Effect of Viral Abundance and Diversity Associated with Mycoplasma hyopneumoniae on the Severity of Lung Lesions in Slaughtered Pigs: A Case-Control Study

Respiratory diseases in swine are mostly infectious sources, and Mycoplasma hyopneumoniae (Mhyo) is one of the most prevalent agents in pig farms, often associated with coinfections with viruses as well as other bacteria. This interaction results in the Porcine Respiratory Disease Complex (PRDC) that can lead to significant economic losses to the swine industry. In this study, bronchial swabs were collected from 30 slaughtered pigs, divided into three groups according to the lung lesion score and Mhyo detection by PCR: Control: without lesions and Mhyo negative; Group 1: mild lesions and Mhyo positive; Group 2: severe lesions and Mhyo positive. Ten samples per group were pooled and high-throughput sequencing (HTS) was performed. The analyses revealed the presence of the viral families: Anelloviridae, Circoviridae, Parvoviridae , and Picornaviridae. The number of identified viral reads was significantly higher (11.6x) in the group with severe lung lesions and Mhyo-positive compared to the group with mild lesions and Mhyo-positive. Also, group 2 presented the highest viral diversity. No viruses were detected in samples from the group without lesions. Based on these findings, the study suggests that the presence of Mhyo in lungs at slaughter may increase the susceptibility of pigs to viral infection, resulting in severe pulmonary lesions.