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Mannonen L, Jokela P, Kragh Thomsen M, Yerly S, Cilla G, Jarem D, Canchola JA, Hopkins M. Performance of the cobas EBV and cobas BKV assays: multi-site comparison of standardized quantitation. J Clin Microbiol 2024; 62:e0026724. [PMID: 39046255 PMCID: PMC11323559 DOI: 10.1128/jcm.00267-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024] Open
Abstract
Guidelines recommend monitoring of Epstein-Barr virus (EBV) and BK virus (BKV) in solid organ and hematopoietic stem cell transplant patients. The majority of quantitative DNA testing for EBV and BKV employs unstandardized individual laboratory-developed testing solutions (LDTs), with implications for accuracy, reproducibility, and comparability between laboratories. The performance of the cobas EBV and cobas BKV assays was assessed across five laboratories, using the World Health Organization International Standards (WHO IS) for EBV and BKV, and the National Institute of Standards and Technology Quantitative Standard for BKV, and results were compared with the LDTs in use at the time. Methods were also compared using locally sourced clinical specimens. Variation was high when laboratories reported EBV or BKV DNA values using LDTs, where quantitative values were observed to differ by up to 1.5 log10 unit/mL between sites. Conversely, results from the cobas EBV and cobas BKV assays were accurate and reproducible across sites and on different testing days. Adjustment of LDTs using the international standards led to closer alignment between the assays; however, day-to-day reproducibility of LDTs remained high. In addition, BKV continued to show bias, indicating challenges with the commutability of the BKV International Standard. The cobas EBV and cobas BKV assays are automated, aligned to the WHO IS, and have the potential to reduce the variability in viral load testing introduced by differences in LDTs. Standardization of reporting values may eventually allow different centers to compare data to allow clinical decision thresholds to be established supporting improvements in patient management.IMPORTANCEThe application of center-specific cut-offs for clinical decisions and the variability of LDTs often hinder interpretation; thus, the findings reported here support the need for standardization in the field of post-transplant monitoring of EBV and BKV to improve patient management. Alongside the choice of assay, it is also important to consider which standard to use when deciding upon a testing methodology. This is a call to action for standardization, as treatment for EBV and BKV is driven by viral load test results, and the more accurate and comparable the test results are across institutions, the more informed and better the treatment decisions can be.
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Affiliation(s)
- Laura Mannonen
- Department of Clinical Microbiology, HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pia Jokela
- Department of Clinical Microbiology, HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Sabine Yerly
- Laboratory of Virology, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - Gustavo Cilla
- Department of Microbiology, Donostia University Hospital and Biodonostia Health Research Institute, San Sebastián, Spain
| | - Daniel Jarem
- Clinical Development and Medical Affairs, Roche Molecular Systems, Inc., Pleasanton, California, USA
| | - Jesse A. Canchola
- CDMA Biometrics, Biostatistics Group, Roche Molecular Systems, Inc., Pleasanton, California, USA
| | - Mark Hopkins
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- Department of Infection and Immunity, Liverpool University Hospitals NHS Trust, Liverpool, United Kingdom
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2
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Lee C, Lim Y, Saintine D, Babady NE. Analytical and clinical evaluation of the cobas Epstein-Barr virus test at a tertiary care cancer hospital. J Clin Virol 2024; 173:105680. [PMID: 38728796 DOI: 10.1016/j.jcv.2024.105680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Epstein-Barr Virus (EBV) viral loads in hematopoietic stem cell transplant (HSCT) recipients are typically monitored using quantitative molecular assays. The Cobas EBV test (Roche Molecular, Pleasanton, CA) has recently been FDA-cleared for the monitoring of EBV viral loads in plasma samples of transplant patients. In this study, we compared the viral loads obtained by a laboratory-developed test (EBV LDT) using Altona Analyte specific reagents (ASR) to those obtained on the Cobas EBV test. METHODS The analytical performance of the assay was established using the EBV verification panel from Exact Diagnostics and the EBV ATCC strain B95-8. The clinical evaluation was performed using 343 plasma samples initially tested on the EBV LDT. RESULTS The analytical sensitivity (<18.8 IU/mL), precision (SD < 0.17 log) and linear range (35.0 IU/mL to 1E + 08 IU/mL) of the Cobas EBV assay established by the manufacturers were confirmed. The strength of the qualitative agreement was substantial between the cobas EBV and the EBV LDT (85.6 %; κ = 0.71) and almost perfect when discordant results were resolved (96.4 %; κ = 0.93). The quantitative agreement was moderate (82.9 %; κ = 0.53) with the viral load obtained on the Cobas EBV test being lower across the linear range of the two tests (mean log difference of 1.0). While the absolute values of the viral loads were markedly different, the overall trends observed in patients with multiple consecutive results were similar between the two tests. CONCLUSIONS The Cobas EBV test provides an accurate and valid, in vitro diagnostic (IVD) option for monitoring of EBV viral loads in transplant patients and should provide an opportunity for increased standardization and commutability of tests results across laboratories.
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Affiliation(s)
- Cindy Lee
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Younmin Lim
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Deborah Saintine
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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3
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Chang CK, Chen CS, Jian MJ, Chung HY, Chang FY, Lin JC, Hsieh SS, Tang SH, Perng CL, Chen CW, Chiu CH, Shang HS. Monitoring coronavirus disease progression and clinical impact through quantitative viral load testing. Clin Chim Acta 2024; 560:119731. [PMID: 38754576 DOI: 10.1016/j.cca.2024.119731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The viral load (VL) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals is critical for improving clinical treatment strategies, care, and decisions. Several studies have reported that the initial SARS-CoV-2 VL is associated with disease severity and mortality. Cycle threshold (Ct) values and/or copies/mL are often used to quantify VL. However, a multitude of platforms, primer/probe sets of different SARS-CoV-2 target genes, and reference material manufacturers may cause inconsistent interlaboratory interpretations. The first International Standard for SARS-CoV-2 RNA quantitative assays has allowed diagnostic laboratories to transition SARS-CoV-2 VL results into international units per milliliter (IU/mL). The Cobas SARS-CoV-2 Duo quantitative assay provides VL results expressed in IU/mL. MATERIALS AND METHODS We enrolled 145 and 50 SARS-CoV-2-positive, hospitalized and 50-negative individuals at the Tri-Service General Hospital, Taiwan from January to May 2022. Each participant's electronic medical record was reviewed to determine asymptomatic, mild, moderate, and severe cases. Nasopharyngeal swabs were collected using universal transport medium. We investigated the association of SARS-CoV-2 VL with disease severity using the Cobas SARS-CoV-2 Duo quantitative assay and its functionality in clinical assessment and decision making to further improve clinical treatment strategies. Limit of detection (LOD) was assessed. RESULTS All 50 SARS-CoV-2-negative samples confirmed negative for SARS-CoV-2, demonstrating 100 % specificity of the Cobas SARS-CoV-2 Duo assay. Patients with severe symptoms had longer hospital stays, and the length of hospital stay (30.56 days on average) positively correlated with the VL (8.22 ± 1.21 log10 IU/mL). Asymptomatic patients had the lowest VL (5.54 ± 2.06 log10 IU/mL) at admission and the shortest hospital stay (14.1 days on average). CONCLUSIONS VL is associated with disease severity and duration of hospitalization; therefore, its quantification should be considered when making clinical care decisions and treatment strategies. The Cobas SARS-CoV-2 Duo assay provides a commutable unitage IU/mL for interlaboratory interpretations.
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Affiliation(s)
- Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chun-Hsiang Chiu
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China.
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4
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Leber AL. Maternal and congenital human cytomegalovirus infection: laboratory testing for detection and diagnosis. J Clin Microbiol 2024; 62:e0031323. [PMID: 38391188 PMCID: PMC11005381 DOI: 10.1128/jcm.00313-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Human cytomegalovirus (CMV) is the leading cause of congenital infection worldwide and the most common cause of non-genetic sensorineural hearing loss. As there is no vaccine or other specific intervention to prevent congenital CMV infection, there is a need to identify maternal and congenital infections with sensitive and specific testing as early as possible. There is no widely accepted practice for screening during pregnancy or in all newborns for identification of possible cases of congenital CMV. Currently, screening during pregnancy is limited to those identified as at risk followed by fetal and/or neonatal testing when congenital infection is suspected. This review focuses primarily on the current status of laboratory testing for diagnosis of maternal and congenital CMV infections. Primary maternal infection is best diagnosed using serologic testing, including CMV IgM, IgG, and avidity testing, while fetal infection should be assessed by nucleic acid amplification testing (NAAT) of amniotic fluid. Urine and saliva NAATs are the mainstay for diagnosis of congenital CMV in the first 3 weeks of life. Testing of dried blood spots can be useful for diagnosis of congenital CMV outside of the newborn period. The gaps in knowledge such as the prognostic value of viral loads in various sample types are addressed.
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Affiliation(s)
- Amy L. Leber
- Departments of Pathology and Laboratory Medicine and Pediatrics, Nationwide Children’s Hospital, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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5
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Preiksaitis J, Allen U, Bollard CM, Dharnidharka VR, Dulek DE, Green M, Martinez OM, Metes DM, Michaels MG, Smets F, Chinnock RE, Comoli P, Danziger-Isakov L, Dipchand AI, Esquivel CO, Ferry JA, Gross TG, Hayashi RJ, Höcker B, L'Huillier AG, Marks SD, Mazariegos GV, Squires J, Swerdlow SH, Trappe RU, Visner G, Webber SA, Wilkinson JD, Maecker-Kolhoff B. The IPTA Nashville Consensus Conference on Post-Transplant lymphoproliferative disorders after solid organ transplantation in children: III - Consensus guidelines for Epstein-Barr virus load and other biomarker monitoring. Pediatr Transplant 2024; 28:e14471. [PMID: 37294621 DOI: 10.1111/petr.14471] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/10/2022] [Accepted: 01/02/2023] [Indexed: 06/11/2023]
Abstract
The International Pediatric Transplant Association convened an expert consensus conference to assess current evidence and develop recommendations for various aspects of care relating to post-transplant lymphoproliferative disorders after solid organ transplantation in children. In this report from the Viral Load and Biomarker Monitoring Working Group, we reviewed the existing literature regarding the role of Epstein-Barr viral load and other biomarkers in peripheral blood for predicting the development of PTLD, for PTLD diagnosis, and for monitoring of response to treatment. Key recommendations from the group highlighted the strong recommendation for use of the term EBV DNAemia instead of "viremia" to describe EBV DNA levels in peripheral blood as well as concerns with comparison of EBV DNAemia measurement results performed at different institutions even when tests are calibrated using the WHO international standard. The working group concluded that either whole blood or plasma could be used as matrices for EBV DNA measurement; optimal specimen type may be clinical context dependent. Whole blood testing has some advantages for surveillance to inform pre-emptive interventions while plasma testing may be preferred in the setting of clinical symptoms and treatment monitoring. However, EBV DNAemia testing alone was not recommended for PTLD diagnosis. Quantitative EBV DNAemia surveillance to identify patients at risk for PTLD and to inform pre-emptive interventions in patients who are EBV seronegative pre-transplant was recommended. In contrast, with the exception of intestinal transplant recipients or those with recent primary EBV infection prior to SOT, surveillance was not recommended in pediatric SOT recipients EBV seropositive pre-transplant. Implications of viral load kinetic parameters including peak load and viral set point on pre-emptive PTLD prevention monitoring algorithms were discussed. Use of additional markers, including measurements of EBV specific cell mediated immunity was discussed but not recommended though the importance of obtaining additional data from prospective multicenter studies was highlighted as a key research priority.
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Affiliation(s)
- Jutta Preiksaitis
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Upton Allen
- Division of Infectious Diseases and the Transplant and Regenerative Medicine Center, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Hospital, The George Washington University, Washington, District of Columbia, USA
| | - Vikas R Dharnidharka
- Department of Pediatrics, Division of Pediatric Nephrology, Hypertension & Pheresis, Washington University School of Medicine & St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Daniel E Dulek
- Division of Pediatric Infectious Diseases, Monroe Carell Jr. Children's Hospital at Vanderbilt and Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael Green
- Division of Pediatric Infectious Diseases, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Olivia M Martinez
- Department of Surgery and Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Diana M Metes
- Departments of Surgery and Immunology, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Marian G Michaels
- Division of Pediatric Infectious Diseases, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Françoise Smets
- Pediatric Gastroenterology and Hepatology, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | | | - Patrizia Comoli
- Cell Factory & Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico, Pavia, Italy
| | - Lara Danziger-Isakov
- Division of Infectious Disease, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Anne I Dipchand
- Labatt Family Heart Centre, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | | | - Judith A Ferry
- Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Thomas G Gross
- Center for Cancer and Blood Diseases, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Robert J Hayashi
- Division of Pediatric Hematology/Oncology, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Britta Höcker
- University Children's Hospital, Pediatrics I, Heidelberg, Germany
| | - Arnaud G L'Huillier
- Faculty of Medicine, Pediatric Infectious Diseases Unit and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
| | - Stephen D Marks
- Department of Paediatric Nephrology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health, London, UK
| | - George Vincent Mazariegos
- Department of Surgery, Hillman Center for Pediatric Transplantation, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James Squires
- Division of Gastroenterology, Hepatology and Nutrition, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Steven H Swerdlow
- Division of Hematopathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ralf U Trappe
- Department of Hematology and Oncology, DIAKO Ev. Diakonie-Krankenhaus Bremen, Bremen, Germany
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Gary Visner
- Division of Pulmonary Medicine, Boston Children's Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Steven A Webber
- Department of Pediatrics, Vanderbilt School of Medicine, Nashville, Tennessee, USA
| | - James D Wilkinson
- Department of Pediatrics, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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Kim SR, Waghmare A, Hijano DR. Approach to hematopoietic cell transplant candidates with respiratory viral detection. Front Pediatr 2024; 11:1339239. [PMID: 38304442 PMCID: PMC10830789 DOI: 10.3389/fped.2023.1339239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant parameters, and the specific respiratory virus (RV). In the setting of adenovirus (ADV), human metapneumovirus (HMPV), influenza, parainfluenza virus (PIV), and respiratory syncytial virus (RSV) detection prior to hematopoietic cell transplant (HCT), clinical practice guidelines recommend transplant delay when possible; however, there is much more ambiguity when other respiratory viruses, such as seasonal coronaviruses (CoVs), human rhinovirus (HRV), and SARS-CoV-2, are detected. Our aims for this review include detailing clinical practical guidelines and reviewing current literature on pre-transplant respiratory viral infections (RVIs), including antiviral therapies and prevention strategies, when available. We will center our discussion on three representative clinical scenarios, with the goal of providing practical guidance to clinicians.
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Affiliation(s)
- Sara R. Kim
- Division of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Alpana Waghmare
- Division of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Diego R. Hijano
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, United States
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7
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Hijano DR, Ferrolino JA, Gu Z, Brazelton JN, Zhu H, Suganda S, Glasgow HL, Dallas RH, Allison KJ, Maron G, Darji H, Tang L, Fabrizio TP, Webby RJ, Hayden RT. Digital PCR to Measure SARS-CoV-2 RNA, Variants, and Outcomes in Youth. J Pediatric Infect Dis Soc 2023; 12:618-626. [PMID: 37956414 PMCID: PMC10725239 DOI: 10.1093/jpids/piad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND The role of SARS-CoV-2 viral load in predicting contagiousness, disease severity, transmissibility, and clinical decision-making continues to be an area of great interest. However, most studies have been in adults and have evaluated SARS-CoV-2 loads using cycle thresholds (Ct) values, which are not standardized preventing consistent interpretation critical to understanding clinical impact and utility. Here, a quantitative SARS-CoV-2 reverse-transcription digital PCR (RT-dPCR) assay normalized to WHO International Units was applied to children at risk of severe disease diagnosed with COVID-19 at St. Jude Children's Research Hospital between March 28, 2020, and January 31, 2022. METHODS Demographic and clinical information from children, adolescents, and young adults treated at St. Jude Children's Research Hospital were abstracted from medical records. Respiratory samples underwent SARS-CoV-2 RNA quantitation by RT-dPCR targeting N1 and N2 genes, with sequencing to determine the genetic lineage of infecting virus. RESULTS Four hundred and sixty-two patients aged 0-24 years (median 11 years old) were included during the study period. Most patients were infected by the omicron variant (43.72%), followed by ancestral strain (22.29%), delta (13.20%), and alpha (2.16%). Viral load at presentation ranged from 2.49 to 9.14 log10 IU/mL, and higher viral RNA loads were associated with symptoms (OR 1.32; CI 95% 1.16-1.49) and respiratory disease (OR 1.23; CI 95% 1.07-1.41). Viral load did not differ by SARS-CoV-2 variant, vaccination status, age, or baseline diagnosis. CONCLUSIONS SARS-CoV-2 RNA loads predict the presence of symptomatic and respiratory diseases. The use of standardized, quantitative methods is feasible, allows for replication, and comparisons across institutions, and has the potential to facilitate consensus quantitative thresholds for risk stratification and treatment.
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Affiliation(s)
- Diego R Hijano
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jose A Ferrolino
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Zhengming Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jessica N Brazelton
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haiqing Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Sri Suganda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Heather L Glasgow
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ronald H Dallas
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Himani Darji
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Thomas P Fabrizio
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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8
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Leuzinger K, Hirsch HH. Amplicon size and non-encapsidated DNA fragments define plasma cytomegalovirus DNA loads by automated nucleic acid testing platforms: A marker of viral cytopathology? J Med Virol 2023; 95:e29139. [PMID: 37804497 DOI: 10.1002/jmv.29139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Management of cytomegalovirus (CMV) in transplant patients relies on measuring plasma CMV-loads using quantitative nucleic acid testing (QNAT). We prospectively compared the automated Roche-cobas®6800-CMV and Roche-CAP/CTM-CMV with laboratory-developed Basel-CMV-UL54-95bp, and Basel-CMV-UL111a-77bp. Roche-cobas®6800-CMV and Roche-CAP/CTM-CMV were qualitatively concordant in 142/150 cases (95%). In-depth comparison revealed higher CMV-loads of the laboratory-developed assay and correlated with smaller amplicon size. After calibration to the 1.WHO-approved CMV international standard, differences were reduced but remained significant. DNase-I pretreatment significantly reduced CMV-loads for both automated Roche-CAP/CTM-CMV and Roche-cobas®6800-CMV assays, whereby 90% and 95% of samples became undetectable. DNase-I pretreatment also reduced CMV-loads quantified by Basel-CMV-UL54-95bp and Basel-CMV-UL111a-77bp, but remaining detectable in 20% and 35%, respectively. Differences were largest for 110 samples with low-level CMV-DNAemia being detectable but not-quantifiable by Roche-cobas®6800-CMV, whereby the smaller amplicon sizes yielded higher viral loads for concordant positives. We conclude that non-encapsidated fragmented CMV-DNA is the major form of plasma CMV-loads also measured by fully-automated platforms. Amplicons of <150 bp and calibrators are needed for reliable and commutable QNAT-results. We hypothesize that non-encapsidated fragmented CMV-DNA results from lysis of CMV-replicating cells and represent a direct marker of viral cell damage, which contribute to delayed viral load responses despite effective antivirals.
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Affiliation(s)
- Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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9
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Lütgehetmann M, Albert E, Hamilton A, Jarem D, Pfefferle S, Stucki H, Navarro D. Evaluation of a Quantitative Dual-Target EBV DNA Test on a Fully Automated Molecular Testing System. J Clin Microbiol 2023; 61:e0051823. [PMID: 37432105 PMCID: PMC10446858 DOI: 10.1128/jcm.00518-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/07/2023] [Indexed: 07/12/2023] Open
Abstract
The measurement of Epstein-Barr virus (EBV) deoxyribonucleic acid (DNA) is key to diagnosing and managing EBV-associated complications in transplant recipients. The performance of the new Conformité Européenne (CE) and Food and Drug Administration (FDA)-cleared quantitative Roche cobas EBV real-time PCR assay was determined by using EDTA-plasma dilution panels and clinical samples that were spiked with either the World Health Organization's EBV international standard or high-titer EBV lambda stock. Correlation with the Abbott Realtime EBV assay was assessed in clinical specimens and conducted at two independent laboratories. An in silico analysis revealed that the dual-target test (EBNA1 and BMRF2) was 100% inclusive for the known diversity of EBV. The overall limit of detection (LoD) was 16.6 IU/mL for genotype 1 (GT1). GT2 LoD was verified at 18.8 IU/mL. The linear ranges were from 1.40 × 101 to 2.30 × 108 IU/mL and from 2.97 × 101 to 9.90 × 107 IU/mL for GT1 and GT2, respectively. Accuracy was confirmed across the linear range (mean difference not exceeding ±0.18 log10). Precision was not influenced by the factors analyzed (standard deviation of 0.02 to 0.17 log10), including the presence of potentially interfering endogenous or exogenous substances. Plasma samples were stable under several conditions (variable time points, storage, and freeze/thaw cycles). In clinical EBV DNA-positive samples, correlation between the cobas EBV test and the comparator was high (n = 126 valid results; R2 = 0.96) with a 0.1 mean log10 titer difference. The cobas EBV test is an accurate, sensitive, specific, and reproducible assay for the detection of EBV DNAemia in plasma. In general, high levels of automation and calibration to the international standard will lead to improvements in the harmonization of quantitative EBV DNA test results across laboratories.
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Affiliation(s)
| | - Eliseo Albert
- Hospital Clínico Universitario, Fundación INCLIVA, School of Medicine, Valencia, Spain
| | | | - Daniel Jarem
- Roche Molecular Systems, Pleasanton, California, USA
| | | | - Heinz Stucki
- Roche Diagnostics International, Rotkreuz, Switzerland
| | - David Navarro
- Hospital Clínico Universitario, Fundación INCLIVA, School of Medicine, Valencia, Spain
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10
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Miller JA, Huang C, Yamamoto F, Sahoo MK, Le QT, Pinsky BA. Comparison of Real-Time PCR and Digital PCR for Detection of Plasma Epstein-Barr Virus DNA in Nasopharyngeal Carcinoma. J Mol Diagn 2023; 25:490-501. [PMID: 37068736 DOI: 10.1016/j.jmoldx.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/26/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
Plasma Epstein-Barr virus (EBV) DNA is an established biomarker for endemic nasopharyngeal carcinoma. However, existing real-time quantitative PCR (qPCR) assays are limited by poor interlaboratory reproducibility. This is a barrier to biomarker integration into staging systems and management. It was hypothesized that EBV digital PCR (dPCR) would have similar sensitivity but improved precision relative to qPCR. Using the World Health Organization EBV standard and patient specimens, the NRG-HN001 BamHI-W qPCR, two commercial EBNA-1 qPCR assays, and two laboratory-developed dPCR assays amplifying the BamHI-W, EBNA-1, and EBER targets were compared. Testing was conducted in the North American reference laboratory for the NRG-HN001 randomized trial. The EBV dPCR assays achieved similar performance compared with qPCR. Although dPCR does not require quantitation standards, different dPCR thresholding algorithms yielded significant qualitative and quantitative variation. This was most evident with low levels of EBV DNA. No-template control-informed thresholding (ddpcRquant) mitigated false-positive/false-negative findings. The NRG-HN001 BamHI-W qPCR and laboratory-developed BamHI-W droplet dPCR offered higher sensitivity, lower limit of blank, higher precision at low plasma EBV DNA levels (≤1500 IU/mL), and higher overall agreement with clinical specimens versus single-copy qPCR/dPCR targets (EBNA-1/EBER). These data confirm the rationale for using the BamHI-W target to define prognostic thresholds and indicate that both qPCR and dPCR methods harmonized to the World Health Organization standard can provide the necessary analytical performance.
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Affiliation(s)
- Jacob A Miller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California.
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11
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Govind S, Fritzsche M, Jenkins A, Cleveland MH, Vallone PM, Almond N, Morris C, Berry N. Deep Sequencing and Molecular Characterisation of BK Virus and JC Virus WHO International Reference Materials for Clinical Diagnostic Use. Viruses 2023; 15:1289. [PMID: 37376589 DOI: 10.3390/v15061289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Reactivation of JC and BK polyomaviruses during immunosuppression can lead to adverse clinical outcomes. In renal transplant recipients, BKV-associated nephropathy can result in graft loss, while in patients with autoimmune disorders, prolonged immunomodulatory drug use can cause rare onset of progressive multifocal leukoencephalopathy due to JCV reactivation. In such patients, accurate BK and JC viral load determinations by molecular technologies are important for diagnosis and clinical management; however, comparability across centres requires effective standardisation of diagnostic molecular detection systems. In October 2015, the WHO Expert Committee for Biological Standardisation (ECBS) established the 1st WHO International Standards (ISs) for use as primary-order calibrants for BKV and JCV nucleic acid detection. Two multi-centre collaborative studies confirmed their utility in harmonising agreement across the wide range of BKV and JCV assays, respectively. Previous Illumina-based deep sequence analysis of these standards, however, identified deletions in different regions, including the large T-antigen coding region. Hence, further detailed characterization was warranted. METHODS Comprehensive sequence characterisation of each preparation using short- and long-read next-generation sequencing technologies was performed with additional corroborative independent digital PCR (dPCR) determinations. Potential error rates associated with long-read sequencing were minimised by applying rolling circle amplification (RCA) protocols for viral DNA (circular dsDNA), generating a full validation of sequence identity and composition and delineating the integrity of full-length BK and JC genomes. RESULTS The analysed genomes displayed subpopulations frequently characterised by complex gene re-arrangements, duplications and deletions. CONCLUSIONS Despite the recognition of such polymorphisms using high-resolution sequencing methodologies, the ability of these reference materials to act to enhance assay harmonisation did not appear significantly impacted, based on data generated by the 2015 WHO collaborative studies, but highlights cautionary aspects of IS generation and commutability for clinical molecular diagnostic application.
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Affiliation(s)
- Sheila Govind
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Martin Fritzsche
- Division of Analytical and Biological Sciences, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare Product Regulatory Agency (MHRA), South Mimms EN6 3QG, UK
| | - Adrian Jenkins
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Megan H Cleveland
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Clare Morris
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Neil Berry
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
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12
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Monk CH, Youngquist BM, Brady AD, Shaffer JG, Hu TY, Ning B, Zwezdaryk KJ. Development of a CRISPR-Cas12a rapid diagnostic for human cytomegalovirus. Antiviral Res 2023; 215:105624. [PMID: 37150408 DOI: 10.1016/j.antiviral.2023.105624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Despite decades of research, human cytomegalovirus (CMV) continues to contribute to significant morbidity and mortality in transplant settings and remains the leading cause of viral congenital infections. Clinical diagnosis of CMV infection and/or reactivation under these settings is completed using real time quantitative polymerase chain reaction (RT-qPCR). This assay performs well but is hampered by poor sensitivity and a lack of standardization among testing facilities. A point-of-care rapid diagnostic to determine CMV viremia could address these issues and improve patient care. In this manuscript, we introduce clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a technology to design and validate a rapid diagnostic for CMV. This system was tested using CMV spiked human saliva and urine samples. Sensitivity of the assay was ∼10 infectious units (IU)/mL. Specificity of the assay was robust and failed to detect other herpesviruses. Collectively, we have designed and validated a rapid diagnostic for CMV that overcomes limitations of the current standard diagnostic. This assay has the potential to be used as a point-of-care screening tool in transplant and neonatal settings.
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Affiliation(s)
- Chandler H Monk
- Bioinnovation Program, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Brady M Youngquist
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Alyson D Brady
- Neurosceince Program, Tulane University, New Orleans, LA, 70112, United States
| | - Jeffrey G Shaffer
- Department of Biostatistics and Data Science, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Bo Ning
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Kevin J Zwezdaryk
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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13
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Palavecino EL, Ridley T, Hester L, Blosser SJ. Analytical evaluation of the cobas® 6800 system for the detection and quantification of BK Virus (BKV) and Epstein Barr Virus (EBV) at a US solid organ and hematopoietic stem cell transplant center. Diagn Microbiol Infect Dis 2023; 105:115884. [PMID: 36630742 DOI: 10.1016/j.diagmicrobio.2022.115884] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
The cobas® EBV and BKV assays are the first FDA-approved, quantitative assays for monitoring posttransplant reactivation of these viruses. In this study, we assessed performance of the fully-automated cobas® assays, compared with Diasorin Molecular ASR, our laboratory developed test, and demonstrated a strong interassay correlation for BK and EBV monitoring.
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Affiliation(s)
- Elizabeth L Palavecino
- Department of Pathology, Wake Forest School of Medicine, Winston Salem, NC, USA; Department of Pathology, Atrium Health -Wake Forest Baptist, Winston Salem, NC, USA.
| | - Tonika Ridley
- Department of Pathology, Atrium Health -Wake Forest Baptist, Winston Salem, NC, USA
| | - Louise Hester
- Department of Pathology, Atrium Health -Wake Forest Baptist, Winston Salem, NC, USA
| | - Sara J Blosser
- Medical and Scientific Affairs, Roche Diagnostics Corporation, Indianapolis, IN, USA
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14
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Buchta C, Kollros D, Jovanovic J, Huf W, Delatour V, Puchhammer-Stöckl E, Mayerhofer M, Müller MM, Shenoy S, Griesmacher A, Aberle SW, Görzer I, Camp JV. Converting to an international unit system improves harmonization of results for SARS-CoV-2 quantification: Results from multiple external quality assessments. J Clin Virol 2023; 158:105352. [PMID: 36525853 PMCID: PMC9733965 DOI: 10.1016/j.jcv.2022.105352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The detection of SARS-CoV-2 vRNA in clinical samples has relied almost exclusively on RT-qPCR as the gold standard test. Published results from various external quality assessments ("ring trials") worldwide have shown that there is still a large variability in results reported for the same samples. As reference standards of SARS-CoV-2 RNA are available, we tested whether using standard curves to convert Ct values into copies/mL (cp/mL) improved harmonization. METHODS Nine laboratories using 23 test systems (15 of which were unique) prepared standard dilution curves to convert Ct values of 13 SARS-CoV-2 positive samples to cp/mL (hereafter IU/mL). The samples were provided in three rounds of a virus genome detection external quality assessment (EQA) scheme. We tested the precision and accuracy of results reported in IU/mL, and attempted to identify the sources of variability. RESULTS Reporting results as IU/mL improved the precision of the estimated concentrations of all samples compared to reporting Ct values, although some inaccuracy remained. Variance analysis showed that nearly all variability in data was explained by individual test systems within individual laboratories. When controlling for this effect, there was no significant difference between all other factors tested (test systems, EQA rounds, sample material). CONCLUSIONS Converting results to copies/mL improved precision across laboratory test systems. However, it seems the results are still very specific to test systems within laboratories. Further efforts could be made to improve accuracy and achieve full harmonization across diagnostic laboratories.
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Affiliation(s)
- Christoph Buchta
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Dominik Kollros
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Jovana Jovanovic
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Wolfgang Huf
- Karl Landsteiner Institute for Clinical Risk Management, Vienna, Austria
| | - Vincent Delatour
- Laboratoire National de Métrologie et d'Essais (LNE), Paris, France
| | | | - Maximilian Mayerhofer
- Armament and Defence Technology Agency, NBC & Environmental Protection Technology Division, Vienna, Austria
| | - Mathias M. Müller
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Santosh Shenoy
- Department of Surgery, Kansas City Veterans Medical Center, University of Missouri at Kansas City, Kansas City, MO, USA
| | - Andrea Griesmacher
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | | | - Irene Görzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Jeremy V. Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria,Corresponding author at: Center for Virology, Medizinische Universitat Wien, Kinderspitalgasse 15, 1095 Vienna, Austria
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15
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Cui J, Zhao K, Sun Y, Wen R, Zhang X, Li X, Long B. Diagnosis and treatment for the early stage of cytomegalovirus infection during hematopoietic stem cell transplantation. Front Immunol 2022; 13:971156. [PMID: 36211358 PMCID: PMC9537469 DOI: 10.3389/fimmu.2022.971156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Cytomegalovirus (CMV) infection remains a frequent complication after hematopoietic stem cell transplantation (HSCT) and causes significant morbidity and mortality in transplantation recipients. In this review, we highlight the role of major risk factors that are associated with the incidence of CMV infection. Advances in immunosurveillance may predict CMV infection, allowing early interventions to prevent severe infection. Furthermore, numerous therapeutic strategies against CMV infection after HSCT are summarized. A comprehensive understanding of the current situation of CMV treatment may provide a hint for clinical practice and even promote the development of novel strategies for precision medicine.
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Affiliation(s)
| | | | | | | | | | - Xudong Li
- *Correspondence: Bing Long, longb3@ mail.sysu.edu.cn; Xudong Li,
| | - Bing Long
- *Correspondence: Bing Long, longb3@ mail.sysu.edu.cn; Xudong Li,
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16
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Hayden RT, Su Y, Boonyaratanakornkit J, Cook L, Gu Z, Jerome KR, Pinsky BA, Sam SS, Tan SK, Zhu H, Tang L, Caliendo AM. Matrix Matters: Assessment of Commutability among BK Virus Assays and Standards. J Clin Microbiol 2022; 60:e0055522. [PMID: 35997500 PMCID: PMC9491175 DOI: 10.1128/jcm.00555-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Quantitative testing of BK virus (BKPyV) nucleic acid has become the standard of care in transplant patients. While the relationship between interassay harmonization and commutability has been well characterized for other transplant-related viruses, it has been less well studied for BKPyV, particularly regarding differences in commutability between matrices. Here, interassay agreement was evaluated among six real-time nucleic acid amplification tests (NAATs) and one digital PCR (dPCR) BKPyV assay. Differences in the commutability of three quantitative standards was examined across all assays using a variety of statistical approaches. Panels, including 40 samples each of plasma and urine samples previously positive for BKPyV, together with one previously negative plasma sample and four previously negative urine samples, were tested using all assays, with each real-time NAAT utilizing its usual quantitative calibrators. Serial dilutions of WHO, National Institute for Standards and Technology (NIST), and commercially produced (Exact/Bio-Rad) reference materials were also run by each assay as unknowns. The agreement of the clinical sample values was assessed as a group and in a pairwise manner. The commutability was estimated using both relativistic and quantitative means. The quantitative agreement across assays in the urine samples was within a single log10 unit across all assays, while the results from the plasma samples varied by 2 to 3 log10 IU/mL. The commutability showed a similar disparity between the matrices. Recalibration using international standards diminished the resulting discrepancies in some but not all cases. Differences in the sample matrix can affect the commutability and interassay agreement of quantitative BKPyV assays. Differences in commutability between matrices may largely be due to factors other than those such as amplicon size, previously described as important in the case of cytomegalovirus. Continued efforts to standardize viral load measurements must address multiple sources of variability and account for differences in assay systems, quantitative standards, and sample matrices.
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Affiliation(s)
- R. T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Y. Su
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - L. Cook
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Z. Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - K. R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseaese Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - B. A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - S. S. Sam
- Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - S. K. Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - H. Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - L. Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - A. M. Caliendo
- Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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17
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Human cytomegalovirus: a survey of end-organ diseases and diagnostic challenges in solid organ transplant recipients. Curr Opin Organ Transplant 2022; 27:243-249. [PMID: 36354249 DOI: 10.1097/mot.0000000000000992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PURPOSE OF REVIEW Human cytomegalovirus (CMV) infection is one of the most important infectious complications in solid organ transplant (SOT) recipients, leading to significant morbidity and mortality. Therefore, early detection and prompt treatment are imperative to improve transplant outcomes. This article highlights the clinical characteristics of the most common CMV end-organ diseases in SOT recipients and their diagnostic modalities and challenges. RECENT FINDINGS CMV can cause a variety of end-organ diseases in SOT recipients. Although CMV nucleic acid amplification by polymerase chain reaction (PCR) is frequently employed to detect CMV reactivation or infection, its predictive value for various CMV end-organ diseases remains uncertain. Given the limitation of PCR or other noninvasive tests, confirmation of CMV end-organ disease may require tissue biopsy, which may not be feasible or available, or may cause untoward complications. SUMMARY The utility of PCR to diagnose CMV end-organ disease is limited. As CMV can infect any organ system(s), clinicians caring for SOT recipients need to maintain vigilance for any signs and symptoms of end-organ disease to allow early recognition and prompt treatment. Invasive procedures might be needed to confirm the diagnosis and minimize the empirical use of antiviral therapy that may have substantial drug toxicities.
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18
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Park Y, Roh J, Kim S. Performance Evaluation of the Aptima Assays in Comparison with the cobas 6800 Assays for the Detection of HIV-1, HBV, and HCV in Clinical Samples. Ann Lab Med 2022; 42:447-456. [PMID: 35177565 PMCID: PMC8859551 DOI: 10.3343/alm.2022.42.4.447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/06/2021] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Background Accurate and consistent viral load (VL) quantitation of HIV type 1 (HIV-1), hepatitis B virus (HBV), and hepatitis C virus (HCV) is important for diagnosis and clinical monitoring. Assay results have to be concordant and compatible across laboratories. We evaluated the performance of three Aptima assays (Hologic, San Diego, CA, USA) and compared their VL values with corresponding cobas 6800 assay (Roche Diagnostics, Mannheim, Germany) results, using 840 clinical samples. Methods The correlation between VL results obtained using the two assays was evaluated in terms of analytical sensitivity, precision/reproducibility, linearity, and cross-reactivity. Agreement rates were determined using kappa statistics. The overall agreement of VL values was examined using Passing–Bablok regression analysis. Results All CVs were within 5%; the assays had good precision for detecting all three viruses. The linearity of quantitation assessed using three AccuSpan linearity panels (Seracare, Milford, MA, USA), was excellent for the Aptima assays. For HIV-1 and HCV, the results of both assays showed excellent agreement (κ=0.89 and 0.90, respectively) while for HBV, the results showed good agreement (κ=0.69). For analytical sensitivity, the VLs required for a 100% detection rate of HIV-1, HBV, and HCV were 20 copies/mL, 7.5 IU/mL, and 5.0 IU/mL, respectively. The results for HIV-1, HBV, and HCV obtained using both assays correlated strongly (R2=0.97, 0.93, and 0.95, respectively). Conclusions The cobas 6800 and Aptima assays, with fully automated and high-throughput molecular platforms for HIV-1, HBV, and HCV VL measurements, show good analytical performance and a strong correlation between results. The study results suggest that the assays can be used interchangeably for long-term monitoring of chronic infections.
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Affiliation(s)
- Younhee Park
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Juhye Roh
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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19
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Ngouth N, Monaco MC, Walker L, Corey S, Ikpeama I, Fahle G, Cortese I, Das S, Jacobson S. Comparison of qPCR with ddPCR for the Quantification of JC Polyomavirus in CSF from Patients with Progressive Multifocal Leukoencephalopathy. Viruses 2022; 14:v14061246. [PMID: 35746716 PMCID: PMC9229850 DOI: 10.3390/v14061246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Lytic infection of oligodendrocytes by the human JC polyomavirus (JCPyV) results in the demyelinating disease called progressive multifocal leukoencephalopathy (PML). The detection of viral DNA in the cerebrospinal fluid (CSF) by PCR is an important diagnostic tool and, in conjunction with defined radiological and clinical features, can provide diagnosis of definite PML, avoiding the need for brain biopsy. The main aim of this study is to compare the droplet digital PCR (ddPCR) assay with the gold standard quantitative PCR (qPCR) for the quantification of JC viral loads in clinical samples. Methods: A total of 62 CSF samples from 31 patients with PML were analyzed to compare the qPCR gold standard technique with ddPCR to detect conserved viral DNA sequences in the JCPyV genome. As part of the validation process, ddPCR results were compared to qPCR data obtained in 42 different laboratories around the world. In addition, the characterization of a novel triplex ddPCR to detect viral DNA sequence from both prototype and archetype variants and a cellular housekeeping reference gene is described. Triplex ddPCR was used to analyze the serum from six PML patients and from three additional cohorts, including 20 healthy controls (HC), 20 patients with multiple sclerosis (MS) who had never been treated with natalizumab (no-NTZ-treated), and 14 patients with MS who were being treated with natalizumab (NTZ-treated); three from this last group seroconverted during the course of treatment with natalizumab. Results: JCPyV DNA was detected only by ddPCR for 5 of the 62 CSF samples (8%), while remaining undetected by qPCR. For nine CSF samples (15%), JCPyV DNA was at the lower limit of quantification for qPCR, set at <250 copies/mL, and therefore no relative quantitation could be determined. By contrast, exact copies of JCPyV for each of these samples were quantified by ddPCR. No differences were observed between qPCR and ddPCR when five standardized plasma samples were analyzed for JCPyV in 42 laboratories in the United States and Europe. JCPyV-DNA was undetected in all the sera from HC and MS cohorts tested by triplex ddPCR, while serum samples from six patients with PML tested positive for JCPyV. Conclusion: This study shows strong correlation between ddPCR and qPCR with increased sensitivity of the ddPCR assay. Further work will be needed to determine whether multiplex ddPCR can be useful to determine PML risk in natalizumab-treated MS patients.
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Affiliation(s)
- Nyater Ngouth
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (N.N.); (M.C.M.)
| | - Maria Chiara Monaco
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (N.N.); (M.C.M.)
| | - Lorenzo Walker
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Sydney Corey
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (S.C.); (I.C.)
| | - Ijeoma Ikpeama
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Gary Fahle
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Irene Cortese
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (S.C.); (I.C.)
| | - Sanchita Das
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (N.N.); (M.C.M.)
- Correspondence:
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20
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Phung Q, Lin MJ, Xie H, Greninger AL. Fragment Size-Based Enrichment of Viral Sequences in Plasma Cell-Free DNA. J Mol Diagn 2022; 24:476-484. [PMID: 35569878 PMCID: PMC9127460 DOI: 10.1016/j.jmoldx.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Sequencing of plasma cell-free DNA (cfDNA) is a promising milieu for broad-based cancer and infectious disease diagnostics. The performance of cfDNA sequencing for infectious disease diagnostics is chiefly limited by inadequate analytical sensitivity. The current study investigated whether the analytical sensitivity of cfDNA sequencing for viral diagnostics could be improved by selective sequencing of short cfDNA fragments, given prior observations of shorter fragment size distribution in microbial and cytomegalovirus-derived cfDNA compared with human-derived cfDNA. It shows that the shorter plasma cfDNA fragment size distribution is a general feature of multiple DNA viruses, including adenovirus [interquartile range (IQR), 87 to 165 bp], herpes simplex virus 2 (IQR, 114 to 195 bp), human herpesvirus 6 (IQR, 145 to 176 bp), and varicella zoster virus (IQR, 98 to 182 bp), compared with human (IQR, 148 to 178 bp). It was used to further optimize a size selection-based cfDNA sequencing method, demonstrating an enrichment of viral sequences up to 16.6-fold, with a median fold enrichment of 6.7×, 4.6×, 2.2×, and 10.3× for adenovirus, herpes simplex virus 2, human herpesvirus 6, and varicella zoster virus, respectively. These findings demonstrate a simple yet scalable method for enhanced detection of DNA viremia that maintains the unbiased nature of cfDNA sequencing.
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Affiliation(s)
- Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
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21
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Linthorst J, Baksi MMM, Welkers MR, Sistermans EA. The cell‐free DNA virome of 108,349 Dutch pregnant women. Prenat Diagn 2022; 43:448-456. [PMID: 35403226 DOI: 10.1002/pd.6143] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Viral infections during pregnancy are a major health concern to mother and fetus. By repurposing cell-free Non Invasive Prenatal Testing (NIPT) sequencing data, we investigated prevalence and abundance of viral DNA in a cohort of 108,349 pregnant women. METHOD Cell-free DNA (cfDNA) sequencing reads that did not map to any of the human chromosomes or mitochondrial DNA of the human reference genome build GRCh38 were aligned to 224 DNA viruses selected from the NCBI refseq viral database. RESULTS In total 443,665 reads of viral origin were detected across 42,273 samples representing 165 viral species. Several are known to be potentially harmful during pregnancy and/or childbirth, including Cytomegalovirus, Parvovirus B19 and Hepatitis B. Viral sequences were mostly detected at very low abundance. However, several cases had exceptionally high viral loads for Parvovirus B19, Hepatitis B and others. We found statistically significant associations between presence of viral DNA and gestational age, maternal age, fetal fraction, cfDNA concentration and others. CONCLUSION We demonstrate the feasibility to detect viral DNA from typical genome-wide NIPT cfDNA sequencing and describe the main characteristics of the viral DNA in our cohort. Our dataset of detected viral sequence reads is made publicly available to guide future clinical implementations.
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Affiliation(s)
- Jasper Linthorst
- Amsterdam UMC location Vrije Universiteit Amsterdam Dept. of Human Genetics De Boelelaan1117 Amsterdam The Netherlands
- Amsterdam Reproduction & Development Amsterdam The Netherlands
| | - Moezammin M. M. Baksi
- Amsterdam UMC location Vrije Universiteit Amsterdam Dept. of Human Genetics De Boelelaan1117 Amsterdam The Netherlands
| | - Matthijs R.A. Welkers
- Amsterdam UMC location University of Amsterdam Dept. of Medical Microbiology and Infection Prevention Meibergdreef 9 Amsterdam The Netherlands
| | - Erik A. Sistermans
- Amsterdam UMC location Vrije Universiteit Amsterdam Dept. of Human Genetics De Boelelaan1117 Amsterdam The Netherlands
- Amsterdam Reproduction & Development Amsterdam The Netherlands
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22
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Geris JM, Spector LG, Roesler M, Hernandez-Alvarado N, Blackstad M, Nelson HH, Schleiss MR. High prevalence of asymptomatic CMV shedding in healthy children attending the minnesota state fair. J Clin Virol 2022; 148:105102. [PMID: 35158280 PMCID: PMC8918022 DOI: 10.1016/j.jcv.2022.105102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Young children in the household are a known risk factor for maternal CMV infection and consequently, congenital infection in infants. However, little is known about viral shedding in pre-school aged children. OBJECTIVES To estimate the prevalence of CMV DNA shedding and CMV antibodies among healthy children and their mothers. STUDY DESIGN A study of children ages 0 through 5 years was undertaken at the 2019 Minnesota State Fair. Children and their mothers were assessed for CMV shedding by procurement of a saliva swab for CMV PCR testing. An optional finger-stick for capillary blood was used to assess CMV antibodies. RESULTS A total of 109 children and 85 mothers were enrolled. The prevalence of CMV saliva shedding among children (mean age 3.1 years, SE=0.16) and their mothers was 12/109 (11.0%) and 1/85 (1.2%), respectively. The prevalence of CMV DNA among children peaked at 3 years of age (26%) while the mean viral load was greatest at one year of age (236,693 IU/mL). CMV IgG antibodies among those who agreed to a finger-stick were detected in 16/35 mothers (45.7%) and 0/7 children (0%). Mothers of children aged 5 years or greater had the highest seroprevalence (61.5%). CONCLUSIONS The prevalence of CMV salivary shedding in this unselected sample of young children was approximately 11.0%. The overall maternal seroprevalence in our sample was <50%, suggesting these women are at risk for acquisition of a primary CMV infection in subsequent pregnancies.
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Affiliation(s)
- Jennifer M Geris
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis MN, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis MN, USA.
| | - Logan G Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis MN, USA
| | - Michelle Roesler
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis MN, USA
| | - Nelmary Hernandez-Alvarado
- Division of Pediatric Infectious Diseases and Immunology, Department of Pediatrics, University of Minnesota, Minneapolis MN, USA
| | - Mark Blackstad
- Division of Pediatric Infectious Diseases and Immunology, Department of Pediatrics, University of Minnesota, Minneapolis MN, USA
| | - Heather H Nelson
- Division of Epidemiology & Community Health, University of Minnesota School of Public Health, Minneapolis MN, USA
| | - Mark R Schleiss
- Institute for Molecular Virology, University of Minnesota, Minneapolis MN, USA; Division of Pediatric Infectious Diseases and Immunology, Department of Pediatrics, University of Minnesota, Minneapolis MN, USA
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23
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Abstract
Introduction: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged as a novel viral agent that quickly spread worldwide. SARS-CoV-2 is responsible for the human coronavirus disease 2019 (COVID-19) which has claimed hundreds of thousands of lives and had an immeasurable toll on the economy. Currently, most clinical cases are identified by qualitative molecular testing. However, the need for quantitative assessment is gaining traction. Areas covered: In this review, the current state and future perspective of SARS-CoV-2 viral load quantification is presented. Expert opinion: Viral load quantification is a critical measure that informs clinicians of treatment response, actionable viral load levels, and guidance on patient management. Additionally, for pathogens with epidemiological consequences, viral load can provide information to guide infection control measures and policies. While qualitative detection is sufficient to identify cases and initiate containment and mitigation measures in the vast majority of COVID-19 cases, in certain situations, SARS-CoV-2 quantification is needed to assess viral load trending. However, there are obstacles to quantification, including variability in respiratory specimen collection and the lack of commutable reference material. At the same time, the need for quantification for clinical and epidemiological management is growing, especially concerning individuals with prolonged RNA shedding.
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Affiliation(s)
- Mark J Lee
- Department of Pathology, Duke University, Durham, USA
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24
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Jakharia N, Howard D, Riedel DJ. CMV Infection in Hematopoietic Stem Cell Transplantation: Prevention and Treatment Strategies. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2021; 13:123-140. [PMID: 34305463 PMCID: PMC8294301 DOI: 10.1007/s40506-021-00253-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Purpose of Review Cytomegalovirus (CMV) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (Allo-HSCT). New strategies and methods for prevention and management of CMV infection are urgently needed. We aim to review the new developments in diagnostics, prevention, and management strategies of CMV infection in Allo-HSCT recipients. Recent Findings The approval of the novel anti-CMV drug letermovir in 2017 has led to an increase in the use of antiviral prophylaxis as a preferred approach for prevention in many centers. Real-world studies have shown efficacy similar to the clinical trial. CMV-specific T cell-mediated immunity assays identify patients with immune reconstitution and predict disease progression. Phase 2 trials of maribavir have shown its efficacy as preemptive therapy and treatment of resistant and refractory CMV infections. Adoptive T cell therapy is an emerging option for treatment of refractory and resistant CMV. Of the different CMV vaccine trials, PepVax has shown promising results in a phase 1 trial. Summary CMV cell-mediated immunity assays have potential to be used as an adjunctive test to develop individualized management plan by identifying the patients who develop immune reconstitution; however, further prospective interventional studies are needed. Maribavir and adoptive T cell therapy are promising new therapies for treatment of CMV infections. CMV vaccine trials for prevention are also under way.
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Affiliation(s)
- Niyati Jakharia
- Department of Internal Medicine, Section of Infectious Diseases, Stanford University Hospital, 300 Pasteur Dr., Lane L 134, Stanford, CA 94305 USA
| | - Dianna Howard
- Department of Internal Medicine, Section of Hematology-Oncology, Wake Forest Baptist Medical Center, Winston-Salem, NC USA
| | - David J Riedel
- Department of Internal Medicine, Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore, MD USA
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25
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Wu X, Tay JK, Goh CK, Chan C, Lee YH, Springs SL, Wang DY, Loh KS, Lu TK, Yu H. Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids. Biomaterials 2021; 274:120876. [PMID: 34034027 DOI: 10.1016/j.biomaterials.2021.120876] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Rapid diagnostics of adventitious agents in biopharmaceutical/cell manufacturing release testing and the fight against viral infection have become critical. Quantitative real-time PCR and CRISPR-based methods rapidly detect DNA/RNA in 1 h but suffer from inter-site variability. Absolute quantification of DNA/RNA by methods such as digital PCR reduce this variability but are currently too slow for wider application. Here, we report a RApid DIgital Crispr Approach (RADICA) for absolute quantification of nucleic acids in 40-60 min. Using SARS-CoV-2 as a proof-of-concept target, RADICA allows for absolute quantification with a linear dynamic range of 0.6-2027 copies/μL (R2 value > 0.99), high accuracy and low variability, no cross-reactivity to similar targets, and high tolerance to human background DNA. RADICA's versatility is validated against other targets such as Epstein-Barr virus (EBV) from human B cells and patients' serum. RADICA can accurately detect and absolutely quantify EBV DNA with similar dynamic range of 0.5-2100 copies/μL (R2 value > 0.98) in 1 h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based detection. RADICA therefore enables rapid and sensitive absolute quantification of nucleic acids which can be widely applied across clinical, research, and biomanufacturing areas.
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Affiliation(s)
- Xiaolin Wu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Chuan Keng Goh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Cheryl Chan
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Yie Hou Lee
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Stacy L Springs
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - De Yun Wang
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Timothy K Lu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA.
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Institute of Bioengineering and Bioimaging, A*STAR, The Nanos, #04-01, 31, Biopolis Way, 138669, Singapore; Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, 117411, Singapore; Department of Physiology & the Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, 117593, Singapore.
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26
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Yong MK, Gottlieb D, Lindsay J, Kok J, Rawlinson W, Slavin M, Ritchie D, Bajel A, Grigg A. New advances in the management of cytomegalovirus in allogeneic haemopoietic stem cell transplantation. Intern Med J 2021; 50:277-284. [PMID: 31403736 DOI: 10.1111/imj.14462] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
Cytomegalovirus (CMV) viraemia continues to be a frequent complication in the post-haemopoietic stem cell transplantation period despite a low incidence of CMV end-organ disease. Several significant advances in the understanding and management of CMV infection have occurred in the last few years including improved diagnostics, monitoring of CMV immunity, availability of novel anti-CMV drugs, and emerging use of immunotherapies including CMV-specific T-cell infusions. In addition to reviewing these advances we also explore some of the more practical prescribing issues of the older and newer CMV drugs including cost, toxicity and drug interactions to help clinicians navigate this new era of CMV management.
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Affiliation(s)
- Michelle K Yong
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Gottlieb
- Department of Haematology and Bone Marrow Transplantation, Westmead Hospital, Sydney, New South Wales, Australia.,Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia.,Sydney Cellular Therapies Laboratory, Westmead Hospital, Sydney, New South Wales, Australia
| | - Julian Lindsay
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Pharmacy Department, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - William Rawlinson
- NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Monica Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Ritchie
- Department of Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashish Bajel
- Department of Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Andrew Grigg
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Haematology and Olivia Newton John Cancer Research Institute, Austin Hospital, Melbourne, Victoria, Australia
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27
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Dollard SC, Dreon M, Hernandez-Alvarado N, Amin MM, Wong P, Lanzieri TM, Osterholm EA, Sidebottom A, Rosendahl S, McCann MT, Schleiss MR. Sensitivity of Dried Blood Spot Testing for Detection of Congenital Cytomegalovirus Infection. JAMA Pediatr 2021; 175:e205441. [PMID: 33523119 PMCID: PMC7851756 DOI: 10.1001/jamapediatrics.2020.5441] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IMPORTANCE The sensitivity of dried blood spots (DBS) to identify newborns with congenital cytomegalovirus (cCMV) infection has not been evaluated in screening studies using the current, higher-sensitivity methods for DBS processing. OBJECTIVE To assess the sensitivity of DBS polymerase chain reaction (PCR) for newborn screening for cCMV infection using saliva as the reference standard for screening, followed by collection of a urine sample for confirmation of congenital infection. DESIGN, SETTING, AND PARTICIPANTS This population-based cohort study took place at 5 newborn nurseries and 3 neonatal intensive care units in the Minneapolis/Saint Paul area in Minnesota from April 2016 to June 2019. Newborns enrolled with parental consent were screened for cCMV using DBS obtained for routine newborn screening and saliva collected 1 to 2 days after birth. Dried blood spots were tested for CMV DNA by PCR at both the University of Minnesota (UMN) and the US Centers for Disease Control and Prevention (CDC). Saliva swabs were tested by CMV DNA PCR at the UMN laboratory only. Newborns who screened positive by saliva or DBS had a diagnostic urine sample obtained by primary care professionals, tested by PCR within 3 weeks of birth. Analysis began July 2019. EXPOSURES Detection of CMV from a saliva swab using a PCR assay. MAIN OUTCOMES AND MEASURES Number of children with urine-confirmed cCMV and the proportion of them who were CMV positive through DBS screening. RESULTS Of 12 554 individuals enrolled through June 2019 (of 25 000 projected enrollment), 56 newborns were confirmed to have cCMV (4.5 per 1000 [95% CI, 3.3-5.7]). Combined DBS results from either UMN or CDC had a sensitivity of 85.7% (48 of 56; 95% CI, 74.3%-92.6%), specificity of 100.0% (95% CI, 100.0%-100.0%), positive predictive value (PPV) of 98.0% (95% CI, 89.3%-99.6%), and negative predictive value (NPV) of 99.9% (95% CI, 99.9%-100.0%). Dried blood spot results from UMN had a sensitivity of 73.2% (95% CI, 60.4%-83.0%), specificity of 100.0% (100.0%-100.0%), PPV of 100.0% (95% CI, 91.4%-100.0%), and NPV of 99.9% (95% CI, 99.8%-99.9%). Dried blood spot results from CDC had a sensitivity of 76.8% (95% CI, 64.2%-85.9%), specificity of 100.0% (95% CI, 100.0%-100.0%), PPV of 97.7% (95% CI, 88.2%-99.6%), and NPV of 99.9% (95% CI, 99.8%-99.9%). Saliva swab results had a sensitivity of 92.9% (52 of 56; 95% CI, 83.0%-97.2%), specificity of 99.9% (95% CI, 99.9%-100.0%), PPV of 86.7% (95% CI, 75.8%-93.1%), and NPV of 100.0% (95% CI, 99.9%-100.0%). CONCLUSIONS AND RELEVANCE This study demonstrates relatively high analytical sensitivity for DBS compared with previous studies that performed population-based screening. As more sensitive DNA extraction and PCR methods continue to emerge, DBS-based testing should remain under investigation as a potential low-cost, high-throughput option for cCMV screening.
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Affiliation(s)
| | - Maggie Dreon
- Public Health Laboratory, Newborn Screening, Minnesota Department of Health, Saint Paul
| | - Nelmary Hernandez-Alvarado
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis
| | - Minal M. Amin
- US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Phili Wong
- US Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Erin A. Osterholm
- Division of Neonatology, University of Minnesota Medical School, Minneapolis
| | | | - Sondra Rosendahl
- Public Health Laboratory, Newborn Screening, Minnesota Department of Health, Saint Paul
| | - Mark T. McCann
- Public Health Laboratory, Newborn Screening, Minnesota Department of Health, Saint Paul
| | - Mark R. Schleiss
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis
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28
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Abstract
Quality assurance measures ensure competence and reliability in the laboratories procedures from patient specimen receipt (pre-analytical phase), specimen handling and testing (analytical phase), to the analysis and reporting of patient results (post-analytical phase). However, when faced with new challenges such as Coronavirus pandemic, the virology laboratory has to dynamic and responsive as well as able to adapt existing protocols, implement new technologies in response to the risks posed by the most recent threats to public health, while ensuring that the quality of the testing services provided, demonstrates clinical utility and meets appropriate regulatory requirements
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29
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Limaye AP, Babu TM, Boeckh M. Progress and Challenges in the Prevention, Diagnosis, and Management of Cytomegalovirus Infection in Transplantation. Clin Microbiol Rev 2020; 34:34/1/e00043-19. [PMID: 33115722 PMCID: PMC7920732 DOI: 10.1128/cmr.00043-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hosts with compromised or naive immune systems, such as individuals living with HIV/AIDS, transplant recipients, and fetuses, are at the highest risk for complications from cytomegalovirus (CMV) infection. Despite substantial progress in prevention, diagnostics, and treatment, CMV continues to negatively impact both solid-organ transplant (SOT) and hematologic cell transplant (HCT) recipients. In this article, we summarize important developments in the field over the past 10 years and highlight new approaches and remaining challenges to the optimal control of CMV infection and disease in transplant settings.
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Affiliation(s)
- Ajit P Limaye
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Tara M Babu
- Division of Infectious Diseases, University of Rochester Medical Center, Rochester, New York, USA
- Department of Infectious Diseases, Overlake Medical Center, Bellevue, Washington, USA
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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30
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Minz RW, Kumar M, Kanwar DB, Sharma A, Singh P, Singh J, Singh S, Anand S, Sakhuja V, Minz M. Cytomegalovirus Infection in Postrenal Transplant Recipients: 18 Years’ Experience From a Tertiary Referral Center. Transplant Proc 2020; 52:3173-3178. [DOI: 10.1016/j.transproceed.2020.02.162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/09/2020] [Indexed: 12/19/2022]
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31
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Persistent Challenges of Interassay Variability in Transplant Viral Load Testing. J Clin Microbiol 2020; 58:JCM.00782-20. [PMID: 32554479 DOI: 10.1128/jcm.00782-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While quantification of viruses that cause important infections in transplant recipients has been the standard of care for years, important challenges related to standardization remain. The issues are wide ranging, and until they are adequately addressed, the full impact of viral load testing regarding clinical management decisions will not be realized. This review focuses on a broad array of problems, including the lack of available FDA-approved/cleared tests, limited uptake of international standards, accurate quantification of secondary standards, specific assay characteristics, and commutability. Though some of these topics are nuanced, taken together they greatly influence the clinical utility of testing. For example, it has not been possible to define thresholds that predict the risk of developing disease and determine significant changes in serial viral load values for a given patient. Moreover, the utility of international guidelines may be limited due to the lack of a standardized assay. By summarizing the issues, the hope is that commercial companies, regulatory agencies, and professional societies can come together to advance the field and solve these problems.
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32
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Skipper C, Schleiss MR, Bangdiwala AS, Hernandez-Alvarado N, Taseera K, Nabeta HW, Musubire AK, Lofgren SM, Wiesner DL, Rhein J, Rajasingham R, Schutz C, Meintjes G, Muzoora C, Meya DB, Boulware DR. Cytomegalovirus Viremia Associated With Increased Mortality in Cryptococcal Meningitis in Sub-Saharan Africa. Clin Infect Dis 2020; 71:525-531. [PMID: 31504335 PMCID: PMC7384323 DOI: 10.1093/cid/ciz864] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cryptococcal meningitis and tuberculosis are both important causes of death in persons with advanced human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). Cytomegalovirus (CMV) viremia may be associated with increased mortality in persons living with HIV who have tuberculosis. It is unknown whether concurrent CMV viremia is associated with mortality in other AIDS-related opportunistic infections. METHODS We prospectively enrolled Ugandans living with HIV who had cryptococcal meningitis from 2010-2012. Subsequently, we analyzed stored baseline plasma samples from 111 subjects for CMV DNA. We compared 10-week survival rates among those with and without CMV viremia. RESULTS Of 111 participants, 52% (58/111) had detectable CMV DNA (median plasma viral load 498 IU/mL, interquartile range [IQR] 259-2390). All samples tested were positive on immunoglobin G serology. The median CD4+ T cell count was 19 cells/µL (IQR 9-70) and did not differ by the presence of CMV viremia (P = .47). The 10-week mortality rates were 40% (23/58) in those with CMV viremia and 21% (11/53) in those without CMV viremia (hazard ratio 2.19, 95% confidence interval [CI] 1.07-4.49; P = .03), which remained significant after a multivariate adjustment for known risk factors of mortality (adjusted hazard ratio 3.25, 95% CI 1.49-7.10; P = .003). Serum and cerebrospinal fluid cytokine levels were generally similar and cryptococcal antigen-specific immune stimulation responses did not differ between groups. CONCLUSIONS Half of persons with advanced AIDS and cryptococcal meningitis had detectable CMV viremia. CMV viremia was associated with an over 2-fold higher mortality rate. It remains unclear whether CMV viremia in severely immunocompromised persons with cryptococcal meningitis contributes directly to this mortality or may reflect an underlying immune dysfunction (ie, cause vs effect). CLINICAL TRIALS REGISTRATION NCT01075152.
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Affiliation(s)
- Caleb Skipper
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Mark R Schleiss
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | | | | | - Kabanda Taseera
- Department of Medicine, Mbarara University of Science and Technology, Uganda
| | - Henry W Nabeta
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Abdu K Musubire
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Sarah M Lofgren
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Darin L Wiesner
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Joshua Rhein
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | | | - Charlotte Schutz
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, South Africa
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, South Africa
| | - Conrad Muzoora
- Department of Medicine, Mbarara University of Science and Technology, Uganda
| | - David B Meya
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - David R Boulware
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
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HERQ-9 Is a New Multiplex PCR for Differentiation and Quantification of All Nine Human Herpesviruses. mSphere 2020; 5:5/3/e00265-20. [PMID: 32581076 PMCID: PMC7316487 DOI: 10.1128/msphere.00265-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
By adulthood, almost all humans become infected by at least one herpesvirus (HHV). The maladies inflicted by these microbes extend beyond the initial infection, as they remain inside our cells for life and can reactivate, causing severe diseases. The diagnosis of active infection by these ubiquitous pathogens includes the detection of DNA with sensitive and specific assays. We developed the first quantitative PCR assay (HERQ-9) designed to identify and quantify each of the nine human herpesviruses. The simultaneous detection of HHVs in the same sample is important since they may act together to induce life-threatening conditions. Moreover, the high sensitivity of our method is of extreme value for assessment of the effects of these viruses persisting in our body and their long-term consequences on our health. Infections with the nine human herpesviruses (HHVs) are globally prevalent and characterized by lifelong persistence. Reactivations can potentially manifest as life-threatening conditions for which the demonstration of viral DNA is essential. In the present study, we developed HERQ-9, a pan-HHV quantitative PCR designed in triplex reactions to differentiate and quantify each of the HHV-DNAs: (i) herpes simplex viruses 1 and 2 and varicella-zoster virus; (ii) Epstein-Barr virus, human cytomegalovirus, and Kaposi’s sarcoma-associated herpesvirus; and (iii) HHV-6A, -6B, and -7. The method was validated with prequantified reference standards as well as with mucocutaneous swabs and cerebrospinal fluid, plasma, and tonsillar tissue samples. Our findings highlight the value of multiplexing in the diagnosis of many unsuspected, yet clinically relevant, herpesviruses. In addition, we report here frequent HHV-DNA co-occurrences in clinical samples, including some previously unknown. HERQ-9 exhibited high specificity and sensitivity (LOD95s of ∼10 to ∼17 copies/reaction), with a dynamic range of 101 to 106 copies/μl. Moreover, it performed accurately in the coamplification of both high- and low-abundance targets in the same reaction. In conclusion, we demonstrated that HERQ-9 is suitable for the diagnosis of a plethora of herpesvirus-related diseases. Besides its significance to clinical management, the method is valuable for the assessment of hitherto-unexplored synergistic effects of herpesvirus coinfections. Furthermore, its high sensitivity enables studies on the human virome, often dealing with minute quantities of persisting HHVs. IMPORTANCE By adulthood, almost all humans become infected by at least one herpesvirus (HHV). The maladies inflicted by these microbes extend beyond the initial infection, as they remain inside our cells for life and can reactivate, causing severe diseases. The diagnosis of active infection by these ubiquitous pathogens includes the detection of DNA with sensitive and specific assays. We developed the first quantitative PCR assay (HERQ-9) designed to identify and quantify each of the nine human herpesviruses. The simultaneous detection of HHVs in the same sample is important since they may act together to induce life-threatening conditions. Moreover, the high sensitivity of our method is of extreme value for assessment of the effects of these viruses persisting in our body and their long-term consequences on our health.
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High-resolution profiling of human cytomegalovirus cell-free DNA in human plasma highlights its exceptionally fragmented nature. Sci Rep 2020; 10:3734. [PMID: 32111931 PMCID: PMC7048871 DOI: 10.1038/s41598-020-60655-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/14/2020] [Indexed: 11/14/2022] Open
Abstract
Human cytomegalovirus (CMV) infections comprise a leading cause of newborn impairments worldwide and are pervasive concerns among the immunocompromised. Quantification of CMV viral loads is increasingly used to guide definitions of CMV disease but standardization of CMV quantitation remains problematic, mostly due to differences in qPCR amplicon sizes between clinical laboratories. Here, we used plasma cfDNA sequencing data from 2,208 samples sent for non-invasive prenatal aneuploidy screening to detect CMV and precisely measure the length of CMV fragments in human plasma. CMV reads were identified in 120 (5.4%) samples. Median cfDNA fragment size derived from CMV was significantly shorter than cfDNA derived from human chromosomes (103 vs 172 bp, p < 0.0001), corresponding to the 3rd percentile of human cfDNA. Sequencing of cfDNA from seven plasma samples from transplant patients positive for CMV confirmed the extraordinarily short nature of CMV cfDNA fragment size with a median length of 149 bp. We further show that these high-resolution measurements of CMV DNA fragment size accurately predict measured discrepancies in serum viral load measurements by different qPCR assays. These results highlight the exceptionally fragmented nature of CMV cfDNA and illustrate the promise of plasma cfDNA sequencing for quantitating viral loads through detection of fragments that would be unrecoverable by qPCR.
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35
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Mullane KM. Human Cytomegalovirus Prophylaxis and Treatment in Lung Transplantation in the Current Era. CURRENT PULMONOLOGY REPORTS 2020. [DOI: 10.1007/s13665-020-00246-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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37
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Impact of Fragmentation on Commutability of Epstein-Barr Virus and Cytomegalovirus Quantitative Standards. J Clin Microbiol 2019; 58:JCM.00888-19. [PMID: 31619529 DOI: 10.1128/jcm.00888-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022] Open
Abstract
Despite the adaptation of international standards, quantitative viral load testing of transplant-associated viruses continues to be limited by interlaboratory disagreement. Studies have suggested that this disagreement and the poor commutability of standards may, in some cases, be linked to amplicon size and the fragmentation of circulating viral DNA. We evaluated target fragmentation as a cause of noncommutability and pretest fragmentation of quantitative standards as a potential means of increasing commutability and interassay agreement. Forty-two cytomegalovirus (CMV)-positive and 41 Epstein-Barr virus (EBV)-positive plasma samples, together with two different quantitative standards for each virus, were tested as unknowns using 10 different quantitative PCR assays at 5 different laboratories. Standards were tested both intact and after intentional fragmentation by ultrasonication. Quantitative agreement between methods was assessed, together with commutability, using multiple statistical approaches. Most assays yielded results within 0.5 log10 IU/ml of the mean for CMV, while for EBV a greater variability of up to 1.5 log10 IU/ml of the mean was shown. Commutability showed marked improvement following fragmentation of both CMV standards but not after fragmentation of the EBV standards. These findings confirm the impact of amplicon size and target fragmentation on commutability for CMV and suggest that for some (but not all) viruses, interlaboratory harmonization can be improved through the use of fragmented quantitative standards.
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38
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Metagenomic Next-Generation Sequencing for Identification and Quantitation of Transplant-Related DNA Viruses. J Clin Microbiol 2019; 57:JCM.01113-19. [PMID: 31554674 PMCID: PMC6879295 DOI: 10.1128/jcm.01113-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
Infections with DNA viruses are frequent causes of morbidity and mortality in transplant recipients. Infections with DNA viruses are frequent causes of morbidity and mortality in transplant recipients. This study describes the analytical and clinical performance characteristics of the Arc Bio Galileo Pathogen Solution, an all-inclusive metagenomic next-generation sequencing (mNGS) reagent and bioinformatics pipeline that allows the simultaneous quantitation of 10 transplant-related double-stranded DNA (dsDNA) viruses (adenovirus [ADV], BK virus [BKV], cytomegalovirus [CMV], Epstein-Barr virus [EBV], human herpesvirus 6A [HHV-6A], HHV-6B, herpes simplex virus 1 [HSV-1], HSV-2, JC virus [JCV], and varicella-zoster virus [VZV]). The mNGS 95% limit of detection ranged from 14 copies/ml (HHV-6) to 191 copies/ml (BKV), and the lower limit of quantitation ranged from 442 international units (IU)/ml (EBV) to 661 copies/ml (VZV). An evaluation of 50 residual plasma samples with at least one DNA virus detected in prior clinical testing showed a total percent agreement of mNGS and quantitative PCR (qPCR) of 89.2% (306/343), with a κ statistic of 0.725. The positive percent agreement was 84.9% (73/86), and the negative percent agreement was 90.7% (233/257). Furthermore, mNGS detected seven subsequently confirmed coinfections that were not initially requested by qPCR. Passing-Bablok regression revealed a regression line of y = 0.953x + 0.075 (95% confidence interval [CI] of the slope, 0.883 to 1.011; intercept, −0.100 to 0.299), and Bland-Altman analysis (mNGS − qPCR) showed a slight positive bias (0.28 log10 concentration; 95% limits of agreement, −0.62 to 1.18). In conclusion, the mNGS-based Galileo pipeline demonstrates analytical and clinical performance comparable to that of qPCR for transplant-related DNA viruses.
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Leuzinger K, Naegele K, Schaub S, Hirsch HH. Quantification of plasma BK polyomavirus loads is affected by sequence variability, amplicon length, and non-encapsidated viral DNA genome fragments. J Clin Virol 2019; 121:104210. [PMID: 31759262 DOI: 10.1016/j.jcv.2019.104210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Klaudia Naegele
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Stefan Schaub
- Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland; Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
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40
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Grossi PA, Baldanti F, Andreoni M, Perno CF. CMV infection management in transplant patients in Italy. J Clin Virol 2019; 123:104211. [PMID: 31879243 DOI: 10.1016/j.jcv.2019.104211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 10/01/2019] [Accepted: 11/04/2019] [Indexed: 12/27/2022]
Abstract
Transplant represents an effective strategy in the management of chronic organ dysfunction. Nonetheless, life threatening risks remain, especially in the post-transplant; among them, human cytomegalovirus (CMV) is a major concern, currently causing active infections in at least one-third of transplant recipients. Microbiologist and transplant scientific societies redefined guidance on CMV disease prevention and the best use for universal prophylaxis and pre-emptive virological monitoring. Developments in molecular diagnostic supported the spread of the pre-emptive strategy, and quantitative Real Time-PCR assays has unravelled the potential of viral load measurement as a predictor of the infection development in CMV post-transplant management. However, despite the WHO 1st CMV International Standard, the standardization of diagnostic and clinical practice has been limited by the absence of algorithms for calculating conversion factor to International Units and the lack of shared monitoring procedure, both at national and international level. At a regional level, the Italian scientific societies, AMCLI (Italian Clinical Microbiologist Association), SITO (Organ Transplant Italian Society), GITMO (Italian Group for Bone Marrow Transplant), recently tried to define a consensus for post-transplant monitoring. The concerted practice encompasses molecular quantitative PCR assays technical aspects and endorses the relevance of immunologic monitoring for improvement in patient risk stratification and prognosis. Here, we provide an overview of the state of the art of CMV management strategies, with a specific focus on the clinical practices and on the scientific societies' initiatives that aim to implement international standardization guidelines at a national level.
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Affiliation(s)
- Paolo Antonio Grossi
- Infectious Diseases Section, Department of Medicine and Surgery, University of Insubria, Varese; National Center for Transplantation, Rome, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Policlinic IRCCS Foundation San Matteo, Pavia, Italy
| | - Massimo Andreoni
- Infectious Disease Unit, Policlinic Foundation Tor Vergata, Rome, Italy; Department of Oncology and Oncohematology, University of Milan, Italy; Department of Clinical Virology, ASST Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Infectious Disease Unit, Policlinic Foundation Tor Vergata, Rome, Italy; Department of Oncology and Oncohematology, University of Milan, Italy; Department of Clinical Virology, ASST Niguarda, Milan, Italy.
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41
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Gerna G, Baldanti F. Brief molecular diagnostic criteria for human cytomegalovirus infection/disease. Expert Rev Mol Diagn 2019; 19:773-775. [DOI: 10.1080/14737159.2019.1657010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Giuseppe Gerna
- Laboratories of Genetics, Transplantology and Cardiovascular Diseases, and Biotechnology Laboratories, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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42
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Allen UD, Preiksaitis JK. Post-transplant lymphoproliferative disorders, Epstein-Barr virus infection, and disease in solid organ transplantation: Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant 2019; 33:e13652. [PMID: 31230381 DOI: 10.1111/ctr.13652] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
PTLD with the response-dependent sequential use of RIS, rituximab, and cytotoxic chemotherapy is recommended. Evidence gaps requiring future research and alternate treatment strategies including immunotherapy are highlighted.
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Affiliation(s)
- Upton D Allen
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Research Institute, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, ON, Canada
| | - Jutta K Preiksaitis
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada
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43
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Govind S, Hockley J, Morris C, Almond N. The development and establishment of the 1st WHO BKV International Standard for nucleic acid based techniques. Biologicals 2019; 60:75-84. [DOI: 10.1016/j.biologicals.2019.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/15/2019] [Accepted: 04/25/2019] [Indexed: 12/25/2022] Open
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44
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Aretzweiler G, Leuchter S, García-Álvarez M, Simon C, Marins E, Paxinos E, Canchola J, Delgado R, Frontzek A. Analytical performance of four molecular platforms used for HIV-1, HBV and HCV viral load determinations. Expert Rev Mol Diagn 2019; 19:941-949. [PMID: 31159598 DOI: 10.1080/14737159.2019.1624162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background: Viral load (VL) quantification is important for the management of HBV, HCV, and HIV-1-infected patients. Several semi- or fully automated systems and assays are available that can be used to measure VL for these and other targets. Research design and methods: We assessed the accuracy, genotype/subtype inclusivity, and precision of four VL assays for three viral targets: cobas 4800 (Roche), cobas 6800 (Roche), Aptima (Hologic) and VERIS (Beckman), using WHO standards, cell culture supernatants and clinical samples. Results: Most results were close to expected values, except for significant under-quantification of HIV-1 group O, HBV genotype C, and D at high VL, and HCV genotype 3 by Aptima, and of HIV-1 CRF01_AE and group N and HCV genotype 3 by VERIS. Precision was comparable between tests except for VERIS HCV, which showed more variability. Aptima and cobas 6800 results agreed well with each other except HBV VL at lower VL (<10,000 IU/mL) where Aptima results tended to be higher. Conclusions: Results from different VL assays may not always agree in certain subsets of patients. Clinicians should we aware of these findings when making treatment decisions.
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Affiliation(s)
- Gudrun Aretzweiler
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
| | - Susanne Leuchter
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
| | - Mónica García-Álvarez
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas 12) , Madrid , Spain
| | - Christian Simon
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Ed Marins
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Ellen Paxinos
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Jesse Canchola
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Rafael Delgado
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas 12) , Madrid , Spain
| | - Andre Frontzek
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
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Hirsch HH, Randhawa PS. BK polyomavirus in solid organ transplantation-Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant 2019; 33:e13528. [PMID: 30859620 DOI: 10.1111/ctr.13528] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
The present AST-IDCOP guidelines update information on BK polyomavirus (BKPyV) infection, replication, and disease, which impact kidney transplantation (KT), but rarely non-kidney solid organ transplantation (SOT). As pretransplant risk factors in KT donors and recipients presently do not translate into clinically validated measures regarding organ allocation, antiviral prophylaxis, or screening, all KT recipients should be screened for BKPyV-DNAemia monthly until month 9, and then every 3 months until 2 years posttransplant. Extended screening after 2 years may be considered in pediatric KT. Stepwise immunosuppression reduction is recommended for KT patients with plasma BKPyV-DNAemia of >1000 copies/mL sustained for 3 weeks or increasing to >10 000 copies/mL reflecting probable and presumptive BKPyV-associated nephropathy, respectively. Reducing immunosuppression is also the primary intervention for biopsy-proven BKPyV-associated nephropathy. Hence, allograft biopsy is not required for treating BKPyV-DNAemic patients with baseline renal function. Despite virological rationales, proper randomized clinical trials are lacking to generally recommend treatment by switching from tacrolimus to cyclosporine-A, from mycophenolate to mTOR inhibitors or leflunomide or by the adjunct use of intravenous immunoglobulins, leflunomide, or cidofovir. Fluoroquinolones are not recommended for prophylaxis or therapy. Retransplantation after allograft loss due to BKPyV nephropathy can be successful if BKPyV-DNAemia is definitively cleared, independent of failed allograft nephrectomy.
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Affiliation(s)
- Hans H Hirsch
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Parmjeet S Randhawa
- Division of Transplantation Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Thomas E Starzl Transplantation Institute, Pittsburgh, Pennsylvania
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46
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Piñana JL, Giménez E, Gómez MD, Pérez A, González EM, Vinuesa V, Hernández-Boluda JC, Montoro J, Salavert M, Tormo M, Amat P, Moles P, Carretero C, Balaguer-Roselló A, Sanz J, Sanz G, Solano C, Navarro D. Pulmonary cytomegalovirus (CMV) DNA shedding in allogeneic hematopoietic stem cell transplant recipients: Implications for the diagnosis of CMV pneumonia. J Infect 2019; 78:393-401. [PMID: 30797790 PMCID: PMC7126576 DOI: 10.1016/j.jinf.2019.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 12/07/2018] [Accepted: 02/18/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To date no definitive cut-off value for cytomegalovirus (CMV) DNA load in bronchoalveolar lavage (BAL) fluid specimens has been established to discriminate between CMV pneumonia and pulmonary CMV DNA shedding in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients. METHODS The current retrospective study is aimed at assessing the range of CMV DNA loads quantified in BAL fluid specimens from allo-HSCT patients with pneumonia in which different microorganisms were causally involved. RESULTS A total of 144 BAL specimens from 123 patients were included. CMV DNA was detected in 56 out of 144 BAL fluid specimens and the median CMV DNA load from patients in whom CMV pneumonia was unlikely or could be tentatively ruled out was 1210 (31-68, 920) IU/ml. The frequency of CMV DNA detection and median CMV DNA loads were comparable, irrespective of the attributable cause of pneumonia. Detection of CMV DNA loads in BAL fluid specimens >500 IU/ml was independently associated with pneumonia-attributable mortality. CONCLUSIONS The current study highlights the difficulty in establishing universal CMV DNA load thresholds in BAL fluid specimens for distinguishing between CMV pneumonia and pulmonary CMV DNA shedding, and suggests that the presence of CMV DNA in BAL fluid specimens beyond a certain level may have a deleterious impact on patient outcome.
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Affiliation(s)
- José Luis Piñana
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - María Dolores Gómez
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Ariadna Pérez
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Eva María González
- Microbiology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Víctor Vinuesa
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | | | - Juan Montoro
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Miguel Salavert
- Department of Infectious Diseases, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Mar Tormo
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Paula Amat
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Paula Moles
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Carlos Carretero
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | - Jaime Sanz
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Guillermo Sanz
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain; Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibáñez 17, 46010 Valencia, Spain.
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The Third International Consensus Guidelines on the Management of Cytomegalovirus in Solid-organ Transplantation. Transplantation 2019; 102:900-931. [PMID: 29596116 DOI: 10.1097/tp.0000000000002191] [Citation(s) in RCA: 708] [Impact Index Per Article: 141.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite recent advances, cytomegalovirus (CMV) infections remain one of the most common complications affecting solid organ transplant recipients, conveying higher risks of complications, graft loss, morbidity, and mortality. Research in the field and development of prior consensus guidelines supported by The Transplantation Society has allowed a more standardized approach to CMV management. An international multidisciplinary panel of experts was convened to expand and revise evidence and expert opinion-based consensus guidelines on CMV management including prevention, treatment, diagnostics, immunology, drug resistance, and pediatric issues. Highlights include advances in molecular and immunologic diagnostics, improved understanding of diagnostic thresholds, optimized methods of prevention, advances in the use of novel antiviral therapies and certain immunosuppressive agents, and more savvy approaches to treatment resistant/refractory disease. The following report summarizes the updated recommendations.
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Standardization of Nucleic Acid Tests: the Approach of the World Health Organization. J Clin Microbiol 2019; 57:JCM.01056-18. [PMID: 30257900 DOI: 10.1128/jcm.01056-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The first World Health Organization (WHO) international standards (ISs) for nucleic acid amplification techniques were established two decades ago, with the initial focus on blood screening for three major viral targets, i.e., hepatitis C virus, hepatitis B virus, and human immunodeficiency virus 1. These reference materials have subsequently found utility in the diagnosis and monitoring of a wide range of infectious diseases in clinical microbiology laboratories worldwide. WHO collaborating centers develop ISs and coordinate international studies for their evaluation. The WHO Expert Committee on Biological Standardization is responsible for the endorsement of new standardization projects and the establishment of new and replacement ISs. Potencies of ISs are defined in international units (IU); the reporting in IU for assays calibrated with an IS (or secondary standards traceable to the IS) facilitates comparability of results for different assays and determination of assay parameters such as analytical sensitivities.
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Impacts and Challenges of Advanced Diagnostic Assays for Transplant Infectious Diseases. PRINCIPLES AND PRACTICE OF TRANSPLANT INFECTIOUS DISEASES 2019. [PMCID: PMC7121269 DOI: 10.1007/978-1-4939-9034-4_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advanced technologies described in this chapter should allow for full inventories to be made of bacterial genes, their time- and place-dependent expression, and the resulting proteins as well as their outcome metabolites. The evolution of these molecular technologies will continue, not only in the microbial pathogens but also in the context of host-pathogen interactions targeting human genomics and transcriptomics. Their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.
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Cytomegalovirus Viral Load in Bronchoalveolar Lavage to Diagnose Lung Transplant Associated CMV Pneumonia. Transplantation 2018; 102:326-332. [PMID: 28846557 DOI: 10.1097/tp.0000000000001927] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The diagnostic yield for cytomegalovirus (CMV) polymerase chain reaction (PCR) viral load in bronchoalveolar lavage (BAL) or in plasma to diagnose CMV pneumonia in lung transplant recipients remains uncertain and was investigated in a large cohort of consecutive lung transplant recipients. METHODS Bronchoscopies within the first year of lung transplantation with CMV detectable in BAL by PCR (ie, viral load, ≥273 IU/mL) were included (66 recipients; 145 bronchoscopies); at each bronchoscopy episode, 2 independent experts reviewed clinical and laboratory information to determine whether the patient at that time fulfilled the criteria for CMV pneumonia per current international recommendations. Corresponding plasma CMV PCR viral load determined at time of the bronchoscopy (n = 126) was also studied. Optimal CMV PCR viral load cutoff for CMV pneumonia diagnosis was determined using receiver operating characteristics. RESULTS CMV was detected in BAL with CMV PCR in 145 episodes, and 34 (23%) of these episodes fulfilled the criteria for CMV pneumonia. The area under the curve-receiver operating characteristics for CMV in BAL was 90% at the optimum cutoff (4545 IU/mL) with a corresponding sensitivity of 91% and specificity of 77% (in plasma the corresponding values were 274 IU/mL, 63% and 76%, respectively). CONCLUSIONS CMV PCR viral load in BAL had a high performance to diagnose CMV pneumonia in lung transplant recipients; plasma CMV viral load did not reliably aid as a diagnostic tool.
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