Characterization of porcine endogenous retrovirus insertion in Jeju native pigs and commercial breeds

Objective: This study aimed to characterize the genomic distribution and amino acid homology of porcine endogenous retrovirus (PERV) subtypes in three pig breeds, Jeju native pigs (JNPs), Duroc, and Landrace. Methods: Genomic DNA was extracted from hair and ear tissue samples of JNPs, Duroc, and Landrace breeds using DirEx Fast Hair Kit and Exgene Tissue SV Plus kit (GeneAll). Whole-genome resequencing (WGR) was performed by using the Illumina NovaSeq 6000 platform. Sequencing libraries were prepared using the TruSeq Nano DNA Kit and quality-checked using QUAST and BUSCO, and aligned to the Sus scrofa 11.1 reference genome with Bowtie2. Polymerase chain reaction (PCR) and quantitative real-time PCR were conducted with subtype-specific primers targeting gag, pol, and env regions. Amplicons were verified via agarose gel electrophoresis, purified, and subjected to Sanger sequencing. Results: WGR revealed breed-specific differences in PERV insertion, with JNPs exhibiting a higher frequency compared with the commercial breeds. PERV-B was the most abundant subtype, followed by PERV-CA and PERV-A, whereas PERV-C was absent in all the breeds. Chromosomal mapping highlighted variations in the localization of PERV, with notable absence on chromosomes 10 and 18. Homology analysis of amino acid sequences of PERV-A, PERV-B, and PERV-CA revealed breed-specific variations in the gag, pol, and env regions, indicating potential differences in viral replication and infectivity. The presence of all PERV subtypes were confirmed using polymerase chain reaction, with PERV-C detected in some Western breeds and all the JNPs analyzed. Sequencing of the PERV-C env region revealed single nucleotide polymorphisms, indicating genetic divergence among pig breeds. Conclusion: The study findings highlight the need for breed-specific strategies in PERV inactivation for xenotransplantation applications. The distinct chromosomal distribution patterns and functionally significant PERV insertions identified in this study provide a foundation for future research into host-virus interactions and retroviral evolution.