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Tang HT, Nörz D, Grunwald M, Giersch K, Pfefferle S, Fischer N, Aepfelbacher M, Rohde H, Lütgehetmann M. Analytical and clinical validation of a novel, laboratory-developed, modular multiplex-PCR panel for fully automated high-throughput detection of 16 respiratory viruses. J Clin Virol 2024; 173:105693. [PMID: 38820916 DOI: 10.1016/j.jcv.2024.105693] [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: 02/01/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Viral respiratory Infections pose a health risk, especially to vulnerable patient populations. Effective testing programs can detect and differentiate these infections at an early stage, which is particularly important for high-risk clinical departments. The objective of this study was to develop and validate a multiplex PCR-panel for 16 different respiratory viruses on a fully-automated high-throughput platform. METHODS Three multiplex-PCR assays were designed to run on the cobas5800/6800/8800 systems, consolidating 16 viral targets: RESP1: SARS-CoV-2, influenza-A/B, RSV; RESP2: hMPV, hBoV, hAdV, rhino-/ENV; RESP3: HPIV-1-4, hCoV-229E, hCoV-NL63, hCoV-OC43, hCoV-HKU1. Analytic performance was evaluated using digital-PCR based standards and international reference material. Clinical performance was determined by comparing results from clinical samples with reference assays. RESULTS Analytical sensitivity (i.e. lower limit of detection (LoD), 95 % probability of detection) was determined as follows: SARS-CoV-2: 29.3 IU/ml, influenza-A: 179.9 cp/ml, influenza-B: 333.9 cp/ml and RSV: 283.1 cp/ml. LoDs of other pathogens ranged between 9.4 cp/ml (hCoV-NL63) and 21,419 cp/ml (HPIV-2). Linearity was verified over 4-7 log-steps with pooled standard differentials (SD) ranging between 0.18-0.70ct. Inter-/intra-run variability (precision) was assessed for all targets over 3 days. SDs ranged between 0.13-0.74ct. Positive agreement in clinical samples was 99.4 % and 95 % for SARS-CoV-2 and influenza-A respectively. Other targets were in the 80-100 % range. Negative agreement varied between 96.3-100 %. DISCUSSION Lab-developed tests are a key factor for effective clinical diagnostics. The multiplex panel presented in this study demonstrated high performance and provides an easily scalable high-throughput solution for respiratory virus testing, e.g. for testing in high-risk patient populations.
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Affiliation(s)
- Hui Ting Tang
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Dominik Nörz
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Moritz Grunwald
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Katja Giersch
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Susanne Pfefferle
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Holger Rohde
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Marc Lütgehetmann
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany.
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Mills DC, Huder JB, Bloemberg GV, Huber M. Comparison of three cartridge-based platforms for syndromic testing for respiratory viruses. Diagn Microbiol Infect Dis 2024; 109:116308. [PMID: 38688147 DOI: 10.1016/j.diagmicrobio.2024.116308] [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: 08/16/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Syndromic testing, the simultaneous testing for multiple pathogens causing similar symptoms, has recently gained ground in clinical diagnostics. This approach can significantly shorten time to diagnosis and speed up decision-making, leading to an improved outcome for the patient. Here, we compared three automated multiplex PCR platforms for syndromic testing of respiratory samples in a retrospective study, and assessed their relative sensitivities. The PPA between BioFire and QIAstat compared to ePlex was 98.4 % and 93.8 %, respectively, and 6 discrepant results were observed. The BioFire was identified as the platform with the highest relative sensitivity. Overall, the platforms performed similarly and are all suitable for syndromic testing of respiratory samples.
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Affiliation(s)
| | - Jon Barduot Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Li W, Wang X, Cui W, Yuan L, Hu X. Clinical Evaluation of a Multiplex PCR Assay for Simultaneous Detection of 18 Respiratory Pathogens in Patients with Acute Respiratory Infections. Pathogens 2022; 12:pathogens12010021. [PMID: 36678368 PMCID: PMC9862116 DOI: 10.3390/pathogens12010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Reliable diagnostics are necessary to identify influenza infections, and coronavirus disease 2019 (COVID-19) highlights the need to develop highly specific and sensitive viral detection methods to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens to prevent their further spread. In this prospective study, 1070 clinical respiratory samples were collected from patients with acute respiratory infections from January 2019 to February 2021 to evaluate the diagnostic performance of a multiplex probe amplification (MPA) assay, designed to screen 18 pathogens, mainly those causing acute respiratory infections. Ninety-six positive samples and twenty negative samples for the 18 respiratory pathogens defined by the MPA assay and reverse transcription polymerase chain reaction (RT-PCR) were further confirmed by reference next-generation sequencing (NGS). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the MPA assay were 95.00%, 93.75%, 98.96% and 75.00%, respectively. Additionally, the co-infection rate for these positive samples were 25% (24/95). The MPA assay demonstrated a highly concordant diagnostic performance with NGS in the diagnosis of 18 respiratory pathogens and might play an important role in clinical respiratory pathogen diagnosis.
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Affiliation(s)
- Wenmin Li
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xiaoxiao Wang
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenhao Cui
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Leyong Yuan
- Department of Clinical Laboratory, Southern University of Science and Technology Hospital, Shenzhen 518055, China
- Correspondence: (L.Y.); (X.H.)
| | - Xuejiao Hu
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Correspondence: (L.Y.); (X.H.)
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Kim TY, Bae GE, Kim JY, Kang M, Jang JH, Huh HJ, Chung DR, Lee NY. Evaluation of the Kaira COVID-19/Flu/RSV Detection Kit for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus: A comparative study with the PowerChek SARS-CoV-2, influenza A&B, RSV Multiplex Real-time PCR Kit. PLoS One 2022; 17:e0278530. [PMID: 36516190 PMCID: PMC9750031 DOI: 10.1371/journal.pone.0278530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Co-circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses, such as influenza and respiratory syncytial virus (RSV), can be a severe threat to public health. The accurate detection and differentiation of these viruses are essential for clinical laboratories. Herein, we comparatively evaluated the performance of the Kaira COVID-19/Flu/RSV Detection Kit (Kaira; Optolane, Seongnam, Korea) for detection of SARS-CoV-2, influenza A and B, and RSV in nasopharyngeal swab (NPS) specimens with that of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea). METHODS A total of 250 archived NPS specimens collected for routine clinical testing were tested in parallel by the Kaira and PowerChek assays. RNA standards were serially diluted and tested by the Kaira assay to calculate the limit of detection (LOD). RESULTS The positive and negative percent agreements between the Kaira and PowerChek assays were as follows: 100% (49/49) and 100% (201/201) for SARS-CoV-2; 100% (50/50) and 99.0% (198/200) for influenza A; 100% (50/50) and 100% (200/200) for influenza B; and 100% (51/51) and 100% (199/199) for RSV, respectively. The LODs of the Kaira assay for SARS-CoV-2, influenza A and B, and RSV were 106.1, 717.1, 287.3, and 442.9 copies/mL, respectively. CONCLUSIONS The Kaira assay showed comparable performance to the PowerChek assay for detection of SARS-CoV-2, influenza A and B, and RSV in NPS specimens, indicating that the Kaira assay could be a useful diagnostic tool when these viruses are co-circulating.
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Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Go Eun Bae
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
| | - Doo Ryeon Chung
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Korea
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Halabi KC, Wang H, Leber AL, Sánchez PJ, Ramilo O, Mejias A. Respiratory syncytial virus and SARS-CoV-2 coinfections in children. Pediatr Pulmonol 2022; 57:3158-3160. [PMID: 35997032 PMCID: PMC9538042 DOI: 10.1002/ppul.26127] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Katia C Halabi
- Department of Pediatrics, Division of Infectious Diseases, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Amy L Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Pablo J Sánchez
- Department of Pediatrics, Division of Infectious Diseases, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, Division of Neonatology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Octavio Ramilo
- Department of Pediatrics, Division of Infectious Diseases, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Asuncion Mejias
- Department of Pediatrics, Division of Infectious Diseases, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
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Calderaro A, Buttrini M, Farina B, Montecchini S, De Conto F, Chezzi C. Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays. Microorganisms 2022; 10:microorganisms10091856. [PMID: 36144458 PMCID: PMC9504108 DOI: 10.3390/microorganisms10091856] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/20/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Respiratory tract infections (RTIs) are the focus of developments in public health, given their widespread distribution and the high morbidity and mortality rates reported worldwide. The clinical spectrum ranges from asymptomatic or mild infection to severe or fatal disease. Rapidity is required in diagnostics to provide adequate and prompt management of patients. The current algorithm for the laboratory diagnosis of RTIs relies on multiple approaches including gold-standard conventional methods, among which the traditional culture is the most used, and innovative ones such as molecular methods, mostly used to detect viruses and atypical bacteria. The implementation of molecular methods with syndromic panels has the potential to be a powerful decision-making tool for patient management despite requiring appropriate use of the test in different patient populations. Their use radically reduces time-to-results and increases the detection of clinically relevant pathogens compared to conventional methods. Moreover, if implemented wisely and interpreted cautiously, syndromic panels can improve antimicrobial use and patient outcomes, and optimize laboratory workflow. In this review, a narrative overview of the main etiological, clinical, and epidemiological features of RTI is reported, focusing on the laboratory diagnosis and the potentialities of syndromic panels.
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