understanding the genetic markers involved in the response to the infection is challenging and crucial and represents the main goal of this study. CD163, which encodes the membrane receptor used by the PRRSV to enter macrophages and initiate infection, has been identified as one of the most promising marker genes associated with genetic susceptibility to the disease. In this study, detection by sequencing of the more significant polymorphisms on the CD163 gene was conducted for the first time on 377 pigs reared in different farms distributed in some areas of Central Italy. The genotyping data obtained in this work, together with the assessment of the virological status of the animals and the comparison with the findings from other PRRSV conditioned and experimental infection trials, will allow a better understanding of whether some Italian pig populations can represent a good genetic resource and a reservoir of resistance/“resilience” markers to PRRS. Indeed, marker-assisted selection (MAS) could represent an alternative and a more valid tool than vaccination to control the spread of this impactful disease. ABSTRACT: Porcine Reproductive and Respiratory Syndrome (PRRS) caused by the PRRS virus affects farmed pigs worldwide, causing direct and indirect losses. The most severe manifestations of PRRS infection are observed in piglets and pregnant sows. The clinical outcome of the infection depends on the PRRSV strain’s virulence, the pregnancy state of the female, environmental factors, the presence of protective antibodies due to previous infections, and the host’s genetic susceptibility. The latter aspect was investigated in this study, in particular, evaluating the most significant polymorphisms (SNPs) of the CD163 gene in slaughtered pigs reared in Central Italy. Total RNAs were extracted from 377 swine samples and subjected to RT-PCR targeted to the CD163 gene, followed by sequencing analysis. Contextually, the viral RNA was detected by RT-qPCR in order to phenotypically categorize animals into infected and not infected. In particular, 36 haplotypes were found, and their frequencies ranged from 0.13% to 35.15%. There were 62 resulting genotypes, three of which were associated with a putative resistance to the disease. Both the haplotypes and genotypes were inferred by PHASE v.2.1 software. To the best of our knowledge, this type of investigation was conducted for the first time on pig livestock distributed in different regions of Central Italy. Thus, the obtained findings may be considered very important since they add useful information about swine genetic background in relation to PRRS infection, from the perspective of adopting Marker-Assisted Selection (MAS) as a possible and alternative strategy to control this still widespread disease.