Isolation of a variant of BK virus with altered restriction endonuclease pattern

Pauw, W.; Choufoer, J. C.

doi:10.1007/bf01315635

Cited by 17 publications

(5 citation statements)

References 24 publications

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“…The spontaneous generation of sequence repeats in response to selective pressure is consistent with the known tendency of enhancer mutants of BKV and SV40 to revert by sequence duplication (24,64). It is also consistent with the observation that primary isolates of BKV usually require an extended period of incubation in culture before the first cytopathic effects are observed (7,8,15,19,21,22,26,36,50,51,58,59,69). This would allow time for repeats to be generated and fixed in the population.…”

Section: Discussionsupporting

confidence: 84%

Binding of cellular proteins to the regulatory region of BK virus DNA

Markowitz

Dynan

1988

J Virol

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The human papovavirus BK has a noncoding regulatory region located between the divergently transcribed early and late coding regions. Many strains of BK virus (BKV) have direct DNA sequence repeats in the regulatory region, although the number and extent of these repeats varies widely between independent isolates. Until recently, little was known about the individual functional elements within the BKV regulatory region, and

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Section: Discussionsupporting

confidence: 84%

Binding of cellular proteins to the regulatory region of BK virus DNA

Markowitz

Dynan

1988

J Virol

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“…2) of 50 complete VP1 gene sequences, including the 45 strains shown in Fig. 1; type II strain SB (17); type Ib strains WW (7,18,40), DIK (18,40), and JL (30,40); and type Ic strain MT (39,40). In this VP1 region tree, Jin genotype II (SB) and genotype III (AS) appeared to branch off from a common ancestor, supporting the separate recognition of these two genotypes.…”

Section: Resultsmentioning

confidence: 98%

Phylogenetic Analysis of Polyomavirus BK Sequences

Sharma

Gupta

Vats

et al. 2006

J Virol

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Polyomavirus BK (BKV) has emerged as an important pathogen in kidney transplant patients. Existing taxonomic classifications of BKV come from conventional DNA sequence alignments based on limited data derived from the VP1 gene. We have used a phylogenetic whole-genome approach to examine the pattern of diversity and evolutionary relationships between 45 BKV strains isolated from multiple clinical settings. This analysis supports the classification of BKV into six genotypes, of which types V and VI have not been previously recognized. BKV strains hitherto classified as type I are, in fact, quite heterogeneous, and several cluster with our newly defined genotypes V and VI. The sequence information needed for assigning genotypes can be captured by VP1, VP2, VP3, or large T-gene sequencing. The most polymorphic coding region in the viral genome is VP1, but significant variation is also present in the large T-antigen gene, wherein polymorphisms are found in 11.39% of all nucleotide sites, 46.22% of which are cluster specific. Type-specific amino acid changes within the VP1 region are predicted to map to the BC and DE loops. The number of taxonomically informative amino acid changes in the large T antigen exceeds even that of the VP1 region. Viral strains isolated from healthy subjects and from patients with human immunodeficiency virus infection, WiskottAldrich syndrome, and vasculopathy with capillary leak syndrome formed distinct subclusters. However, within the kidney transplant population, BKV strains derived from patients with asymptomatic viruria did not show complete separation from strains associated with allograft nephropathy.Polyomavirus BK (BKV) has a worldwide seroprevalence of 60 to 80% in humans (10). Primary infection occurs in childhood (11) and leads to viral latency in the urogenital tract and mononuclear cells. Following reactivation, which mostly occurs in immunocompromised patients, the virus is excreted in the urine (5). BKV viruria in renal transplant recipients ranges between 10 to 60% and has been associated with ureteric stenosis (16) and BK viral nephropathy characterized by tubular necrosis and interstitial nephritis (32, 33). In bone marrow transplant recipients, BKV has been linked to hemorrhagic cystitis (13,26,34).Characterization of genetic diversity of BK virus has biologic as well as clinical implications. This information is needed to seek potential relationships between viral genotype and clinical disease. Sequence data are required by diagnostic virology laboratories to ensure that primers and probes being used for amplification of viral DNA can successfully detect all naturally occurring viral strains. One of the most variable regions of the viral genome is the noncoding control region (NCCR), which shows insertions, deletions, duplications, and complex rearrangements involving enhancer and/or promoter sequences (28, 29). Significant variation is also recognized in the VP1 gene, which codes for VP1, a major structural protein that comprises approximately 80% of the total viral c...

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“…2b). The other five additional sequences included one, SB, previously designated as genotype II (Gibson & Gardner, 1983); the other four appeared to be genotype I and consisted of WW (Chauhan et al, 1984), DIK (Goudsmit et al, 1981), JL (Pauw & Choufoer, 1978) and MT (Sugimoto et al, 1989).…”

Section: Phylogenetic Analysis and Genotypic Classification Of Bkv Sementioning

confidence: 99%

Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity

Chen

Sharp

Fowkes

et al. 2004

Journal of General Virology

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To determine the variability of BK virus (BKV) in vivo, the sequences of nine full-length molecular clones from the striated muscle and heart DNA of a patient with BKV-associated capillary leak syndrome (BKV CAP ), as well as three clones each from the urine of one human immunodeficiency virus type 2-positive (BKV HI ) and one healthy control subject (BKV HC ), were analysed. The regulatory region of all clones corresponded to the archetypal regulatory region usually found in urine isolates. Analysis of the predicted conformation of BKV CAP proteins did not suggest any structural differences on the surface of the viral particles compared with BKV HI and BKV HC clones. No amino acid changes common to most BKV CAP clones could be identified that have not already been reported in non-vasculotropic strains. However, the coding region of each clone had unique nucleotide substitutions, and intra-host variability was greater among BKV CAP clones, with a mean difference of 0?29 % per site compared with 0?16 % for BKV HI and 0?14 % for BKV HC . The clones from each strain formed monophyletic clades, suggesting a single source of infection for each subject. The most divergent BKV CAP clones differed at 0?55 % of sites, implying a rate of nucleotide substitution of approximately 5610 "5 substitutions per site per year, which is two orders of magnitude faster than estimated for the other human polyomavirus, JC virus.

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Isolation of a variant of BK virus with altered restriction endonuclease pattern

Cited by 17 publications

References 24 publications

Binding of cellular proteins to the regulatory region of BK virus DNA

Binding of cellular proteins to the regulatory region of BK virus DNA

Phylogenetic Analysis of Polyomavirus BK Sequences

Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity

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