A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping.
BK virus (BKV)-associated diseases in transplant recipients are an emerging issue. However, identification of the various BK virus subtypes/subgroups is a long and delicate process on the basis of currently available data. Therefore, we wanted to define a simple and effective one-step strategy for characterizing all BK virus strains from the VP1 gene sequence. Based on the analysis of 199 available complete DNA VP1 sequences, phylogenetic trees, alignments, and isolated polymorphisms were used to define an effective strategy for distinguishing the 12 different BK virus subtypes/subgroups. Based on the 12 subtypes identified from the 199 complete BKV VP1 sequences (1,089 bp), 60 mutations that can be used to differentiate these various subtypes/subgroups were identified. Some genomic areas were more variable and comprised mutational hot spots. From a subregion of only 100 bp in the VP1 region (1977 through 2076), we therefore constructed an algorithm that enabled rapid determination of all BKV subtypes/subgroups with 99% agreement (197/199) relative to the complete VP1 sequence. We called this domain of the BK viral genome the BK typing and grouping region (BKTGR). Finally, we validated our viral subtype identification process in a population of 100 transplant recipients with 100% efficiency. The new simpler method of BKV subtyping/subgrouping reported here constitutes a useful tool for future studies that will help us to more clearly understand the impact of BKV subtypes/subgroups on diagnosis, infection, and BK virus-associated diseases.
Department of Virology, Amiens University Medical Center, Amiens, France.|EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
Virginie
V
Morel
EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
Elodie
E
Martin
Department of Virology, Amiens University Medical Center, Amiens, France.|EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
Catherine
C
François
EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
François
F
Helle
Department of Nephrology, Amiens University Medical Center, Amiens, France.
Justine
J
Faucher
Normandie Université, Normandy, France.|Université de Rouen, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France.
Thomas
T
Mourez
Department of Nephrology, Amiens University Medical Center, Amiens, France.|INSERM U-1088, Jules Verne University of Picardie, Amiens, France.
Gabriel
G
Choukroun
Department of Virology, Amiens University Medical Center, Amiens, France.|EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
Gilles
G
Duverlie
Department of Virology, Amiens University Medical Center, Amiens, France.|EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
Sandrine
S
Castelain
Department of Virology, Amiens University Medical Center, Amiens, France etienne.brochot@u-picardie.fr.|EA4294 Virology Research Unit, Jules Verne University of Picardie, Amiens, France.
Etienne
E
Brochot
D001739:BK Virus / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D027601:Polyomavirus Infections / Q000821:virology; D017422:Sequence Analysis, DNA; D014412:Tumor Virus Infections / Q000821:virology; D015678:Viral Structural Proteins / Q000235:genetics
D015678:Viral Structural Proteins
BK virus; BK virus strains; subtyping; transplantation