Single-nucleotide polymorphisms within the BK polyomavirus non-coding control region are genotype-associated

Abstract

BK polyomavirus (BKPyV) is a non-enveloped, double-stranded, circular DNA virus that is a member of the Polyomaviridae family. The BKPyV genome is divided into three regions, including the non-coding control region (NCCR), the early region, and the late region. BKPyV has one of the highest mutation rates among DNA viruses, and four genotypes have been identified based on amino acid variation within the VP1 region. Mutations within the NCCR have been noted, and this region exhibits hypervariability. Here, we show that many of the point mutations observed within the NCCR are genotype-associated, termed genotype-associated polymorphisms (GAPs). These GAPs correlate with regions of hypervariability, are inherent to their genotype, and can be used to genotype clinical strains, separate from other genomic regions. We also show that these GAPs fall within predicted transcription factor binding sites and therefore provide targets for further functional studies.IMPORTANCEBK Polyomavirus (BKPyV) is the cause of hemorrhagic cystitis in hematopoietic cell transplant recipients and BKPyV-associated nephropathy in renal transplant recipients and thus is an important determinant of transplant outcome. The viral mechanisms leading to disease manifestation remain to be thoroughly explored, but viral genetic variation has emerged as an area of interest. Understanding genomic diversity between and within BKPyV genotypes can provide sites of interest that may ultimately improve screening strategies and provide insights into the viral factors that contribute to disease.

Keywords: BK polyomavirus; genotype; hematopoietic cell transplantation; non-coding control region; single-nucleotide polymorphisms; subtype; transcription factor binding sites; viral diversity.

Fig 1

The NCCRs of 166 study sequences and 35 reference sequences were analyzed for the presence of SNPs. (A) Diagram depicting all SNPs identified with their locations in each NCCR block. Red triangles depict positions at which only one SNP was observed. Purple squares depict positions where two SNPs were observed. (B) Distribution of SNPs across NCCR blocks. (C) Number of GAPs exhibited by each BKPyV genotype. All subtypes exhibited at least 1 GAP. (D) The positions of each GAP identified and the nucleotide change that occurs when compared to other genotypes. GAPs are denoted by the red letters in each column.

Fig 2

Overall, 166 study sequences and 35 references were used to generate WebLogos showing areas of variation within the BKPyV NCCR O block (A), P block (B), Q block (C), R block (D), and S block (E).

Fig 3

Five patient sample BKPyV sequences were used to examine the validity of the described GAPs. (A) Phylogenetic tree when full-length patient sample sequences are mapped to references of different genotypes. All samples clustered with their respective genotypes regardless of the reference utilized to generate the consensus sequence. References are labeled with their GenBank accession number, country of origin, and genotype. The sample sequences are labeled using a unique identifier and are color-coded according to the sample they were extracted from; sequences for sample 607 are highlighted in yellow, 617 in red, 732 in blue, 776 in green, and 789 in purple. (B–F) Highlighter plots depicting nucleotide differences in the NCCRs of the five patient sample sequences mapped to references of different genotypes.

Fig 4

(A) Phylogenetic tree of full-length sequences excluding the NCCR of 166 study sequences and 21 reference sequences of known BKPyV genotype. (B) Phylogenetic tree of the NCCR from the same patient sample sequences seen in panel A and 35 reference sequences. For both trees, references are labeled with their GenBank accession number, country of origin, and genotype. Patient sample sequences are labeled using a unique identifier. Patient sample sequences are also color coded according to their genotype: red for Ia, yellow for Ib2, green for Ib1, dark blue for II, light blue for III, and purple for IV.