Transcriptome sequencing reveals non-coding RNAs respond to porcine reproductive and respiratory syndrome virus and Haemophilus parasuis concurrent infection in lungs of Kele piglets

Jing Zhang1, Chunping Zhao1, Min Yao2, Jing Qi1, Ya Tan1, Kaizhi Shi1,*, Jing Wang1, Sixuan Zhou1, Zhixin Li3
Author Information & Copyright
1Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang 550002, China.
2 Inspection and Testing Department, Guizhou Testing Center for Livestock and Poultry Germplasm, Guiyang 550002, China.
3College of Animal Science, Guizhou University, Guiyang 550002, China.
*Corresponding Author: Kaizhi Shi, Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang 550002, China. E-mail:

© Copyright 2023 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and<italic> Haemophilus parasuis</italic> (HPS) has severely restricted the healthy development of pig breeding. Exploring disease resistance of non-coding RNAs in pigs co-infected with PRRSV and HPS is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in Kele piglets and to innovate the use of local pig germplasm resources in China. RNA-seq of lungs from Kele piglets with single-infection of PRRSV or HPS and co-infection of both pathogens was performed. Two hundred and twenty-five differentially expressed long non-coding RNAs (DElncRNAs) and 30 DEmicroRNAs (DEmiRNAs) were identified and characterized in the PRRSV and HPS co-infection (PRRSV–HPS) group. Compared with the single-infection groups, 146 unique DElncRNAs, 17 unique DEmiRNAs, and 206 target differentially expressed genes (DEGs) were identified in the PRRSV–HPS group. The expression patterns of 20 DEmiRNAs and DElncRNAs confirmed by real-time quanti-tative PCR were consistent with those determined by high-throughput sequencing. In the PRRSV–HPS group, the target DEGs were enriched in eight immune Gene Ontology terms relating to two unique DEmiRNAs and 16 DElncRNAs, and the unique target DEGs participated the host immune response to pathogens infection by affecting 15 immune-related Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Notably, ceRNA networks of different groups were constructed, and the <italic>ssc-miR-671-5p</italic> miRNA was validated as a potential regulatory factor to regulate <italic>DTX4</italic> and <italic>AEBP1</italic> genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. These results provided insight into further study on the molecular mechanisms of resistance to PRRSV and HPS co-infection in Kele piglets.

Keywords: Kele piglets; PRRSV; Haemophilus parasuis; co-infection; non-coding RNAs; ceRNAs