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Kamminga S, Sidorov IA, Tadesse M, van der Meijden E, de Brouwer C, Zaaijer HL, Feltkamp MC, Gorbalenya AE. Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection. iScience 2022; 25:103613. [PMID: 35036862 PMCID: PMC8749223 DOI: 10.1016/j.isci.2021.103613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/27/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.
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Affiliation(s)
- Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Igor A. Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Michaël Tadesse
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Caroline de Brouwer
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hans L. Zaaijer
- Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Mariet C.W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
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Mormando R, Wolfe AJ, Putonti C. Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets. Viruses 2021; 13:v13061041. [PMID: 34072839 PMCID: PMC8230216 DOI: 10.3390/v13061041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.
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Affiliation(s)
- Rita Mormando
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
- Correspondence:
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Clinical evaluation of a laboratory-developed quantitative BK virus-PCR assay using the cobas® omni Utility Channel. J Virol Methods 2021; 290:114093. [PMID: 33549574 DOI: 10.1016/j.jviromet.2021.114093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND In immunocompromised patients, BK Virus (BKV) reactivation may cause serious disease with high morbidity. Particularly for patient management after solid organ transplantation, monitoring of viral load in different clinical specimens is crucial to ensure early diagnosis and response to reactivation. In this study, we evaluated the clinical performance of a custom designed primer /probe set for detection of BKV on the cobas® 6800, a high-throughput platform, employing the open channel of the system for integration of a lab-developed test (LDT). MATERIALS/METHODS A primer/probe set was optimized for the use on a high-throughput platform. Clinical performance was assessed in EDTA-plasma, serum and urine samples. Limit-of-detection (LOD) was determined by using a dilution series of BKV WHO standard. A CE-labeled PCR test (Altona Diagnostics) was used as a comparison to the assay. RESULTS The LOD for the LDT BKV assay was 6.7 IU/mL. Inter-and intra-run variability (at 5 x LOD) was low (<1.5 Ct in all specimens). All quality control panel specimens (Instand Germany n = 19) were correctly identified. Of 290 clinical samples tested, results were concordant for 280 samples. Sensitivity and specificity of the assay were 96 % and 98 % respectively. The quantitative analysis revealed a strong correlation (linear regression) between the CE-labelled comparator assay and the new BKV LDT assay with r2 = 0.96 for n = 123 urine samples and r2 = 0.98 for n = 167 plasma/serum samples. CONCLUSION Compared to a CE-IVD assay, the adapted LDT showed good analytical and clinical sensitivity and specificity for the detection and quantification of BKV in different clinical specimens. It represents a convenient solution to automate the LDT workflow with low hands-on time and thus facilitates high-throughput screening for BKV reactivation in immunocompromised patients.
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BK Virus-Associated Nephropathy after Renal Transplantation. Pathogens 2021; 10:pathogens10020150. [PMID: 33540802 PMCID: PMC7913099 DOI: 10.3390/pathogens10020150] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023] Open
Abstract
Recent advances in immunosuppressive therapy have reduced the incidence of acute rejection and improved renal transplantation outcomes. Meanwhile, nephropathy caused by BK virus has become an important cause of acute or chronic graft dysfunction. The usual progression of infection begins with BK viruria and progresses to BK viremia, leading to BK virus associated nephropathy. To detect early signs of BK virus proliferation before the development of nephropathy, several screening tests are used including urinary cytology and urinary and plasma PCR. A definitive diagnosis of BK virus associated nephropathy can be achieved only histologically, typically by detecting tubulointerstitial inflammation associated with basophilic intranuclear inclusions in tubular and/or Bowman’s epithelial cells, in addition to immunostaining with anti-Simian virus 40 large T-antigen. Several pathological classifications have been proposed to categorize the severity of the disease to allow treatment strategies to be determined and treatment success to be predicted. Since no specific drugs that directly suppress the proliferation of BKV are available, the main therapeutic approach is the reduction of immunosuppressive drugs. The diagnosis of subsequent acute rejection, the definition of remission, the protocol of resuming immunosuppression, and long-term follow-up remain controversial.
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Yan L, Guo H, Han L, Huang H, Shen Y, He J, Liu J. Sternheimer-Malbin Staining to Detect Decoy Cells in Urine of 213 Kidney Transplant Patients. Transplant Proc 2020; 52:823-828. [PMID: 32111385 DOI: 10.1016/j.transproceed.2020.01.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/11/2019] [Accepted: 01/25/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Human polyoma virus-associated nephropathy frequently refers to allograft failure after kidney transplant. Thus, the early detection of viral activation is extremely important for these immunocompromised patients. METHODS Previously, urine polyoma virus-infected cells (decoy cells) were indicated as the virus action, usually screened by the routine papanicolaou cytology in renal biopsy, but these methods are complex and the positive rate is low. In this article, the direct microscopy observation method, Wright-Giemsa staining, and Sternheimer-Malbin (SM) staining were all used to screen the decoy cells in urine samples of 213 kidney transplant patients who had used immunosuppressive drugs. RESULTS Among them, decoy cells were detected in 40 cases (18.8%) by the direct observation method, 44 cases (20.7%) by Wright-Giemsa staining and 49 cases (23.0%) by SM staining. Furthermore, the most common polyoma viruses, BK and JC viruses, were also confirmed in 41 (83.7%) cases among these 49 decoy cell-positive samples. Importantly, compared with other decoy cell detection methods, SM staining is fast, easy to operate, and has a high positive rate. CONCLUSION Therefore, SM staining is recommended as a fast and effective method for screening urine decoy cells in kidney transplant patients.
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Affiliation(s)
- Lizhi Yan
- Department of Clinical Laboratory, Inner Mongolia Baogang Hospital, Baotou, Inner Mongolia, China
| | - Hongbo Guo
- Department of Clinical Laboratory, Inner Mongolia Baogang Hospital, Baotou, Inner Mongolia, China
| | - Lizhong Han
- Department of Urology, Inner Mongolia Baogang Hospital, Baotou, Inner Mongolia, China
| | - Hualiang Huang
- Department of Clinical Laboratory, Inner Mongolia Baogang Hospital, Baotou, Inner Mongolia, China
| | - Yan Shen
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jing He
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jinlin Liu
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, China; Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Hangzhou, China.
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Freedman BI, Kistler AL, Skewes-Cox P, Ganem D, Spainhour M, Turner J, Divers J, Langefeld CD, Murea M, Hicks PJ, Hemal AK, Snipes JA, Zhao L, Abend JR, Lyles DS, Ma L, Skorecki KL. JC polyoma viruria associates with protection from chronic kidney disease independently from apolipoprotein L1 genotype in African Americans. Nephrol Dial Transplant 2019; 33:1960-1967. [PMID: 29420808 DOI: 10.1093/ndt/gfx368] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background Viral infections can trigger chronic kidney disease (CKD) and the urine virome may inform risk. The Natural History of APOL1-Associated Nephropathy Study (NHAANS) reported that urine JC polyomavirus (JCPyV) associated with a lower risk of APOL1-associated nephropathy in African Americans. Herein, association was assessed between urine JCPyV with CKD in African Americans independent from the APOL1 genotype. Methods Quantitative polymerase chain reaction was performed for urinary detection of JCPyV and BK polyoma virus (BKPyV) in 200 newly recruited nondiabetic African Americans. A combined analysis was performed in these individuals plus 300 NHAANS participants. Results In the 200 new participants, urine JCPyV was present in 8.8% of CKD cases and 45.8% of nonnephropathy controls (P = 3.0 × 10-8). In those with APOL1 renal-risk genotypes, JCPyV was detected in 5.1% of cases and 40.0% of controls (P = 0.0002). In those lacking APOL1 renal-risk genotypes, JCPyV was detected in 12.2% of cases and 48.8% of controls (P = 8.5 × 10-5). BKPyV was detected in 1.3% of cases and 0.8% of controls (P = 0.77). In a combined analysis with 300 NHAANS participants (n = 500), individuals with urine JCPyV had a 63% lower risk of CKD compared with those without urine JCPyV (odds ratio 0.37; P = 4.6 × 10-6). RNA fluorescence in situ hybridization confirmed the presence of JCPyV genomic DNA and JCPyV messenger RNA (mRNA) in nondiseased kidney. Conclusions Inverse relationships exist between JCPyV viruria and non-diabetic CKD. Future studies should determine whether renal inflammation associated with CKD is less permissive for JCPyV reactivation/replication or whether JCPyV is a marker of reduced host immune responsiveness that diminishes immune pathologic contributions to CKD.
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Affiliation(s)
- Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Amy L Kistler
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Peter Skewes-Cox
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Don Ganem
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Mitzie Spainhour
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Jolyn Turner
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Jasmin Divers
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Mariana Murea
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Pamela J Hicks
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Ashok K Hemal
- Department of Urology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - James A Snipes
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Lihong Zhao
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Johanna R Abend
- Infectious Diseases Area, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Douglas S Lyles
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Lijun Ma
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Karl L Skorecki
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology and Department of Nephrology, Rambam Health Care Campus, Haifa, Israel
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Association Between the Polyomaviruses Titers and Decoy Cell Positivity Rates After Renal Transplantation. Transplant Proc 2017; 48:921-3. [PMID: 27234768 DOI: 10.1016/j.transproceed.2016.02.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/08/2016] [Accepted: 02/18/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Urinary decoy cells develop after renal transplantation and their appearance is attributable primarily to the proliferation of polyomavirus types BK and JC. We measured the levels of these 2 viruses that cause decoy cells to appear in the urine. PATIENTS AND METHODS BK and JC virus levels were quantified in 1182 urine samples from 335 renal transplant patients using a multiplex Taqman real-time polymerase chain reaction assay. Forty-four samples were excluded from analyses because both viruses were present at ≥10(4) copies/mL. We analyzed the relationship between viral load and the presence of urinary decoy cells. RESULTS Decoy cells were observed in 237 of 1138 urine samples (21%) and the BK and JC viruses were positive in 205 (18%) and 455 (40%) samples, respectively. Decoy cells were observed in 0%, 21%, 67%, 87%, 100%, and 96% of urine samples when the BK viral load was <10(4), 10(4)-10(5), 10(5)-10(6), 10(6)-10(7), 10(7)-10(8), and ≥10(8) copies/mL, respectively; and in 1%, 13%, 41%, 59%, 87%, and 97% of urine samples when the JC viral load was <10(4), 10(4)-10(5), 10(5)-10(6), 10(6)-10(7), 10(7)-10(8), and ≥10(8) copies/mL, respectively. CONCLUSIONS BK virus more frequently triggered the appearance of decoy cells than did JC virus at equivalent viral titers.
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Kawashima N, Sekiya Y, Narita A, Kamei M, Muramatsu H, Nishio N, Hama A, Ito Y, Takahashi Y, Kojima S. Kampo patterns and radiology in children receiving choreito for hemorrhagic cystitis after hematopoietic stem cell transplantation. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/tkm2.1053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Nozomu Kawashima
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Yuko Sekiya
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Atsushi Narita
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Michi Kamei
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Hideki Muramatsu
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Nobuhiro Nishio
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Asahito Hama
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Yoshinori Ito
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Seiji Kojima
- Department of Pediatrics; Nagoya University Graduate School of Medicine; Nagoya Japan
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Hasan MR, Tan R, Al-Rawahi G, Thomas E, Tilley P. Comparative evaluation of laboratory developed real-time PCR assays and RealStar(®) BKV PCR Kit for quantitative detection of BK polyomavirus. J Virol Methods 2016; 234:80-6. [PMID: 27091098 DOI: 10.1016/j.jviromet.2016.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 02/25/2016] [Accepted: 04/12/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Quantitative, viral load monitoring for BK virus (BKV) by real-time PCR is an important tool in the management of polyomavirus associated nephropathy in renal transplant patients. However, variability in PCR results has been reported because of polymorphisms in viral genes among different subtypes of BKV, and lack of standardization of the PCR assays among different laboratories. In this study we have compared the performance of several laboratory developed PCR assays that target highly conserved regions of BKV genome with a commercially available, RealStar(®) BKV PCR Kit. METHOD Three real-time PCR assays (i) VP1 assay: selected from the literature that targets the major capsid protein (VP1) gene (ii) VP1MOD assay: VP1 assay with a modified probe, and (iii) BKLTA assay: newly designed assay that targets the large T antigen gene were assessed in parallel, using controls and clinical specimens that were previously tested using RealStar(®) BKV PCR Kit (Altona Diagnostics GmbH, Hamburg, Germany). Nucleic acid from all samples were extracted using the QIA symphony virus/bacteria kit on an automated DNA extraction platform QIA symphony SP (Qiagen). Primer and probe concentration, and reaction conditions for laboratory developed assays were optimized and the limit of detection of different assays was determined. Positive control for laboratory developed BK assays was prepared through construction of a plasmid carrying respective amplicon sequences. RESULTS The 95% detection limit of VP1, VP1MOD and BKLTA assays were 1.8×10(2), 3×10(3) and 3.5×10(2) genomic copies/ml, respectively, as determined by Probit regression analysis of data obtained by testing a dilution series of a titered patient specimen, using RealStar(®) BKV PCR Kit. The inter-assay and intra-assay, coefficient of variations of these assays using calibrated, plasmid standards were <1%. All assays, including the RealStar(®) BKV PCR assay, were highly specific when tested against a panel of external proficiency specimens containing both BK and JC viruses. All assays, except the VP1MOD assay determined BK viral load in proficiency specimens within the same log values. With reference to results obtained by RealStar(®) BKV PCR assay, the sensitivity and specificity of different assays tested in 116 serum specimens submitted for BK viral load assay were 91% and 97% for VP1 assay, 88% and 97% for VP1MOD assay, and 97% and 98% for BKLTA assay, respectively. BK Viral load in positive specimens determined by various assays was highly correlated (R(2)>0.97), based on linear regression analysis. CONCLUSIONS The performance characteristics of the newly designed, BKLTA assay were highly comparable to RealStar(®) BKV PCR assay, and can be used for routine detection and viral load monitoring of BKV in a cost-effective manner.
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Affiliation(s)
- Mohammad R Hasan
- Department of Pathology, Sidra Medical & Research Center, Doha, Qatar; Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Rusung Tan
- Department of Pathology, Sidra Medical & Research Center, Doha, Qatar; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ghada Al-Rawahi
- Children's and Women's Health Centre of BC, PHSA, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eva Thomas
- Department of Pathology, Sidra Medical & Research Center, Doha, Qatar
| | - Peter Tilley
- Children's and Women's Health Centre of BC, PHSA, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Kimura M, Hayashi T. Significance of decoy cells for indicating viral cytopathic effect in urine cytology. Cytopathology 2015; 27:220-1. [DOI: 10.1111/cyt.12261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- M. Kimura
- Department of Pathology; Kinki University Faculty of Medicine; Osaka-Sayama Japan
| | - T. Hayashi
- Department of Urology; Kinki University Faculty of Medicine; Osaka-Sayama Japan
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Huang ASE, Chen WC, Huang WT, Huang ST, Lo YC, Wei SH, Kuo HW, Chan PC, Hung MN, Liu YL, Mu JJ, Yang JY, Liu DP, Chou JH, Chuang JH, Chang FY. Public Health Responses to Reemergence of Animal Rabies, Taiwan, July 16-December 28, 2013. PLoS One 2015; 10:e0132160. [PMID: 26162074 PMCID: PMC4498755 DOI: 10.1371/journal.pone.0132160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/10/2015] [Indexed: 12/25/2022] Open
Abstract
Taiwan had been free of indigenous human and animal rabies case since canine rabies was eliminated in 1961. In July 2013, rabies was confirmed among three wild ferret-badgers, prompting public health response to prevent human rabies cases. This descriptive study reports the immediate response to the reemergence of rabies in Taiwan. Response included enhanced surveillance for human rabies cases by testing stored cerebrospinal fluids (CSF) from patients with encephalitides of unknown cause by RT-PCR, prioritizing vaccine use for postexposure prophylaxis (PEP) during periods of vaccine shortage and subsequent expansion of PEP, surveillance of animal bites using information obtained from vaccine application, roll out of preexposure prophylaxis (PrEP) with vaccine stock restoration, surveillance for adverse events following immunization (AEFI), and ensuring surge capacity to respond to general public inquiries by phone and training for healthcare professionals. Enhanced surveillance for human rabies found no cases after testing 205 stored CSF specimens collected during January 2010-July 2013. During July 16 to December 28, 2013, we received 8,241 rabies PEP application; 6,634 (80.5%) were consistent with recommendations. Among the 6,501 persons who received at least one dose of rabies vaccine postexposure, 4,953 (76.2%) persons who were bitten by dogs; only 59 (0.9%) persons were bitten by ferret-badgers. During the study period, 6,247 persons received preexposure prophylaxis. There were 23 reports of AEFI; but no anaphylaxis, Guillain-Barré syndrome, or acute disseminated encephalomyelitis were found. During the study period, there were 40,312 calls to the Taiwan Centers for Disease Control hotline, of which, 8,692 (22%) were related to rabies. Recent identification of rabies among ferret-badgers in a previously rabies-free country prompted rapid response. To date, no human rabies has been identified. Continued multifaceted surveillance and interministerial collaboration are crucial to achieve the goal of rabies-free status in Taiwan.
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Affiliation(s)
| | - Wan-Chin Chen
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Wan-Ting Huang
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Shih-Tse Huang
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Yi-Chun Lo
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Sung-Hsi Wei
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Hung-Wei Kuo
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Pei-Chun Chan
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Min-Nan Hung
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Yu-Lun Liu
- Office of Preventive Medicine, Centers for Disease Control, Taipei, Taiwan
| | - Jung-Jung Mu
- Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan
| | - Jyh-Yuan Yang
- Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan
| | - Ding-Ping Liu
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Jih-Haw Chou
- Office of Deputy Director, Centers for Disease Control, Taipei, Taiwan
| | - Jen-Hsiang Chuang
- Office of Deputy Director, Centers for Disease Control, Taipei, Taiwan
| | - Feng-Yee Chang
- National Defense Medical Center, Tri-Service General Hospital, Taipei, Taiwan
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Kawashima N, Ito Y, Sekiya Y, Narita A, Okuno Y, Muramatsu H, Irie M, Hama A, Takahashi Y, Kojima S. Choreito Formula for BK Virus–associated Hemorrhagic Cystitis after Allogeneic Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2015; 21:319-25. [DOI: 10.1016/j.bbmt.2014.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
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Funahashi Y, Kato M, Fujita T, Tsuruta K, Inoue S, Gotoh M. Correlation between urine and serum BK virus levels after renal transplantation. Transplant Proc 2014; 46:567-9. [PMID: 24656014 DOI: 10.1016/j.transproceed.2013.11.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/12/2013] [Accepted: 11/27/2013] [Indexed: 02/08/2023]
Abstract
BACKGROUND Quantification of the serum level of BK virus is used as a surrogate marker for the early onset of BK virus nephropathy. However, little is known about the diagnostic value of the urine level of BK virus for nephropathy or the relationship between the serum and urine viral load. We investigated the correlation between urine and serum BK virus levels after renal transplantation. METHODS From November 2008 to August 2013, a total of 270 renal transplant patients who were followed at our institution were included in this study. Urine and serum were collected simultaneously. BK virus levels were quantified in 894 urine and serum samples using a real-time polymerase chain reaction assay. RESULTS BK virus was detected in 178 urine samples and 36 serum samples. Among the BK virus-positive urine subjects, the positive predictive value for viral detection in the serum was 9% (13/147) when the urinary virus level was <10(7) copies/mL and 74% (23/31) when the urinary virus was ≥ 10(7) copies/mL. Serum BK viral levels were ∼2-3 log units lower than those in urine. CONCLUSIONS BK virus was detected more frequently in serum when present in urine at ≥ 10(7) copies/mL after renal transplantation.
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Affiliation(s)
- Y Funahashi
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - M Kato
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Fujita
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Tsuruta
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Inoue
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Gotoh
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Funahashi Y, Kato M, Fujita T, Takai S, Kimura Y, Gotoh M. Prevalence of polyomavirus positivity in urine after renal transplantation. Transplant Proc 2014; 46:564-6. [PMID: 24656013 DOI: 10.1016/j.transproceed.2013.09.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/20/2013] [Indexed: 12/18/2022]
Abstract
BACKGROUND Little is known about the timing of polyomavirus reactivation and its presence in urine after renal transplantation. The purpose of this study was to investigate the prevalence of positive polyomavirus in urine at various time points after renal transplantation. METHODS From November 2008 to August 2013, 279 renal transplant patients from our institution were included in this study. One urine sample was collected at 0-3, 4-6, 7-12, 13-24, 25-60, and ≥ 61 months after renal transplantation. A total of 394 urine samples were assessed for the presence of the BK and JC viruses with the use of a real-time polymerase chain reaction assay. RESULTS BK virus was detected in the urine of one-third of patients during the first 6 months. Thereafter, the positivity rate decreased gradually to 12% >5 years after transplantation. The positivity rate for the JC virus in urine was 33%-49% regardless of the post-transplantation phase. CONCLUSIONS BK virus was detected more frequently in urine during the early phase after renal transplantation, whereas the JC virus was detected more consistently.
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Affiliation(s)
- Y Funahashi
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - M Kato
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Fujita
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Takai
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Kimura
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Gotoh
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Muldrew KL, Lovett JL. An in-house assay for BK polyomavirus quantification using the Abbott m2000 RealTime system. J Med Microbiol 2013; 62:1714-1720. [PMID: 23924663 DOI: 10.1099/jmm.0.058388-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BK polyomavirus (BKPyV) quantification is useful for monitoring renal transplant patient response to therapy. The Abbott m2000 RealTime System employed by some clinical laboratories to perform US Food and Drug Administration-approved assays can also be used to develop in-house assays such as the one presented here. This study aimed to validate an in-house quantitative real-time PCR assay targeting the BKPyV major capsid VP1 gene for assessment of viral load using the Abbott m2000 RealTime System. BKPyV load was measured in 95 urine and plasma samples previously tested for BKPyV by one of three laboratories (46 BKPyV-positive samples consisting of 35 plasma and 11 urine samples; 49 samples negative for BKPyV consisting of 47 plasma and two urine samples). Two additional plasma specimens from the College of American Pathologists proficiency testing survey were also analysed. Precision studies were performed by diluting a high-viral-titre patient sample into BKPyV-negative pooled plasma to create high-positive (6.16 log10 copies ml(-1)) and low-positive (3.16 log10 copies ml(-1)) samples. For precision studies of inter-assay variability, a high-positive (7.0 log10 copies ml(-1)) and a low-positive (3.0 log10 copies ml(-1)) sample were measured in 20 separate runs. The assay's limit of quantification and limit of detection were 2.70 and 2.25 log10 copies ml(-1), respectively. The assay was linear from 2.70 to 9.26 log10 copies ml(-1). Of the 48 known positives, 43 were detected as positive, with three reported by the reference laboratory as values lower than the limit of detection. Two known positives at 3.27 and 3.80 log10 copies ml(-1) tested negative by the m2000 BKPyV assay. Of the 49 known negative samples, 48 were negative by the m2000 BKPyV load assay, with one sample confirmed positive by a reference laboratory. Qualitative analysis prior to discrepancy testing demonstrated a sensitivity of 89.58 % and a specificity of 97.96 %. Precision studies demonstrated inter-assay coefficients of variation of 0.63 % (high positive) and 4.38 % (low positive). Genotyping was performed on 22 patient samples, of which 21 (95.45 %) were type I and one (4.55 %) was type II. In conclusion, the m2000 BKPyV viral load assay sensitivity, specificity, linear range, precision and cost effectiveness make it an attractive methodology for clinical laboratories using the Abbott m2000 RealTime System.
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Affiliation(s)
- Kenneth L Muldrew
- Department of Pathology, University of Toledo Medical Center, Toledo, OH, USA
| | - Jennie L Lovett
- Department of Pathology, University of Toledo Medical Center, Toledo, OH, USA
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Imahashi N, Nishida T, Ito Y, Kawada JI, Nakazawa Y, Toji S, Suzuki S, Terakura S, Kato T, Murata M, Naoe T. Identification of a novel HLA-A*24:02-restricted adenovirus serotype 11-specific CD8+ T-cell epitope for adoptive immunotherapy. Mol Immunol 2013; 56:399-405. [PMID: 23911395 DOI: 10.1016/j.molimm.2013.05.232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 05/22/2013] [Accepted: 05/23/2013] [Indexed: 02/02/2023]
Abstract
Subgroup B adenovirus serotype 11 (Ad11) occasionally causes fatal infections in immunocompromised patients. The present study describes a novel Ad11 epitope presented by HLA-A*24:02 that could be used for adoptive immunotherapy. Ten synthetic Ad11 hexon protein-derived nonamer peptides that bound to HLA-A*24:02 were selected by a computer algorithm and MHC stabilization assay. Stimulation of peripheral blood mononuclear cells from HLA-A*24:02+ donors with each of these synthetic peptides induced peptide-specific CD8(+) T-cells for three peptides. Testing the reactivity of these peptide-specific CD8(+) T-cells against various target cells confirmed that peptide TYFNLGNKF is naturally processed in Ad11-infected cells and is presented by HLA-A*24:02. Emergence of TYFNLGNKF-specific CD8(+) T-cells coincided with the clearance of adenoviruses in a patient with Ad11 disease. Importantly, TYFNLGNKF-specific CD8(+) T-cells were suggested to be not serotype cross-reactive. The novel HLA-A*24:02-restricted Ad11 epitope could be used for anti-Ad11 adoptive immunotherapy and to monitor immunity to Ad11 using MHC tetramers.
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Affiliation(s)
- Nobuhiko Imahashi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan; Research Fellow of Japan Society for the Promotion of Science, Japan
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Ryschkewitsch CF, Jensen PN, Major EO. Multiplex qPCR assay for ultra sensitive detection of JCV DNA with simultaneous identification of genotypes that discriminates non-virulent from virulent variants. J Clin Virol 2013; 57:243-8. [PMID: 23619054 DOI: 10.1016/j.jcv.2013.03.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND JC virus (JCV) is the etiologic agent for progressive multifocal leukoencephalopathy (PML), a demyelinating disease occurring in the brain of patients with underlying immune compromised states. All viable JCV genomes contain a conserved region in the T protein coding nucleotide sequence that when detected by PCR in CSF is a confirmatory diagnostic marker for PML along with clinical and neuroradiological evidence. The non-coding regulatory region (NCRR) is hypervariable, as evidenced by nucleotide sequence of the non-virulent variant, which is predominantly excreted in urine, versus that of virulent variants found in brain and CSF of PML patients. All variants can be found in blood. OBJECTIVE A single assay that quantifies and identifies JCV DNA in clinical samples and discriminates between variants has significant value to physicians and patients at risk for PML. STUDY DESIGN Separate primer pairs were tested together to quantitatively detect conserved viral DNA nucleotide sequence in patient samples, while simultaneously detecting the NCRR specific for the non-virulent variant. RESULTS In testing using control plasmids and patients' CSF, blood, and urine, PML patients predictably demonstrated the non-virulent, archetype NCRR in urine, but virulent NCRR variants in CSF and blood. CONCLUSION The JCV qPCR multiplex assay targets two regions in JCV genomes to simultaneously identify and measure viral DNA, as well as distinguish between variants associated with PML and those that are not. The multiplex results could signal risk for PML if patients are viremic with JCV variants closely associated with PML pathogenesis.
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Affiliation(s)
- Caroline F Ryschkewitsch
- Laboratory of Molecular Medicine and Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Drive, Building 10, Room 3B14, Bethesda, MD 20892, USA.
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