scholarly journals BKTyper—Web Application for VP1 and NCCR Polyoma BK Typing

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 25
Author(s):  
Joan Martí-Carreras ◽  
Piet Maes
Keyword(s):  
Web Application ◽  
Hemorrhagic Cystitis ◽  
Immunosuppressive Agents ◽  
Gc Content ◽  
Epidemiological Studies ◽  
Bk Virus ◽  
Dna Virus ◽  
Diagnostic Assays ◽  
Double Stranded Dna ◽  
Coding Control

Human polyoma BK virus (BKV) prevalence has been increasing due to the introduction of more potent immunosuppressive agents, mostly in immunocompromised patients. BKV has been linked mostly to polyomavirus-associated hemorrhagic cystitis, and polyomavirus-associated nephropathy. BKV is a circular double stranded DNA virus (cdsDNA) with an average genome size of 5100 bp and an average GC content of 40%. Its genome codifies for five proteins: VP1, VP2, VP3, Angio gene, and the antigen T (which includes an event of alternative splicing, yielding a short and a large antigen T transcript). Additionally, it contains the non-coding control region (NCCR), known to be highly repetitive and to vary in number, length, and location of the repeats. Subtyping of BKV has been mainly studied in VP1 and the NCCR. Subtyping and subgrouping of BKV is conducted routinely in diagnostic assays and in epidemiological studies. Recently, Morel et al. published (Journal of Clinical Microbiology 2017; 55, 4) a strategy to subtype BKV through 100 bp VP1 amplicon. NCCR diversity is more complex than VP1, as it is configured by five repeat blocks (O, P, Q, R, and S). NCCR blocks can vary in number and length, resulting in a gradient of infectivity and replication. Rearranged NCCR have been linked to diverse patient etiologies, although any specific arrangement has failed to correlate with disease outcome or to have any predictive value. Due to the high abundance of BKV individuals and the clinical implications for human health that may represent BKV typing, a reliable, automatic, and free typing tool would be of great interest. Here, BKTyper is presented, a whole genome genotyper for polyoma BKV, based on a VP1 typing by Morel’s algorithm and NCCR block identification. BKTyper can accept both whole BKV genome or regions of interest in fasta format to generate the typing profile and phylogenetic analysis.

scholarly journals Survey of BK Virus in Renal Transplant Recipients in Iran: A Systematic Review and Meta-Analysis

Intervirology ◽  
2020 ◽  
pp. 1-9
Author(s):  
Somayeh Shatizadeh Malekshahi ◽  
Hoorieh Soleimanjahi ◽  
Fariba Dorostkar ◽  
Vahid Salimi ◽  
Mohammad Farahmand
Keyword(s):  
Renal Transplant ◽  
Meta Analysis ◽  
Hemorrhagic Cystitis ◽  
Random Effect ◽  
Graft Loss ◽  
Epidemiological Studies ◽  
Bk Virus ◽  
Iranian Population ◽  
Renal Transplant Recipients ◽  
Plasma Samples

<b><i>Introduction:</i></b> BK virus (BKV) infection in renal transplant (RT) recipients can cause hemorrhagic cystitis, transient renal dysfunction, and BKV nephropathy (BKVN). The prevalence and significance of BKV in RT recipients remain to be clarified in the Iranian population. The purpose of this review is to summarize the overall prevalence of BKV infection in RT recipients from previously published studies in Iran. <b><i>Methods:</i></b> We systematically reviewed articles through a comprehensive search of the main electronic and Persian national databases up to November 2019. <b><i>Results:</i></b> The overall pooled prevalence of BKV infection among the Iranian population was 23% (95% CI; 15–33%). Comparing these studies revealed that the prevalence of BKV in plasma samples ranges from 3 to 40%, in renal biopsies 1–13%, and in urine samples 10–49%. Due to substantial heterogeneity among reported studies (<i>I</i><sup>2</sup> = 93%, <i>p</i> &#x3c; 0.01), random-effect meta-analysis was performed. BKV infection rate was slightly higher in women than men (16%, <i>p</i> = 0.04 vs. 14%, <i>p</i> &#x3c; 0.01, respectively). The majority of the studies employed real-time PCR (24%, <i>I</i><sup>2</sup> = 93, <i>p</i> &#x3c; 0.01) and analyzed plasma samples alone or in combination with other types of specimens. BKV prevalence from 5 cities among the Iranian population showed a higher prevalence rate in Guilan. <b><i>Conclusion:</i></b> Our analysis provides a preliminary estimate of the epidemiology of BKV infection in RT recipients in Iran. These results arouse a need for more epidemiological studies of BKV infection in different unanalyzed regions in Iran. Early detection of BKV in RT recipients helps timely nephropathy diagnosis and prevents graft loss.

scholarly journals BKTyper: Free Online Tool for Polyoma BK Virus VP1 and NCCR Typing

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 837
Author(s):  
Joan Martí-Carreras ◽  
Olga Mineeva-Sangwo ◽  
Dimitrios Topalis ◽  
Robert Snoeck ◽  
Graciela Andrei ◽  
...  
Keyword(s):  
Graphical Representation ◽  
Hemorrhagic Cystitis ◽  
Immunosuppressive Agents ◽  
Bk Virus ◽  
Sorting Algorithm ◽  
Cell Transplant ◽  
Structural Protein ◽  
Hematopoietic Stem ◽  
Transplant Patients ◽  
Viral Protein 1

Human BK polyomavirus (BKPyV) prevalence has been increasing due to the introduction of more potent immunosuppressive agents in transplant recipients, and its clinical interest. BKPyV has been linked mostly to polyomavirus-associated hemorrhagic cystitis, in allogenic hematopoietic stem cell transplant, and polyomavirus-associated nephropathy in kidney transplant patients. BKPyV is a circular double-stranded DNA virus that encodes for seven proteins, of which Viral Protein 1 (VP1), the major structural protein, has been extensively used for genotyping. BKPyV also contains the noncoding control region (NCCR), configured by five repeat blocks (OPQRS) known to be highly repetitive and diverse, and linked to viral infectivity and replication. BKPyV genetic diversity has been mainly studied based on the NCCR and VP1, due to the high occurrence of BKPyV-associated diseases in transplant patients and their clinical implications. Here BKTyper is presented, a free online genotyper for BKPyV, based on a VP1 genotyping and a novel algorithm for NCCR block identification. VP1 genotyping is based on a modified implementation of the BK typing and grouping regions (BKTGR) algorithm, providing a maximum-likelihood phylogenetic tree using a custom internal BKPyV database. Novel NCCR block identification relies on a minimum of 12-bp motif recognition and a novel sorting algorithm. A graphical representation of the OPQRS block organization is provided.

scholarly journals An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

2021 ◽  
pp. 193229682098557
Author(s):  
Alysha M. De Livera ◽  
Jonathan E. Shaw ◽  
Neale Cohen ◽  
Anne Reutens ◽  
Agus Salim
Keyword(s):  
Continuous Glucose Monitoring ◽  
Web Application ◽  
Diabetes Management ◽  
Glucose Monitoring ◽  
Epidemiological Studies ◽  
Interactive Software ◽  
Web Based ◽  
Software Applications ◽  
Visualization Of Data ◽  
User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

scholarly journals Circular Double-Stranded Forms of TT Virus DNA in the Liver

2000 ◽  
Vol 74 (11) ◽  
pp. 5161-5167 ◽  
Author(s):  
Hiroaki Okamoto ◽  
Masato Ukita ◽  
Tsutomu Nishizawa ◽  
Junichi Kishimoto ◽  
Yuji Hoshi ◽  
...  
Keyword(s):  
Human Beings ◽  
Specific Primer ◽  
Dna Virus ◽  
S1 Nuclease ◽  
Tt Virus ◽  
Double Stranded Dna ◽  
Replicative Intermediates ◽  
Paired Serum ◽  
Genomic Length ◽  
Liver Tissues

ABSTRACT TT virus (TTV) is an unenveloped, circular, and single-stranded DNA virus commonly infecting human beings worldwide. TTV DNAs in paired serum and liver tissues from three viremic individuals were separated by gel electrophoresis and characterized biophysically. TTV DNAs in sera migrated in sizes ranging from 2.0 to 2.5 kb. TTV DNAs in liver tissues, however, migrated at 2.0 to 2.5 kb as well as at 3.5 to 6.1 kb. Both faster- and slower-migrating forms of TTV DNAs in the liver were found to be circular and of the full genomic length of 3.8 kb. TTV DNAs migrating at 2.0 to 2.5 kb, from either serum or liver tissues, were sensitive to S1 nuclease but resistant to restriction endonucleases, and therefore, they were single-stranded. By contrast, TTV DNAs in liver tissues that migrated at 3.5 to 6.1 kb were resistant to S1 nuclease. They migrated at 3.7 to 4.0 kb after digestion with EcoRI, which suggests that they represent circular, double-stranded replicative intermediates of TTV. When TTV DNAs were subjected to strand-specific primer extension and then amplified by PCR with internal primers, those in serum were found to be minus-stranded DNAs while those in liver tissues were found to be a mixture of plus- and minus-stranded DNAs. These results suggest that TTV replicates in the liver via a circular double-stranded DNA.

scholarly journals BK virus-associated hemorrhagıc cystitis in patients wıth allogeneıc hematopoıetıc cell transplantation: report of three cases

2017 ◽  
Vol 9 (2) ◽  
Author(s):  
Duygu Mert ◽  
Hikmetullah Batgi ◽  
Alparslan Merdin ◽  
Sabahat Çeken ◽  
Mehmet Sinan Dal ◽  
...  
Keyword(s):  
Stem Cell ◽  
Stem Cell Transplantation ◽  
Cell Transplantation ◽  
Allogeneic Stem Cell Transplantation ◽  
Hemorrhagic Cystitis ◽  
Immunosuppressive Treatment ◽  
Active Agent ◽  
Bk Virus ◽  
Cell Transplant ◽  
Hematopoietic Stem

BK virus is a human polyoma virus. It is acquired in early childhood and remains life-long latent in the genitourinary system. BK virus replication is more common in receiving immunosuppressive therapy receiving patients and transplant patients. BK virus could cause hemorrhagic cystitis in patients with allogeneic stem cell transplantation. Hemorrhagic cystitis is a serious complication of hematopoietic stem cell transplantation. Hemorrhagic cystitis could cause morbidity and long stay in the hospital. Diagnosis is more frequently determined by the presence of BK virus DNA detected with quantitative or real-time PCR testing in serum or plasma and less often in urine. The reduction of immunosuppression is effective in the treatment of BK virus infection. There are also several agents with anti-BK virus activity. Cidofovir is an active agent against a variety of DNA viruses including poliomyoma viruses and it is a cytosine nucleotide analogue. Intravenous immunoglobulin IgG (IVIG) also includes antibodies against BK and JC (John Cunningham) viruses. Hereby, we report three cases of hemorrhagic cystitis. Hemorrhagic cystitis developed in all these three cases of allogeneic stem cell transplantation due to acute myeloid leukemia (AML). BK virus were detected as the cause of hemorrhagic cystitis in these patients. Irrigation of the bladder was performed. Then levofloxacin 1×750 mg intravenous and IVIG 0.5 gr/kg were started. But the hematuria did not decreased. In the first case, treatment with leflunomide was started, but patient died due to refractory AML and severe graft-versus-host disease after 4th day of leflunamide and levofloxacin treatments. Cidofovir treatment and the reduction of immunosuppressive treatment decreased the BK virus load and resulted symptomatic improvement in the second case. Initiation of cidofovir was planned in the third case. Administration of cidofovir together with the reduction of immunosuppression in the treatment of hemorrhagic cystitis associated with BK virus in allogeneic stem cell transplant recipients could be a good option.

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