Detection and genetic characterization of Sapelovirus A in Italian swine herds

Background: Porcine sapelovirus A (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV has been isolated worldwide from healthy pigs but also affected with diarrhoea, respiratory signs, encephalitis, skin lesions and fertility disorders. To date little information on the occurrence of PSV in Italian pig herds is available. The objective of this study was to investigate the presence of PSV in three Italian pig farms among animals belonging to different age groups, to clarify the epidemiology and molecular characteristics of the circulating strains. Materials and Methods: Between 2012-2018, 92 pooled fecal samples were collected from healthy pigs of 3 different farms (A, B, C) in Northern Italy. The target of this study was weaned pigs, which is the age class more susceptible to the infection. We also investigated the presence of PSV in adult animals (sows). RNA was extracted by a QiampViral extraction kit (Qiagen) and analyzed by RT-PCR, amplifying a 270 bp fragment in the conserved 5’UTR. One complete genome was obtained by Next Generation Sequencing using Ion Torrent technology and built by Galaxy Aries ( https://aries.iss.it/). To perform phylogenetic analysis, two primers (amplifying a 900 bp fragment) were designed within the VP1 by the alignment of the Italian strain complete genome and those available online (NCBI). The sequences analysis was performed by BLASTn and the phylogenetic analysis by the MEGA7 software. Results: All farms investigated were positive to the virus. PSV was detected in weaned pigs of all farms while only sows from one farm resulted positive. PSV was detected in 67 of 92 fecal samples (73.0%). A unique PSV strain was detected within each farm. Two strains from farm A and B (85% nt. Id. each other) clustered together with another PSV strain detected in Italy in 2015 (88% nt. id.). The strain from farm C did not cluster with any strains reported online showing <88% nucleotide identity with the other PSV strains. Conclusion: Our results indicate that PSV is widespread in Italian farms, as described in other studies conducted in both European and Asian countries. The infection was found in weaned pigs (aged from 2 to 3 months) of all farms investigated while only adult pigs from one farm of two tested resulted positive. These results could be due to the protective immunity in adult animals or to a low percentage of adult animals shedding the virus. Phylogenetic analysis of sequences obtained showed the evolutionary correlation of Italian strains and high heterogeneity of PSV.