ena-STUDY-Centre for Infectious Diseases and Microbiology Laboratory Services-17-11-2018-06:07:35:191-64
Increased diversity of BK Polyomavirus genomes detected by whole genome sequencing in transplant recipients
Historically, BK polyomavirus (BKPyV) has been divided into four major genotypes, BKPyV I-IV, usually based on a 287-bp partial VP1 gene sequence analysis. Using a targeted metagenomics approach, phylogenetic resolution was improved by analyzing BKPyV whole genome sequences (WGS), demonstrating novel virus variants, and differences in the distribution of BKPyV variants in Australian (n=123) and Vietnamese (n=75) transplant recipients. A primer-directed rolling circle amplification (dRCA) method was used to enrich BKPyV DNA directly from clinical samples for accurate BKPyV assembly, resulting in 198 BKPyV genomes. Geographic genotype differences were observed, with all four major genotypes detected in Australia, but only genotypes I and IV in Vietnam. In addition, WGS further differentiated the traditional 12 BKPyV subtypes, identifying 30 novel clusters. This increased resolution allowed common subtypes such as I-b1 to be separated into geographical clusters, providing further evidence for the concept that BKPyV co-evolved with human migration. This study also added a significant number of genotype IV genomes, usually poorly differentiated by traditional partial VP1 or LTag genomic analysis. The improved resolution offered by this simple and cheap method has enabled a more thorough delineation of BKPyV genotypes to investigate BKPyV-associated diseases.
Historically, BK polyomavirus (BKPyV) has been divided into four major genotypes, BKPyV I-IV, usually based on a 287-bp partial VP1 gene sequence analysis. Using a targeted metagenomics approach, phylogenetic resolution was improved by analyzing BKPyV whole genome sequences (WGS), demonstrating novel virus variants, and differences in the distribution of BKPyV variants in Australian (n=123) and Vietnamese (n=75) transplant recipients. A primer-directed rolling circle amplification (dRCA) method was used to enrich BKPyV DNA directly from clinical samples for accurate BKPyV assembly, resulting in 198 BKPyV genomes. Geographic genotype differences were observed, with all four major genotypes detected in Australia, but only genotypes I and IV in Vietnam. In addition, WGS further differentiated the traditional 12 BKPyV subtypes, identifying 30 novel clusters. This increased resolution allowed common subtypes such as I-b1 to be separated into geographical clusters, providing further evidence for the concept that BKPyV co-evolved with human migration. This study also added a significant number of genotype IV genomes, usually poorly differentiated by traditional partial VP1 or LTag genomic analysis. The improved resolution offered by this simple and cheap method has enabled a more thorough delineation of BKPyV genotypes to investigate BKPyV-associated diseases.