ArticleJournal of virology2009
Genotyping schemes for polyomavirus BK, using gene-specific phylogenetic trees and single nucleotide polymorphism analysis.
Article in Journal of virology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 68 citations in OpenAlex.
- Neutralization serotyping of BK polyomavirus infection in kidney transplant recipients.PLoS pathogens · 2012Trial
- BK polyomavirus infection: more than 50 years and still a threat to kidney transplant recipients.Frontiers in transplantation · 2024Review
- Evaluating the Efficiency of the Cobas 6800 System for BK Virus Detection in Plasma and Urine Samples.Diagnostics (Basel, Switzerland) · 2023Article
- Article
- Genomic Mutations of BK Polyomavirus in Patients after Kidney Transplantation: A Cross-Sectional Study in Vietnam.Journal of clinical medicine · 2022Article
- Review
- HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations.Molecular biology and evolution · 2021Article
- Variant morphology and random chromosomal integration of BK polyomavirus in posttransplant urothelial carcinomas.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Article
- BK polyomavirus diversity-Why viral variation matters.Reviews in medical virology · 2020Review
- Source and Relevance of the BK Polyomavirus Genotype for Infection After Kidney Transplantation.Open forum infectious diseases · 2019Article
- Development and evaluation of a BK polyomavirus serotyping assay using Luminex technology.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2019Article
- An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides.PLoS pathogens · 2018Article
- A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping.Journal of clinical microbiology · 2017Article
- Sequence Variation in Amplification Target Genes and Standards Influences Interlaboratory Comparison of BK Virus DNA Load Measurement.Journal of clinical microbiology · 2015Article
- Comparative Evaluation of Three Nucleic Acid-Based Assays for BK Virus Quantification.Journal of clinical microbiology · 2015Article
- The oncogenic potential of BK-polyomavirus is linked to viral integration into the human genome.The Journal of pathology · 2015Article
- Phylogenetic reconstruction and polymorphism analysis of BK virus VP2 gene isolated from renal transplant recipients in China.Experimental and therapeutic medicine · 2015Article
- Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing.Journal of clinical microbiology · 2015Article
- Toward standardization of BK virus monitoring: evaluation of the BK virus R-gene kit for quantification of BK viral load in urine, whole-blood, and plasma specimens.Journal of clinical microbiology · 2014Article
- Replication of oral BK virus in human salivary gland cells.Journal of virology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
BK virus (BKV) genotyping has been historically based on nucleotides 1744 to 1812 in the VP1 gene. We reevaluated this practice by making BKV whole-genome and gene-specific phylogenetic trees as well as performing single nucleotide polymorphism (SNP) analysis of 162 sequences available in the public domain. It was found that currently known BKV subtypes and subgroups can no longer be reliably determined by sequencing certain partial gene sequences. Phylogenetic trees based on large T-antigen (LTA) allow separation of subtype I into subgroups Ia, Ib1, Ib2, and Ic, with bootstrap values of 100%, which are better than bootstraps obtained using VP1 sequences (bootstrap values of 71 to 97%). Subtype IV can be subdivided into subgroups, but LTA bootstrap values (33 to 80%) are lower than those obtained by whole-genome analysis (68 to 87%). Subtypes V and VI provisionally identified earlier on the basis of more limited sequence data are better classified as subgroups Ib2 and Ib1, respectively. LTA positions 3634, 3772, 3934, and 4339 can serve as a minimal SNP set to distinguish between the four major BKV subtypes. No subtype II-, IVa-, or IVb-defining SNPs are available in the VP1 gene. However, the overall congruence of viral strain classification based on either VP1 or LTA phylogenetic analysis indicates that these two areas of the viral genome are genetically linked. Interstrain genetic recombination between distant loci in the VP1 and LTA areas is not a common event.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.