Isolation and complete genome analysis of Porcine Parvovirus 1 from swine with reproductive failure in southern India.

Porcine parvovirus 1 (PPV1) is a major cause of reproductive disorders in swine, leading to stillbirths, mummified fetuses, embryonic death, and infertility, and contributes to significant economic losses worldwide. However, isolation and complete genome molecular data on PPV1 circulating under field conditions in southern India remain scarce. In this study, 100 samples suspected of viral involvement in reproductive failure were collected. These included 70 pooled fetal tissue samples (liver, spleen, and lung) from stillborn or mummified fetuses delivered by dams during farrowing and 30 serum samples from female pigs with a prior history of reproductive failure across five southern Indian states. Molecular screening for PPV1 by VP2 gene–specific PCR detected a positivity rate of 13% (n = 13). Ten PCR-positive samples were propagated in PK-15 cells for PPV1 isolation, and six PPV1 isolates showed characteristic cytopathic changes at the fifth passage and were further confirmed by PPV1-specific PCR. Four isolates were subjected to complete genome amplification using published overlapping primers, followed by Sanger sequencing and contig assembly. Two PPV1 isolates were subjected to whole-genome sequencing using the Illumina NGS platform, and complete PPV1 genomes were generated by reference-based genome mapping. The complete genomes of all six PPV1 isolates were 5,013 nucleotides in length and displayed the characteristic parvoviral organization comprising the NS1 and VP1/VP2 regions. The assembled whole-genome sequences of the six PPV1 isolates were deposited in GenBank under accession numbers PV296187, PV296188, PV296191, PV296192, PV296193, and PV296194. Comparative sequence analysis revealed high nucleotide identity (> 99%) with global PPV1 strains and a highly conserved NS1 region. In contrast, amino acid substitutions at positions I215T, D378G, H383Q, S436P, and R565K in the VP2 capsid protein were consistent with profiles reported in virulent strains, suggesting potential antigenic and pathogenic relevance. Phylogenetic analysis using the Maximum Likelihood method clustered two isolates as genotype C and four as genotype E, whereas the Neighbor-Joining method grouped them as genotypes C and D, respectively, indicating genetic diversity among circulating PPV1 strains. This study reports the isolation and complete genome characterization of PPV1 associated with reproductive failure in pigs in southern India.