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Lakhal-Naouar I, Hack HR, Moradel E, Jarra A, Grove HL, Ismael RM, Padilla S, Coleman D, Ouellette J, Darden J, Storme C, Peachman KK, Hall TL, Huhtanen ME, Scott PT, Hakre S, Jagodzinski LL, Peel SA. Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. PLoS One 2023; 18:e0287576. [PMID: 37384714 PMCID: PMC10309597 DOI: 10.1371/journal.pone.0287576] [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: 04/05/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
OBJECTIVE Validate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality. METHODS Custom-designed primers/probe sets targeting the SARS-CoV-2 Envelope gene (E) and subgenomic E were optimized. A 20-day performance validation following laboratory developed test requirements was conducted to assess assay precision, accuracy, analytical sensitivity/specificity, lower limit of detection and reportable range. RESULTS Quantitative SARS-CoV-2 sgRNA (LDT-Quant sgRNA) assay, which measures intermediates of replication, and viral load (LDT-Quant VLCoV) assay demonstrated acceptable performance. Both assays were linear with an R2 and slope equal to 0.99 and 1.00, respectively. Assay precision was evaluated between 4-6 Log10 with a maximum CV of 2.6% and 2.5% for LDT-Quant sgRNA and LDT-Quant VLCoV respectively. Using negative or positive SARS-CoV-2 human nasopharyngeal swab samples, both assays were accurate (kappa coefficient of 1.00 and 0.92). Common respiratory flora and other viral pathogens were not detected and did not interfere with the detection or quantification by either assay. Based on 95% detection, the assay LLODs were 729 and 1206 Copies/mL for the sgRNA and VL load LDTs, respectively. CONCLUSION The LDT-Quant sgRNA and LDT-Quant VLCoV demonstrated good analytical performance. These assays could be further investigated as alternative monitoring assays for viral replication; and thus, medical management in clinical settings which could inform isolation/quarantine requirements.
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Affiliation(s)
- Ines Lakhal-Naouar
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Holly R. Hack
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Edgar Moradel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Amie Jarra
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Hannah L. Grove
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Rani M. Ismael
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Steven Padilla
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Dante Coleman
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Jason Ouellette
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Janice Darden
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Casey Storme
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kristina K. Peachman
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Tara L. Hall
- Moncrief Army Health Clinic, Fort Jackson, South Carolina, United States of America
| | - Mark E. Huhtanen
- Moncrief Army Health Clinic, Fort Jackson, South Carolina, United States of America
| | - Paul T. Scott
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Shilpa Hakre
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Linda L. Jagodzinski
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sheila A. Peel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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Bernstein DI, Mejias A, Rath B, Woods CW, Deeter JP. Summarizing Study Characteristics and Diagnostic Performance of Commercially Available Tests for Respiratory Syncytial Virus: A Scoping Literature Review in the COVID-19 Era. J Appl Lab Med 2023; 8:353-371. [PMID: 35854475 PMCID: PMC9384538 DOI: 10.1093/jalm/jfac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/07/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Nonpharmaceutical interventions to prevent the spread of coronavirus disease 2019 also decreased the spread of respiratory syncytial virus (RSV) and influenza. Viral diagnostic testing in patients with respiratory tract infections (RTI) is a necessary tool for patient management; therefore, sensitive and specific tests are required. This scoping literature review aimed to summarize the study characteristics of commercially available sample-to-answer RSV tests. CONTENT PubMed and Embase were queried for studies reporting on the diagnostic performance of tests for RSV in patients with RTI (published January 2005-January 2021). Information on study design, patient and setting characteristics, and published diagnostic performance of RSV tests were extracted from 77 studies that met predefined inclusion criteria. A literature gap was identified for studies of RSV tests conducted in adult-only populations (5.3% of total subrecords) and in outpatient (7.5%) or household (0.8%) settings. Overall, RSV tests with analytical time >30 min had higher published sensitivity (62.5%-100%) vs RSV tests with analytical time ≤30 min (25.7%-100%); this sensitivity range could be partially attributed to the different modalities (antigen vs molecular) used. Molecular-based rapid RSV tests had higher published sensitivity (66.7%-100%) and specificity (94.3%-100%) than antigen-based RSV tests (sensitivity: 25.7%-100%; specificity:80.3%-100%). SUMMARY This scoping review reveals a paucity of literature on studies of RSV tests in specific populations and settings, highlighting the need for further assessments. Considering the implications of these results in the current pandemic landscape, the authors preliminarily suggest adopting molecular-based RSV tests for first-line use in these settings.
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Affiliation(s)
- David I Bernstein
- Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Asuncion Mejias
- Department of Pediatrics, Division of Infectious Diseases, Nationwide Children’s Hospital, The Ohio State University, Columbus, OH, USA
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Barbara Rath
- Vienna Vaccine Safety Initiative, Berlin, Germany
- Université de Bourgogne Franche-Comté, Besançon, France
- ESCMID Study Group for Respiratory Viruses (ESGREV), Basel, Switzerland
| | - Christopher W Woods
- ESCMID Study Group for Respiratory Viruses (ESGREV), Basel, Switzerland
- Infectious Diseases Division, Duke University Medical Center, Durham, NC, USA
| | - Jamie Phillips Deeter
- Address correspondence to this author at: 9115 Hague Rd, Indianapolis, IN 46250-0457, USA. Fax: 317-348-4320; E-mail:
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Standardization of SARS-CoV-2 Nucleic Acid Amplification Techniques by Calibration and Quantification to the First WHO International Standard for SARS-CoV-2 RNA. Int J Microbiol 2023; 2023:7803864. [PMID: 36846152 PMCID: PMC9957646 DOI: 10.1155/2023/7803864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Clinical decision-making regarding isolation of SARS-CoV-2 patients is usually based on semiquantitative cycle-threshold (Ct) values without standardization. However, not all molecular assays produce Ct values, and there is ongoing discussion about whether Ct values can be safely used for decision-making. In this study, we standardized two molecular assays which use different nucleic acid amplification techniques (NAAT): the Hologic Aptima SARS-CoV-2/Flu (TMA) and Roche Cobas 6800 SARS-CoV-2 assays. We calibrated these assays against the first WHO international standard for SARS-CoV-2 RNA by using linear regression of log10 dilution series. These calibration curves were used to calculate viral loads for clinical samples. Clinical performance was assessed retrospectively using samples collected between January 2020 and November 2021, including known positives of the wild-type SARS-CoV-2 virus, the VOCs (alpha, beta, gamma, delta, and omicron) and quality control panels. Linear regression and Bland-Altman analysis showed good correlations for SARS-CoV-2 between Panther TMA and Cobas 6800 when standardized viral loads were used. These standardized quantitative results can benefit clinical decision-making and standardization of infection control guidelines.
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Stohr JJJM, Wennekes M, van der Ent M, Diederen BMW, Kluytmans-van den Bergh MFQ, Bergmans AMC, Kluytmans JAJW, Pas SD. Clinical performance and sample freeze-thaw stability of the cobas®6800 SARS-CoV-2 assay for the detection of SARS-CoV-2 in oro-/nasopharyngeal swabs and lower respiratory specimens. J Clin Virol 2020; 133:104686. [PMID: 33221622 PMCID: PMC7648882 DOI: 10.1016/j.jcv.2020.104686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/30/2020] [Accepted: 11/01/2020] [Indexed: 01/14/2023]
Abstract
Naso/oropharygeal swabs and deep respiratory samples, but not feces, show good clinical performance in Cobas®6800 SARS-CoV-2 assay. No significant difference was found after one freeze-thaw cycler with or without lysis buffer. Time-to-result is lower using Cobas®6800 SARS-CoV-2 assay compared to LDA.
Introduction Studies describing the performance characteristics of the cobas®6800 system for SARS-CoV-2 detection in deep respiratory specimens and freeze-thaw stability are limited. The current study compares the clinical performance of the automated SARS-CoV-2 assay on the cobas®6800 system to a lab-developed assay (LDA) and the cobas impact of freeze-thawing combined with lysis buffer. Methods Both retrospective and prospectively selected deep respiratory samples and oro- and nasopharyngeal samples in either E-swab® or GLY- were tested using the SARS-CoV-2 assay on the cobas®6800 System and compared to a lab developed assay. Additonally, SARS-CoV-2 RNA stability was assessed after one freeze-thaw cycle with or without lysis buffer. Results In total, 221 (58.3 %) oro- and nasopharyngeal swabs, 131 (34.6 %) deep respiratory specimens, and n = 25 (6.6 %) swabs of unknown origin were included to study clinical performance. Only 4 samples gave discrepant results, all being positive in the LDA and not the cobas®6800 system. For stability testing, 66 samples without and 110 with lysis buffer were included. No clinically significant difference was found in test results after one freeze-thaw cycle and addition of lysis buffer. Conclusion Based on our findings, the cobas®6800 SARS-CoV-2 RNA assay yielded similar results as the LDA in oro-/nasopharyngeal swabs and deep respiratory specimens. Moreover, the cobas®6800 SARS-CoV-2 RNA assay yielded similar results before and after a freeze-thaw cycle, with better preservation of low viral loads in lysis buffer.
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Affiliation(s)
- Joep J J M Stohr
- Department of Infection Control, Amphia Hospital, Breda, the Netherlands; Microvida Laboratory for Microbiology, Elisabeth-TweeSteden Hospital, Tilburg, the Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, the Netherlands.
| | - Meike Wennekes
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, the Netherlands
| | - Martijn van der Ent
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, the Netherlands
| | - Bram M W Diederen
- Microvida Laboratory for Microbiology, Elisabeth-TweeSteden Hospital, Tilburg, the Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, the Netherlands; Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, the Netherlands
| | - Marjolein F Q Kluytmans-van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, the Netherlands; Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Anneke M C Bergmans
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, the Netherlands
| | - Jan A J W Kluytmans
- Department of Infection Control, Amphia Hospital, Breda, the Netherlands; Microvida Laboratory for Microbiology, Elisabeth-TweeSteden Hospital, Tilburg, the Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, the Netherlands; Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Suzan D Pas
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, the Netherlands; Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, the Netherlands
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Analytical Performances of the Panther Fusion System for the Detection of Respiratory Viruses in the French National Reference Centre of Lyon, France. Microorganisms 2020; 8:microorganisms8091371. [PMID: 32906749 PMCID: PMC7563737 DOI: 10.3390/microorganisms8091371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/04/2023] Open
Abstract
Respiratory infection are mainly caused by viral pathogens. During the 2017-2018 epidemic season, Panther Fusion® Respiratory kits (Influenza virus A&B (FluA&B), respiratory syncytial virus (RSV), adenovirus (ADV), metapneumovirus (MPV), rhinovirus (RV), parainfluenzae virus (PIV), were compared to the Respiratory MultiWells System r-gene. Respiratory clinical specimens were tested retrospectively (n = 268) and prospectively (n = 463). Analytical performances were determined (sensitivity -Sep-, specificity -Spe- and κ) considering concordances of ≥2 molecular testing specific to each viral target (discrepant results were verified at the National Reference Centres for Enteroviruses or Respiratory viruses, Lyon, France). After retrospective (and prospective) testing, Sep, Spe, and κ were 100% (97.7%), 100% (99%) and 100% (94%) for FluA: 100% (95.5%), 100% (99.3%) and 100% (94%) for FluB, and 100% (88.5%), 100% (98.7%) and 100% (89%) for RSV; 82.1% (41.7%), 100% (99.5%) and 86% (54%) for ADV; 94.7% (73.7%), 96.1% (98.0%) and 91% (65%) for MPV; 96.1% (94.6%), 90.2% (98.5%) and 86% (91%) for HRV; and 90% (72.7%), 100% (99.3%) and 91% (72%), respectively, for PIV. Analytical performances were above 85% for all viruses except for ADV, MPV and PIV, confirming the analytical performance of the Panther Fusion system, a high throughput system with reduced turn-around-time, when compared to non-automated systems.
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