Molecular characterization of the BK polyomavirus early coding region in kidney transplant recipients in Vietnam

The early coding region of BK polyomavirus (BKV), encoding the regulatory small T antigen (STAg) and large T antigen (LTAg), has received considerably less attention than the late coding region VP1 capsid gene, which is traditionally employed for BKV genotyping. This study aimed to characterize genetic variation within the BKV early coding region among Vietnamese renal transplant patients and to assess its utility for genotype and subgroup assignment. A total of 42 urine specimens with viral loads ≥10⁴ copies/mL were screened, followed by amplification of full-length (~5.1 kb) viral genomes using long-range PCR. Complete early coding region sequences were obtained from ten clinical samples through Sanger primer walking. Analysis identified 137 single nucleotide variants (SNVs), with 122 localized to LTAg and 15 to STAg. Among these, 95 (77.87%) and 11 (73.33%) SNVs were cluster-defining for LTAg and STAg, respectively. Only ten SNVs resulted in substitutions of amino acids, all of which were genotype-specific. Phylogenetic analyses of STAg, LTAg, and the concatenated early coding region consistently assigned samples to genotype I (subgroup Ib1; n=7) or genotype IV (subgroups IVa1 and IVc1; n=3). Genotype-level bootstrap support was high across the early coding region phylogenies (93%-100%), and the concatenated early coding region tree achieved subgroup-level resolution with greater bootstrap support than the full-length VP1 tree. In contrast, the 327-bp VP1 typing fragment resolved only genotype-level clusters. Phylogenies inferred from the early coding region were fully concordant with VP1-based genotyping, supporting its utility as a complementary marker for BKV molecular surveillance. This study provides the first characterization of BKV early coding region diversity in Vietnam and highlights the potential of this region for enhanced genotyping resolution.