Prevalence and molecular characterization of BK polyomavirus genotypes based on VP1 gene from renal transplant patients in Pakistan

BK polyomavirus (BKPyV) remains a significant threat to graft longevity, primarily reactivating under immunosuppressive conditions to cause BKPyV-associated nephropathy. Despite its clinical importance, high-resolution molecular data regarding the circulating genotypes and mutational landscape in the Pakistani transplant population is critically lacking. This study conducted a blinded molecular investigation to establish baseline prevalence, viral load, and genetic diversity of BKPyV among renal transplant recipients in Pakistan. A total of 100 de-identified specimens (50 urine and 50 blood) were analyzed via real-time PCR for viral quantification. High-titer urine samples were further characterized through conventional PCR amplification and Sanger sequencing of the VP1 BC-loop. BKPyV DNA was detected in 40% of urine and 26% of blood samples, with mean viral loads of 1.3 × 10⁵ IU/ml and 7.8 × 10³ IU/ml respectively. PCR amplification and Sanger sequencing of VP1 gene revealed the presence of genotypes I and IV among the study samples. Phylogenetic analysis of the isolated sequences showed multiple mutations (e.g., N62D, K69R, E82D) overlapping with previously reported mutations. Additional research is needed to explore the consequences of these mutations on disease progression and transplant results for developing personalized treatment approaches and improving patient management protocols.