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Ramirez MM, Zarate MN, Rodriguez LA, Aquino VH. Performance evaluation of Biofire Film Array Respiratory Panel 2.1 for SARS-CoV-2 detection in a pediatric hospital setting. PLoS One 2023; 18:e0292314. [PMID: 37797063 PMCID: PMC10553804 DOI: 10.1371/journal.pone.0292314] [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: 08/12/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
The highly contagious nature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19), requires rapid diagnostic tests to prevent the virus from spreading within hospitals and communities. Reverse transcription followed by the polymerase chain reaction (RT-PCR) test is the gold standard for detecting SARS-CoV-2 infections but is time-consuming, labor-intensive, and restricted to centralized laboratories. There is a growing need to develop and implement point-of-care and rapid tests for SARS-CoV-2 detection to address these limitations. We aimed to evaluate the performance of BioFire Film Array Respiratory Panel 2.1 (BioFire FA-RP2.1) for SARS-CoV-2 detection in a pediatric hospital setting. The BioFire FA-RP2.1 test provides rapid results and can identify several viral and bacterial infections in a single test. This prospective, cross-sectional, diagnostic accuracy study enrolled participants ranging from 0 to 18 years of age, seeking medical consultation for any reason, who had been in contact with individuals confirmed to have COVID-19 or managed at the hospital for medical or surgical reasons. We employed a systematic sampling technique to ensure a representative sample. The study included 339 participants with a median age of 5 years. The BioFire FA-RP2.1 test detected SARS-CoV-2 in 18.6% of cases, while the reference RT-PCR test in 14% of cases. The BioFire FA-RP2.1 sensitivity and specificity for SARS CoV-2 detection were 98% and 94%, respectively. The positive probability coefficient (LR+) was 18. The agreement between the two tests was 0.80. In addition, the BioFire FA-RP2.1 test detected coinfection with two viruses in 7,6% of cases. The BioFire FA-RP2.1 is a reliable solution to meet pediatric healthcare needs and improve prognosis in the post-pandemic era thanks to its friendly interface and rapid testing process.
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Affiliation(s)
| | - Miria Noemi Zarate
- General Pediatric Hospital “Children of Acosta Ñu,” San Lorenzo, Central, Paraguay
| | | | - Victor Hugo Aquino
- Immunology Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
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2
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Ma Y, Wu H, Chen S, Xie C, Hu J, Qi X, Ma X, Chu Y, Shan J, Lu Y, Cui L, Zou B, Zhou G. FEN1-aided recombinase polymerase amplification (FARPA) for one-pot and multiplex detection of nucleic acids with an ultra-high specificity and sensitivity. Biosens Bioelectron 2023; 237:115456. [PMID: 37354713 DOI: 10.1016/j.bios.2023.115456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]
Abstract
Recombinase polymerase amplification (RPA) running at 37-42 °C is fast, efficient and less-implemented; however, the existing technologies of nucleic acid testing based on RPA have some limitations in specificity of single-base recognition and multiplexing capability. Herein, we report a highly specific and multiplex RPA-based nucleic acid detection platform by combining flap endonuclease 1 (FEN1)-catalysed invasive reactions with RPA, termed as FEN1-aided RPA (FARPA). The optimal conditions enable RPA and FEN1-based fluorescence detection to occur automatically and sequentially within a 25-min turnaround time and FARPA exhibits sensitivity to 5 target molecules. Due to the ability of invasive reactions in discriminating single-base variation, this one-pot FARPA is much more specific than the Exo probe-based or CRISPR-based RPA methods. Using a universal primer pair derived from tags in reverse transcription primers, multiplex FARPA was successfully demonstrated by the 3-plex assay for the detection of SARS-CoV-2 pathogen (the ORF1ab, the N gene, and the human RNase P gene as the internal control), the 2-plex assay for the discrimination of SARS-CoV-2 wild-type from variants (Alpha, Beta, Epsilon, Delta, or Omicrons), and the 4-plex assay for the screening of arboviruses (zika virus, tick-borne encephalitis virus, yellow fever virus, and chikungunya virus). We have validated multiplex FARPA with 103 nasopharyngeal swabs for SARS-CoV-2 detection. The results showed a 100% agreement with RT-qPCR assays. Moreover, a hand-held FARPA analyser was constructed for the visualized FARPA due to the switch-like endpoint read-out. This FARPA is very suitable for pathogen screening and discrimination of viral variants, greatly facilitating point-of-care diagnostics.
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Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China; Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Shan Chen
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Chunmei Xie
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Jingjing Hu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Jingwen Shan
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yan Lu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Lunbiao Cui
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China.
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Al-Shaibari KSA, Mousa HAL, Alqumber MAA, Alqfail KA, Mohammed A, Bzeizi K. The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies. Diagnostics (Basel) 2023; 13:3057. [PMID: 37835801 PMCID: PMC10572802 DOI: 10.3390/diagnostics13193057] [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: 06/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process. METHODOLOGY A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes. RESULTS A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively. CONCLUSIONS NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.
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Affiliation(s)
| | | | | | | | | | - Khalid Bzeizi
- Department of Liver Transplantation, King Faisal Specialist Hospital and Research Center, Riyadh 13541, Saudi Arabia
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Yip CCY, Sridhar S, Chan WM, Ip JD, Chu AWH, Leung KH, Cheng VCC, Yuen KY, To KKW. Development and Validation of a Novel COVID-19 nsp8 One-Tube RT-LAMP-CRISPR Assay for SARS-CoV-2 Diagnosis. Microbiol Spectr 2022; 10:e0196222. [PMID: 36445095 PMCID: PMC9769742 DOI: 10.1128/spectrum.01962-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
Accurate and simple diagnostic tests for coronavirus disease 2019 (COVID-19) are essential components of the pandemic response. In this study, we evaluated a one-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay coupled with clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-mediated endpoint detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical samples. RT-LAMP-CRISPR is fast and affordable, does not require bulky thermocyclers, and minimizes carryover contamination risk. Results can be read either visually or with a fluorometer. RT-LAMP-CRISPR assays using primers targeting a highly expressed nsp8 gene and previously described nucleocapsid (N) gene primers were designed. The analytical characteristics and diagnostic performance of RT-LAMP-CRISPR assays were compared to those of a commercial real-time RT-PCR E gene assay. The limits of detection (LODs) of the nsp8 and N RT-LAMP-CRISPR assays were 750 and 2,000 copies/mL, which were higher than that of the commercial real-time RT-PCR assay (31.3 copies/mL). Despite the higher LOD, RT-LAMP-CRISPR assays showed diagnostic sensitivity and specificity of 98.6% and 100%, respectively, equivalent to those of the real-time RT-PCR assay (P = 0.5). The median fluorescence reading from the nsp8 assay (378.3 raw fluorescence unit [RFU] [range, 215.6 to 592.6]) was significantly higher than that of the N gene assay (342.0 RFU [range, 143.0 to 576.6]) (P < 0.0001). In conclusion, we demonstrate that RT-LAMP-CRISPR assays using primers rationally designed from highly expressed gene targets are highly sensitive, specific, and easy to perform. Such assays are a valuable asset in resource-limited settings. IMPORTANCE Accurate tests for the diagnosis of SARS-CoV-2, the virus causing coronavirus disease 2019 (COVID-19), are important for timely treatment and infection control decisions. Conventional tests such as real-time reverse transcription-PCR (RT-PCR) require specialized equipment and are expensive. On the other hand, rapid antigen tests suffer from a lack of sensitivity. In this study, we describe a novel assay format for the diagnosis of COVID-19 that is based on principles of loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas chemistry. A major advantage of this assay format is that it does not require expensive equipment to perform, and results can be read visually. This method proved to be fast, easy to perform, and inexpensive. The test compared well against an RT-PCR assay in terms of the ability to detect SARS-CoV-2 RNA in clinical samples. No false-positive test results were observed. The new assay format is ideal for SARS-CoV-2 diagnosis in resource-limited settings.
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Grants
- Health@InnoHK, Innovation and Technology Commission of Hong Kong
- Donations from Richard Yu and Carol Yu, the Shaw Foundation Hong Kong, Michael Seak-Kan Tong, The Hui Ming, Chan Yin Chuen Memorial Charitable Foundation
- Donations from Marina Man-Wai Lee, the Jessie & George Ho Charitable Foundation, Kai Chong Tong, Tse Kam Ming Laurence, Foo Oi Foundation Limited, Betty Hing-Chu Lee, and Ping Cham So
- Hui Hoy and Chow Sin Lan Charity Fund (許海周倩蘭慈善基金有限公司)
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
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Wu TY, Liao YC, Fuh CS, Weng PW, Wang JY, Chen CY, Huang YM, Chen CP, Chu YL, Chen CK, Yeh KL, Yu CH, Wu HK, Lin WP, Liou TH, Wu MS, Liaw CK. An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection. Front Public Health 2022; 10:994712. [PMID: 36339215 PMCID: PMC9627488 DOI: 10.3389/fpubh.2022.994712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/20/2022] [Indexed: 01/26/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because of its high speed and efficiency. We attempted to implement the hypercube pooling strategy and found it had a large quantization effect. This raised two questions: is hypercube pooling with edge = 3 actually the optimal strategy? If not, what is the best edge and dimension? We used a C++ program to calculate the expected number of PCR tests per patient for different values of prevalence, edge, and dimension. The results showed that every edge had a best performance range. Then, using C++ again, we created a program to calculate the optimal edge and dimension required for pooling samples when entering prevalence into our program. Our program will be provided as freeware in the hope that it can help governments fight the SARS-CoV-2 pandemic.
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Affiliation(s)
- Tai-Yin Wu
- Department of Family Medicine, Zhongxing Branch, Taipei City Hospital, Taipei, Taiwan,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan,General Education Center, University of Taipei, Taipei, Taiwan
| | - Yu-Ciao Liao
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Chiou-Shann Fuh
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Pei-Wei Weng
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan
| | - Jr-Yi Wang
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chih-Yu Chen
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan,International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
| | - Yu-Min Huang
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chung-Pei Chen
- Department of Orthopedics, Cathay General Hospital, Taipei, Taiwan
| | - Yo-Lun Chu
- Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,School of Medicine, College of Medicine, Fu Jen Catholic University, Taipei, Taiwan,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Cheng-Kuang Chen
- Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Kuei-Lin Yeh
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan,Department of Orthopaedics, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan,Department of Long-Term Care and Management, WuFeng University, Chiayi, Taiwan
| | - Ching-Hsiao Yu
- Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan,Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Kang Wu
- Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan,Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan,Department of Nursing, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Wei-Peng Lin
- Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan,Department of Orthopedics, Postal Hospital, Taipei, Taiwan
| | - Tsan-Hon Liou
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chen-Kun Liaw
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan,TMU Biodesign Center, Taipei Medical University, Taipei, Taiwan,*Correspondence: Chen-Kun Liaw ;
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6
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Shirvaliloo M, Sheervalilou R, Ahmadpour E, Safiri S, Bannazadeh Baghi H. Diagnostic accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins in pharyngeal swabs compared to RT-PCR as a reference test. Expert Rev Mol Diagn 2022; 22:881-894. [PMID: 36224104 DOI: 10.1080/14737159.2022.2135434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Nanoparticle-based biosensors (NPBs) are point-of-care diagnostic platforms that can be used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high accuracy. AREAS COVERED EBSCOhost Web, Embase, ProQuest, PubMed/MEDLINE, Scopus, Web of Science, and WHO Global Literature on Coronavirus Disease 2019 (COVID-19) were searched for relevant records published from 1 November 2019 to 30 April 2022. Records reporting original data on the accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins from pharyngeal swab specimens were considered. Findings were reported based on the PRISMA 2020 statement. The QUADAS-2 tool was used for assessment of quality and risk of bias among the included studies. EXPERT OPINION A total of 50 relevant records were identified, of which 13 were included. The included studies explored the diagnostic performance of 13 clinically applied distinct nanoparticle-based biosensors in a total of 789 pharyngeal swabs collected from 376 COVID-19 patients and 413 otherwise healthy individuals. The mean sensitivity, specificity, and accuracy were 97.07%, 94.43%, and 96.91%, respectively, in comparison to RT-qPCR as the reference test. Considering their ease-of-operation, portability, low-cost manufacturing, NPBs could be considered suitable candidate diagnostic platforms for substituting RT-qPCR.
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Affiliation(s)
- Milad Shirvaliloo
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Future Science Group, Unitec House, 2 Albert Place, London, N3 1QB, UK
| | | | - Ehsan Ahmadpour
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeid Safiri
- Neurosciences Research Center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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7
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Cui M, Zhou H, Zhang B, Carr MJ, Guo M, Shi W. Rapid detection of the emerging tick-borne Tamdy virus by TaqMan-based real-time reverse transcription PCR. J Virol Methods 2022; 305:114538. [PMID: 35513136 DOI: 10.1016/j.jviromet.2022.114538] [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: 02/11/2022] [Revised: 04/05/2022] [Accepted: 04/30/2022] [Indexed: 10/18/2022]
Abstract
Tamdy virus (TAMV) is an emerging zoonotic tick-borne arbovirus in the genus Orthonairovirus. Reports of human infections with TAMV have been increasing and development of a rapid detection assay is thus urgently required. In the present study, singleplex and dual-target real-time reverse transcription PCR (qRT-PCR) assays were established for the detection of TAMV. Sensitivity and specificity were evaluated and demonstrated high sensitivity of both the singleplex and dual-target qRT-PCR assays with no cross-reaction with common bunyaviruses and tick-borne viruses. The TaqMan-based qRT-PCR methodology established in this study can be employed for epidemiological surveillance and pathogenesis studies of TAMV.
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Affiliation(s)
- Mingxue Cui
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, 271000, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, 271000, China
| | - Bin Zhang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot, Inner Mongolia, 010022, China
| | - Michael J Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020, Japan
| | - Moujian Guo
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, 271000, China
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, 271000, China; School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, 271000, China
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