Detection of swine emerging viruses by Real-time PCR and histopathological examination of tissue lesions in domestic pigs (Sus scrofa domesticus) in Sardinia

Population growth caused global meat consumption to increase, and pork production occupies more than 30% of the overall meat demand. This sector plays a very important economic role in Italy. In Sardinia, most pork-producing farms are for self-consumption, but intensive farms are likely uncommon. Intensive pig farms are stress-inducing systems that lead to an increased susceptibility to diseases. Swine pathologies affecting pig farms are a serious concern causing death in pig herds and leading to very important losses. Porcine Reproductive and Respiratory Syndrome (PRRS), Foot and Mouth Disease (FMD), and Porcine Circovirus 2 (PCV2) are some of the most common viruses reported in swine-intensive rearing systems. Although emerging viruses are omnipresent in the swine population, they are scarcely investigated leading to limited knowledge of their pathological aspects. A multidisciplinary approach is advised to investigate the swine emerging viruses’ presence and pathogenic effect to prevent and control diseases. To accomplish this goal, we evaluated lesions in swine organs by gross and histopathology examinations and investigated the presence of the most common viruses (PRRS and PCV2), and of the emerging viruses such as Torque Teno Sus virus (TTSuV), Senecavirus A (SVA), Atypical Porcine Pestivirus (APPeV), LINDA virus, Porcine Circovirus 3 (PCV3), Parvoviruses (PPV) 2, 3, 4, 5, 6, 7, Swine Enteric Alphacoronavirus (SEACoV), and Porcine Deltacoronavirus (PDCoV), by RT-PCR. Additionally, we evaluated viral co-infections in pig tissues. Two hundred thirty-two samples from 29 pigs (10 adult pigs, 10 post-weaning pigs, and 9 piglets) were collected from a Sardinian intensive farm. Moderate to severe chronic lymphoplasmacytic bronchitis and interstitial pneumonia were found in all swine categories. Adult pigs and piglets were characterized by more severe bronchiolar lesions than post-weaning pigs, whereas this last category showed more severe lesions in the lung interstitium than adults. PCV2 was detected in adult, post-weaning pigs and piglets’ organs showing, in the lung, a higher viral load than PRRSV. This data suggested that interstitial pneumonia in our cases could be more related to PCV2 infections than PRRSV. PCV3 was detected in all swine tissues with no statistically significant differences between organs suggesting a broad tropism of PCV3. Notably, TTSuV was detected in 100% of the three age categories of swine, with the highest viral load in the lung and spleen suggesting that TTSuV may play a role in swine lung lesions, enhancing the development of disease caused by other pathogenic agents. PPV2 was found in most examined tissues of adults and piglets, and to less extent in post-weaning pigs. Moreover, since interstitial pneumonia is the most representative lung lesion, and all cases are 100% positive for PPV2, we can propose that this virus could be an important contributor to the development of lung lesions in swine. APPeV was detected in adult pigs’ mediastinal and mesenteric lymph nodes with a high viral load. PPV3-7 have been also detected, whereas SVA, LINDAV, PDCoV, and SEACoV were not discovered in swine tissues. Co-infections with PPV2, TTSuV, and PCV2 in lung samples from all pig categories were found. We propose including emerging viruses such as TTSuV and PPV2 in the routine diagnostic investigation of respiratory swine disease. Our work offered the first report of several newly emerging viruses, which haven’t been previously reported in the domestic pig population farmed in Sardinia (PPV2-7, APPeV), and of the co-infection between emerging and common viruses (PPV2, TTSuV, and PCV2) in lungs of pigs with pneumonia, regardless of age categories. Further investigations are needed to localize specific viruses in the organs of co-infected pigs, to better clarify the role of each pathogen and its impact on swine health and industry.

Population growth leads to global meat consumption and production increase. In Italy, pork production plays an important economic role. In Sardinia, pork-producing farms are familiar, and intensive farms are uncommon. Intensive pig farms are stress-inducers leading to increased disease susceptibility. The most common viruses affecting pigs are Porcine Reproductive and Respiratory Syndrome (PRRS), Foot and Mouth Disease (FMD), and Porcine Circovirus 2 (PCV2). Emerging viral diseases in pigs are understudied. Our work aimed to evaluate pathological lesions in organs, and to detect the presence of viruses by RT-PCR (PRRSV, PCV2, Torque Teno Sus virus (TTSuV), Senecavirus A (SVA), Atypical Porcine Pestivirus (APPeV), LINDA virus, Porcine Circovirus 3 (PCV3), Parvoviruses (PPV2-7), Swine Enteric Alphacoronavirus (SEACoV), Porcine Deltacoronavirus (PDCoV). Swine samples (N=232) from different age categories were collected from a Sardinian intensive farm. Moderate to severe chronic lymphoplasmacytic bronchitis and interstitial pneumonia were found in all samples. PCV2 was detected in all categories, suggesting that interstitial pneumonia could be related to PCV2. Notably, TTSuV showed the lowest Ct in the lung suggesting that it may play a role in lung lesions. PPV2 was found in all lungs, suggesting that this virus may be associated to lesions in swine. PPV3-7 and APPeV were also detected, whereas the remaining viruses were not found. Co-infections with PPV2, TTSuV, and PCV2 in lung samples were found. Our work proposed including TTSuV and PPV2 in the routine diagnostic investigation of respiratory swine disease in addition to common viruses and represented the first report of PPV2-7, and APPeV in Sardinia.