Subtypes of BK virus prevalent in Japan and variation in their transcriptional control region

Abstract

BK polyomavirus (BKV) is ubiquitous in the human population, infecting children without obvious symptoms, and persisting in the kidney in a latent state. In immunosuppressed patients, BKV is reactivated and excreted in urine. BKV isolates have been classified into four subtypes (I-IV) using either serological or genotyping methods. To elucidate the subtypes of BKV prevalent in Japan, the 287 bp typing region in the viral genome was PCR-amplified from urine samples of 45 renal transplant (RT) and 31 bone-marrow transplant (BMT) recipients. The amplified fragments were subjected to a phylogenetic or RFLP analysis to determine the subtypes of BKV isolates in urine samples. Subtypes I, II, III and IV were detected, respectively, in 70-80, 0, 2-3 and 10-20 % of the BKV-positive patients in both patient groups. This pattern of distribution was virtually identical to patterns previously demonstrated in England, Tanzania and the United States, suggesting that BKV subtypes are distributed similarly in various human populations. Furthermore, transcriptional control regions (TCRs) were PCR-amplified from the urine samples of 25 RT and 20 BMT recipients, and their nucleotide sequences were determined. The basic TCR structure (the so-called archetype configuration) was observed in most isolates belonging to subtypes I, III and IV (subtype II isolates were not available), albeit with several nucleotide substitutions and a few single-nucleotide deletions (or insertions). Only three TCRs carried extensive sequence rearrangements. Thus, it was concluded that the archetypal configuration of the BKV TCR has been conserved during the evolution of BKV.

Mutations in the BC‐loop of the BKV VP1 region do not influence viral load in renal transplant patients

“…No sequences could be assigned to subtype II or III. Subtype I is further classified into the three subclusters Ia, Ib, and Ic [Takasaka et al, 2004]. Twenty-eight of the 30 subtype I sequences belonged to the cluster of Ib, two BKV isolates clustered within the subgroup Ia (Table II).…”

“…Subtype I is worldwide predominant and is divided into the subgroups Ia, Ib, and Ic. Subtype IV is detected at lower rates and the subtypes II and III only rarely occur [Takasaka et al, 2004;Ikegaya et al, 2006]. Strains of subtype I replicate in cell culture more efficiently than strains of subtype IV [Nukuzuma et al, 2006].…”

Genotyping Schemes for Polyomavirus BK, Using Gene-Specific Phylogenetic Trees and Single Nucleotide Polymorphism Analysis

“…As our knowledge of BKV genomic diversity expanded, difficulties were encountered in assigning viral strains to existing subtypes (1,27). Investigators proposed additional subgroups within the four major subtypes, such as subgroups Ia and Ib (35); Ic (36); and IVa, IVb, and IVc (14,25). Robust biologic and statistical support was not always available for the proposed subgroups.…”

A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping

“…Based on DNA sequence variations, four subgroups of subtype I have been identified (Ia, Ib-1, Ib-2, and Ic), and six subgroups of subtype IV have been identified (IVa-1, IVa-2, IVb-1, IVb-2, IVc-1, and IVc-2) (5, 6). The distribution of BKV subtypes and subgroups in human populations has been studied in many countries (7)(8)(9). BKV subtype I subgroup distributions vary across countries; subgroup Ia is highly prevalent in Africa, subgroup Ib-1 is highly prevalent in southeast Asia, subgroup Ib-2 is highly prevalent in Europe, and subgroup Ic is highly prevalent in northeast Asia (10,11).…”