A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping

Morel, Vincent; Martin, Élodie; François, Clément; Helle, François; Faucher, Justine; Mourez, Thomas; Choukroun, Gabriel; Duverlie, Gilles; Castelain, Sandrine; Brochot, Étienne

doi:10.1128/jcm.01180-16

Cited by 36 publications

(59 citation statements)

References 19 publications

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“…The influenza B virus lineage was determined based on the sequence as described previously (32). Polyomavirus BK (BKPyV) subtypes were determined using the algorithm of genomic variants described by Morel et al (33). The metapneumovirus lineage was determined based on the genomic determinants described by van den Hoogen et al (34).…”

Section: Methodsmentioning

confidence: 99%

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Wylie

Buller

et al. 2018

J Clin Microbiol

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Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.

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Section: Methodsmentioning

confidence: 99%

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Wylie

Buller

et al. 2018

J Clin Microbiol

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“…So far, four subtypes (I‐IV) of BKV have been identified based on the viral genome nucleotide sequence in the viral major capsid protein 1 (VP1) . Additionally, based on DNA sequence variations, four subgroups of genotype I have been identified (Ia, Ib1, Ib2, and Ic), and six subgroups of genotype IV have been identified (IVa1, IVa2, IVb1, IVb2, IVc1, and IVc2) …”

Section: Discussionmentioning

confidence: 99%

“…BKV genotypes have an uneven geographical distribution with subtype I accounting for 70‐80% of BKV worldwide, subtype IV responsible for around 10‐20% of BKV, and relatively smaller numbers due to types II and III BKV . BKV genotype I subgroup (Ia‐Ic) distributions vary across continents; subgroup Ia is highly prevalent in Africa, subgroup Ib‐1 in southeast Asia, subgroup Ib‐2 in Europe and West Asia, and subgroup Ic in northeast Asia . In line with BKV subtype 1, the genotype IV subgroups (Iva1‐IVc2) also have a varied geographic distribution .…”

Section: Discussionmentioning

confidence: 99%

“…56,57 So far, four subtypes (I-IV) of BKV have been identified based on the viral genome nucleotide sequence in the viral major capsid protein 1 (VP1). 58 33,38,60 In line with BKV subtype 1, the genotype IV subgroups (Iva1-IVc2) also have a varied geographic distribution. 1,61 In our meta-analysis, we are the first to summarize the epidemiology of BKV subtype in the United States.…”

Section: Evaluation For Publication Biasmentioning

confidence: 99%

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BK polyomavirus genotypes in renal transplant recipients in the United States: A meta‐analysis

Khoury

Aeddula

Boonpheng

et al. 2019

J Evidence Based Medicine

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Background In the United States, increasing ethnic diversity has been apparent. However, the epidemiology and trends of BKV genotypes remain unclear. This meta‐analysis was conducted with the aim to assess the prevalence of BKV genotypes among kidney transplant (KTx) recipients in the United States. Methods A comprehensive literature review was conducted through October 2018 utilizing MEDLINE, Embase, and Cochrane Database to identify studies that reported the prevalence of BKV subtypes and/or subgroups in KTx recipients in the United States. Pooled prevalence rates were combined using random effects, generic inverse variance method. The protocol for this study is registered with PROSPERO (no. CRD42019134582). Results A total of eight observational studies with a total of 193 samples (urine, blood, and kidney tissues) from 188 BKV‐infected KTX recipients were enrolled. Overall, the pooled estimated prevalence rates of BKV subtypes were 72.2% (95% confidence of interval [CI]: 62.7‐80.0%) for subtype I, 6.8% (95% CI: 2.5‐16.9%) for subtype II, 8.3% (95% CI: 4.4‐15.1%) for subtype III, and 16.1% (95% CI: 10.4‐24.2%) for subtype IV, respectively. While metaregression analysis demonstrated a significant positive correlation between year of study and the prevalence of BKV subtype I (slopes = +0.1023, P = .01), there were no significant correlations between year of study and percentages of BKV subtype II‐IV (P > .05). Among KTx recipients with BKV subtype I, the pooled estimated percentages of BKV subgroups were 22.4% (95% CI: 13.7‐34.5%) for subgroup Ia, 30.6% (95% CI: 17.7‐47.5%) for subgroup Ib1, 47.7% (95% CI: 35.8‐59.9%) for subgroup Ib2, and 4.1% (95% CI:1.2‐13.3%) for subgroup Ic, respectively. Conclusion BKV subtype I is the most prevalent subtype among KTx recipients in the United States and its prevalence seems to increasing overtime. Subgroup Ib2 is the most common subgroup among BKV subtype I.

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“…Despite the low variability seen in BKPyV, nonconserved regions of VP1 gene have been used to subtype BKPyV and also to molecular studies . The noncoding control region (NCCR) is also considered when diversity among isolates is investigated .…”

Section: Introductionmentioning

confidence: 99%

Variable sources of Bk virus in renal allograft recipients

Urbano

Nali

Oliveira

et al. 2019

Journal of Medical Virology

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BK virus is the causative agent of polyomavirus‐associated nephropathy, a major cause of kidney transplant failure affecting 1%‐10% of recipients. Previous studies that investigated the viral source on the kidney recipient pointed that the donor is implicated in the origin of human polyomavirus BK (BKPyV) infection in recipients, but giving the low genetic variability of BKPyV this subject is still controversial. The aim of this study was to determine if BKPyV replicating in kidney recipients after transplantation is always originated from the donor. Urine and blood samples from 68 pairs of living donors and kidney recipients who underwent renal transplantation from August 2010‐September 2011 were screened for BKPyV by real time polymerase chain reaction. Only three recipients presented viremia. When both donors and recipients were BKPyV positive, a larger fragment of VP1 region was obtained and sequenced to determine the level of similarity between them. A phylogenetic tree was built for the 12 pairs of sequences obtained from urine and high level of similarity among all sequences was observed, indicating that homology inferences for donor and recipient viruses must be cautiously interpreted. However, a close inspection on the donor‐recipient pairs sequences revealed that 3 of 12 pairs presented considerably different viruses and 4 of 12 presented mixed infection, indicating that the source of BKPyV infection is not exclusively derived from the donor. We report that about 60% of the renal recipients shed BKPyV genetically distinct from the donor, confronting the accepted concept that the donor is the main source of recipients’ infection.

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A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping

Cited by 36 publications

References 19 publications

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

BK polyomavirus genotypes in renal transplant recipients in the United States: A meta‐analysis

Variable sources of Bk virus in renal allograft recipients

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