1
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [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: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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2
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Jiang KP, Bennett S, Heiniger EK, Kumar S, Yager P. UbiNAAT: a multiplexed point-of-care nucleic acid diagnostic platform for rapid at-home pathogen detection. LAB ON A CHIP 2024; 24:492-504. [PMID: 38164805 DOI: 10.1039/d3lc00753g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The COVID-19 pandemic increased demands for respiratory disease testing to facilitate treatment and limit transmission, demonstrating in the process that most existing test options were too complex and expensive to perform in point-of-care or home scenarios. Lab-based molecular techniques can detect viral RNA in respiratory illnesses but are expensive and require trained personnel, while affordable antigen-based home tests lack sensitivity for early detection in newly infected or asymptomatic individuals. The few home RNA detection tests deployed were prohibitively expensive. Here, we demonstrate a point-of-care, paper-based rapid analysis device that simultaneously detects multiple viral RNAs; it is demonstrated on two common respiratory viruses (COVID-19 and influenza A) spiked onto a commercial nasal swab. The automated device requires no sample preparation by the user after insertion of the swab, minimizing user operation steps. We incorporated lyophilized amplification reagents immobilized in a porous matrix, a novel thermally actuated valve for multiplexed fluidic control, a printed circuit board that performs on-device lysis and amplification within a cell-phone-sized disposable device. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized via fluorescent dyes using a modified cell phone, resulting in detection of as few as 104 viral copies per swab across both pathogens within 30 minutes. This integrated platform could be commercialized in a form that would be inexpensive, portable, and sensitive; it can readily be multiplexed to detect as many as 8 different RNA or DNA sequences, and adapted to any desired RNA or DNA detection assays.
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Affiliation(s)
- Kevin P Jiang
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Steven Bennett
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Erin K Heiniger
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Sujatha Kumar
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Paul Yager
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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3
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Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [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: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
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Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
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4
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DeJaco RF, Roberts MJ, Romsos EL, Vallone PM, Kearsley AJ. Reducing Bias and Quantifying Uncertainty in Fluorescence Produced by PCR. Bull Math Biol 2023; 85:83. [PMID: 37574503 PMCID: PMC10423706 DOI: 10.1007/s11538-023-01182-z] [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: 11/16/2022] [Accepted: 06/20/2023] [Indexed: 08/15/2023]
Abstract
We present a new approach for relating nucleic-acid content to fluorescence in a real-time Polymerase Chain Reaction (PCR) assay. By coupling a two-type branching process for PCR with a fluorescence analog of Beer's Law, the approach reduces bias and quantifies uncertainty in fluorescence. As the two-type branching process distinguishes between complementary strands of DNA, it allows for a stoichiometric description of reactions between fluorescent probes and DNA and can capture the initial conditions encountered in assays targeting RNA. Analysis of the expected copy-number identifies additional dynamics that occur at short times (or, equivalently, low cycle numbers), while investigation of the variance reveals the contributions from liquid volume transfer, imperfect amplification, and strand-specific amplification (i.e., if one strand is synthesized more efficiently than its complement). Linking the branching process to fluorescence by the Beer's Law analog allows for an a priori description of background fluorescence. It also enables uncertainty quantification (UQ) in fluorescence which, in turn, leads to analytical relationships between amplification efficiency (probability) and limit of detection. This work sets the stage for UQ-PCR, where both the input copy-number and its uncertainty are quantified from fluorescence kinetics.
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Affiliation(s)
- Robert F. DeJaco
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Dr., College Park, MD 20742-4454 USA
| | - Matthew J. Roberts
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Cost Analysis and Research Division, Institute for Defense Analyses, 730 E. Glebe Rd., Alexandria, VA 22305-3086 USA
| | - Erica L. Romsos
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Peter M. Vallone
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Anthony J. Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
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5
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Yu H, Zhang H, Li J, Zhao Z, Deng M, Ren Z, Li Z, Xue C, Li MG, Chen Z. Rapid and Unamplified Detection of SARS-CoV-2 RNA via CRISPR-Cas13a-Modified Solution-Gated Graphene Transistors. ACS Sens 2022; 7:3923-3932. [PMID: 36472865 PMCID: PMC9745736 DOI: 10.1021/acssensors.2c01990] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
The disease caused by severe acute respiratory syndrome coronavirus, SARS-CoV-2, is termed COVID-19. Even though COVID-19 has been out for more than two years, it is still causing a global pandemic. Due to the limitations of sample collection, transportation, and kit performance, the traditional reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method has a long detection period and high testing costs. An increased risk of infection is inevitable, since many patients may not be diagnosed in time. The CRISPR-Cas13a system can be designed for RNA identification and knockdown, as a promising platform for nucleic acid detection. Here, we designed a solution-gated graphene transistor (SGGT) biosensor based on the CRISPR-Cas13a system. Using the gene-targeting capacity of CRISPR-Cas13a and gate functionalization via multilayer modification, SARS-CoV-2 nucleic acid sequences can be quickly and precisely identified without the need for amplification or fluorescence tagging. The limit of detection (LOD) in both buffer and serum reached the aM level, and the reaction time was about 10 min. The results of the detection of COVID-19 clinical samples from throat swabs agree with RT-PCR. In addition, the interchangeable gates significantly minimize the cost and time of device fabrication. In a nutshell, our biosensor technology is broadly applicable and will be suitable for point-of-care (POC) testing.
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Affiliation(s)
- Haiyang Yu
- State Key Laboratory of Advanced Technology for
Materials Synthesis and Processing, Wuhan University of
Technology, Wuhan430070, China
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Huibin Zhang
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Jinhua Li
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Zheng Zhao
- State Key Laboratory of Advanced Technology for
Materials Synthesis and Processing, Wuhan University of
Technology, Wuhan430070, China
- Sanya Science and Education Innovation Park
of Wuhan University of Technology, Sanya572000,
China
| | - Minhua Deng
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Zhanpeng Ren
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Ziqin Li
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Chenglong Xue
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Mitch Guijun Li
- Division of Integrative Systems and Design,
The Hong Kong University of Science and Technology, Clear
Water Bay, Kowloon, Hong Kong SAR999077, China
| | - Zhaowei Chen
- Division of Nephrology, Renmin Hospital
of Wuhan University, Wuhan430060, China
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Tohari TR, Anshori I, Baroroh U, Nugroho AE, Gumilar G, Kusumawardani S, Syahruni S, Yuliarto B, Arnafia W, Faizal I, Hartati YW, Subroto T, Yusuf M. Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein. BIOSENSORS 2022; 12:1133. [PMID: 36551102 PMCID: PMC9776105 DOI: 10.3390/bios12121133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Two years after SARS-CoV-2 caused the first case of COVID-19, we are now in the "new normal" period, where people's activity has bounced back, followed by the easing of travel policy restrictions. The lesson learned is that the wide availability of accurate and rapid testing procedures is crucial to overcome possible outbreaks in the future. Therefore, many laboratories worldwide have been racing to develop a new point-of-care diagnostic test. To aid continuous innovation, we developed a plasmonic-based biosensor designed explicitly for portable Surface Plasmon Resonance (SPR). In this study, we designed a single chain variable fragment (scFv) from the CR3022 antibody with a particular linker that inserted a cysteine residue at the second position. It caused the linker to have a strong affinity to the gold surface through thiol-coupling and possibly become a ready-to-use bioreceptor toward a portable SPR gold chip without purification steps. The theoretical affinity of this scFv on spike protein was -64.7 kcal/mol, computed using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method from the 100 ns molecular dynamics trajectory. Furthermore, the scFv was produced in Escherichia coli BL21 (DE3) as a soluble protein. The binding activity toward Spike Receptor Binding Domain (RBD) SARS-CoV-2 was confirmed with a spot-test, and the experimental binding free energy of -10.82 kcal/mol was determined using portable SPR spectroscopy. We hope this study will be useful in designing specific and low-cost bioreceptors, particularly early in an outbreak when the information on antibody capture is still limited.
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Affiliation(s)
- Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Biomedical Engineering Department, Institute of Technology, Bandung 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Bandung 40266, Indonesia
| | - Antonius Eko Nugroho
- Lab-on-Chip Group, Biomedical Engineering Department, Institute of Technology, Bandung 40132, Indonesia
| | - Gilang Gumilar
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
- Advanced Functional Material Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
- Research and Development Division, PT. Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Shinta Kusumawardani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Sari Syahruni
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
| | - Brian Yuliarto
- Research Center for Nanoscience and Nanotechnology (RCNN), Institut Teknologi Bandung, Bandung 40132, Indonesia
- Advanced Functional Material Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Wyanda Arnafia
- Research and Development Division, PT. Tekad Mandiri Citra, Bandung 40292, Indonesia
| | - Irvan Faizal
- Centre for Vaccine and Drug Research, National Research and Innovation Agency Republic of Indonesia, Kawasan Puspiptek Serpong, Tangerang Selatan 15314, Indonesia
- Department of Biotechnology, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang 15345, Indonesia
| | - Yeni Wahyuni Hartati
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Toto Subroto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Muhammad Yusuf
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
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7
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The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk. Int J Mol Sci 2022; 23:ijms232214110. [PMID: 36430586 PMCID: PMC9693045 DOI: 10.3390/ijms232214110] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.
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Qaqish B, Sallam M, Al-Khateeb M, Reisdorf E, Mahafzah A. Assessment of COVID-19 Molecular Testing Capacity in Jordan: A Cross-Sectional Study at the Country Level. Diagnostics (Basel) 2022; 12:diagnostics12040909. [PMID: 35453957 PMCID: PMC9024853 DOI: 10.3390/diagnostics12040909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic control measures rely on the accurate and timely diagnosis of infected individuals. Real-time polymerase chain reaction (qPCR) remains the gold-standard method for laboratory diagnosis of the disease. Delayed diagnosis due to challenges that face laboratories performing COVID-19 testing can hinder public health control measures. Such challenges may be related to shortages in staff, equipment or materials, improper inventory management, flawed workflow, or long turnaround time (TAT). The aim of the current study was to assess the overall COVID-19 molecular testing capacity in Jordan as of April 2021. In addition, the study’s objectives included the identification of potential defects that could comprise the utility of the COVID-19 molecular testing capacity in the country. All laboratories certified by the Ministry of Health (MoH) in Jordan to conduct molecular testing for SARS-CoV-2 were invited to participate in this study. Data were obtained from the participating laboratories (those which agreed to participate) by either telephone interviews or a self-reported written questionnaire with items assessing the key aspects of COVID-19 molecular testing. The full molecular testing capacity in each laboratory was self-reported considering 24 working hours. The total number of participating laboratories was 51 out of 77 (66.2%), with the majority being affiliated with MoH (n = 17) and private laboratories (n = 20). The total molecular COVID-19 testing capacity among the participating laboratories was estimated at 574,441 tests per week, while the actual highest number of tests performed over a single week was 310,047 (54.0%, reported in March 2021). Laboratories affiliated with the MoH were operating at a level closer to their maximum capacity (87.2% of their estimated full capacity for COVID-19 testing) compared to private hospital laboratories (41.3%, p = 0.004), private laboratories (20.8%, p < 0.001), and academic/research laboratories (14.7%, p < 0.001, ANOVA). The national average daily COVID-19 molecular testing was 349.2 tests per 100,000 people in April 2021. The average TAT over the first week of April 2021 for COVID-19 testing was 932 min among the participating laboratories, with the longest TAT among MoH laboratories (mean: 1959 min) compared to private laboratories (mean: 333 min, p < 0.001). Molecular COVID-19 testing potential in Jordan has not been fully utilized, particularly for private laboratories and those belonging to academic/research centers. Supply-chain challenges and shortages in staff were identified as potential obstacles hindering the exploitation of full molecular testing capacity for COVID-19 in the country.
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Affiliation(s)
- Bara’a Qaqish
- Abt Associates, United States Agency for International Development (USAID) Funded Local Health System Sustainability Project (LHSS), Amman 11822, Jordan;
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmo, Sweden
- Correspondence: (M.S.); (A.M.)
| | | | - Erik Reisdorf
- Infectious Disease Detection and Surveillance (IDDS), Rockville, MD 20894, USA;
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Correspondence: (M.S.); (A.M.)
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9
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Biotechnological Perspectives to Combat the COVID-19 Pandemic: Precise Diagnostics and Inevitable Vaccine Paradigms. Cells 2022; 11:cells11071182. [PMID: 35406746 PMCID: PMC8997755 DOI: 10.3390/cells11071182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
The outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause for the ongoing global public health emergency. It is more commonly known as coronavirus disease 2019 (COVID-19); the pandemic threat continues to spread aroundthe world with the fluctuating emergence of its new variants. The severity of COVID-19 ranges from asymptomatic to serious acute respiratory distress syndrome (ARDS), which has led to a high human mortality rate and disruption of socioeconomic well-being. For the restoration of pre-pandemic normalcy, the international scientific community has been conducting research on a war footing to limit extremely pathogenic COVID-19 through diagnosis, treatment, and immunization. Since the first report of COVID-19 viral infection, an array of laboratory-based and point-of-care (POC) approaches have emerged for diagnosing and understanding its status of outbreak. The RT-PCR-based viral nucleic acid test (NAT) is one of the rapidly developed and most used COVID-19 detection approaches. Notably, the current forbidding status of COVID-19 requires the development of safe, targeted vaccines/vaccine injections (shots) that can reduce its associated morbidity and mortality. Massive and accelerated vaccination campaigns would be the most effective and ultimate hope to end the COVID-19 pandemic. Since the SARS-CoV-2 virus outbreak, emerging biotechnologies and their multidisciplinary approaches have accelerated the understanding of molecular details as well as the development of a wide range of diagnostics and potential vaccine candidates, which are indispensable to combating the highly contagious COVID-19. Several vaccine candidates have completed phase III clinical studies and are reported to be effective in immunizing against COVID-19 after their rollout via emergency use authorization (EUA). However, optimizing the type of vaccine candidates and its route of delivery that works best to control viral spread is crucial to face the threatening variants expected to emerge over time. In conclusion, the insights of this review would facilitate the development of more likely diagnostics and ideal vaccines for the global control of COVID-19.
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10
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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11
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Alotaibi B, El-Masry TA, Seadawy MG, Farghali MH, El-Harty BE, Saleh A, Mahran YF, Fahim JS, Desoky MS, Abd El-Monsef MM, El-Bouseary MM. SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. Heliyon 2022; 8:e08864. [PMID: 35128118 PMCID: PMC8801622 DOI: 10.1016/j.heliyon.2022.e08864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
COVID-19 is an infectious disease caused by SARS-CoV-2 and has spread globally, resulting in the ongoing coronavirus pandemic. The current study aimed to analyze the clinical and epidemiological features of COVID-19 in Egypt. Oropharyngeal swabs were collected from 197 suspected patients who were admitted to the Army Hospital and confirmation of the positivity was performed by rRT-PCR assay. Whole genomic sequencing was conducted using Illumina iSeq 100® System. The average age of the participants was 48 years, of which 132 (67%) were male. The main clinical symptoms were pneumonia (98%), fever (92%), and dry cough (66%). The results of the laboratory showed that lymphocytopenia (79.2%), decreased levels of haemoglobin (77.7%), increased levels of interleukin 6, C-reactive protein, serum ferritin, and D-dimer (77.2%, 55.3%, 55.3%, and 25.9%, respectively), and leukocytopenia (25.9%) were more common. The CT findings showed that scattered opacities (55.8%) and ground-glass appearance (27.9%) were frequently reported. The recovered validated sequences (n = 144) were submitted to NCBI Virus GenBank. All sequenced viruses have at least 99% identity to Wuhan-Hu-1. All variants were GH clade, B.1 PANGO lineage, and L.GP.YP.HT haplotype. The most predominant subclade was D614G/Q57H/V5F/G823S. Our findings have aided in a deep understanding of COVID-19 evolution and identifying strains with unique mutational patterns in Egypt. Isolation and clinical characterization of SARS-CoV-2 from Egyptian patients. Whole Genome Sequencing of recovered isolates revealed unique sequences. Egyptian SARS-CoV-2 variants in 2020 with at least 99% identity to Wuhan-Hu-1. Egyptian SARS-CoV-2 variants were GH clade and L.GP.YP.HT haplotype. A unique mutation (D614G/Q57H/V5F/G823S) pattern was predominant among SARS-CoV-2.
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Affiliation(s)
- Badriyah Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thanaa A. El-Masry
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Mahmoud H. Farghali
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Pharmacy, Al Azhar University, Cairo, Egypt
| | - Yasmen F. Mahran
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | | | | | | | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
- Corresponding author.
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12
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Chavda VP, Vuppu S, Mishra T, Kamaraj S, Patel AB, Sharma N, Chen ZS. Recent review of COVID-19 management: diagnosis, treatment and vaccination. Pharmacol Rep 2022; 74:1120-1148. [PMID: 36214969 PMCID: PMC9549062 DOI: 10.1007/s43440-022-00425-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 02/06/2023]
Abstract
The idiopathic Coronavirus disease 2019 (COVID-19) pandemic outbreak caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached global proportions; the World Health Organization (WHO) declared it as a public health emergency during the month of January 30, 2020. The major causes of the rise of new variants of SARS-CoV-2 are genetic mutations and recombination. Some of the variants with high infection and transmission rates are termed as variants of concern (VOCs) like currently Omicron variants. Pregnant women, aged people, and immunosuppressed and compromised patients constitute the most susceptible human population to the SARS-CoV-2 infection, especially to the new evolving VOCs. To effectively manage the pathological condition of infection, the focus should be directed towards prevention and prophylactic approach. In this narrative review, we aimed to analyze the current scenario of COVID-19 management and discuss the treatment and prevention strategies. We also focused on the complications prevalent during the COVID-19 and post-COVID period and to discuss the novel approaches developed for mitigation of the global pandemic. We have also emphasized on the COVID-19 management approaches for the special population including children, pregnant women, aged groups, and immunocompromised patients. We conclude that the advancements in therapeutic and pharmacological domains have provided opportunities to develop and design novel diagnosis, treatment, and prevention strategies. New advanced techniques such as RT-LAMP, RT-qPCR, High-Resolution Computed Tomography, etc., efficiently diagnose patients with SARS-CoV-2 infection. In the case of treatment options, new drugs like paxlovid, combinations of β-lactum drugs and molnupiravir are found to be effective against even the new emerging variants. In addition, vaccination is an essential approach to prevent the infection or to reduce its severity. Vaccines for against COVID-19 from Comirnaty by Pfizer-BioNTech, SpikeVax by Moderna, and Vaxzevria by Oxford-AstraZeneca are approved and used widely. Similarly, numerous vaccines have been developed with different percentages of effectiveness against VOCs. New developments like nanotechnology and AI can be beneficial in providing an efficient and reliable solution for the suppression of SARS-CoV-2. Public health concerns can be efficiently treated by a unified scientific approach, public engagement, and better diagnosis.
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Affiliation(s)
- Vivek P. Chavda
- grid.419037.80000 0004 1765 7930Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat India
| | - Suneetha Vuppu
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Toshika Mishra
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Sathvika Kamaraj
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Aayushi B. Patel
- grid.419037.80000 0004 1765 7930Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat India
| | - Nikita Sharma
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Zhe-Sheng Chen
- grid.264091.80000 0001 1954 7928Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, St. John’s University, New York, NY 11439 USA
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13
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Martínez MJ, Basile L, Sisó-Almirall A, Cristino V, Cuesta G, Hurtado JC, Fernandez-Pittol M, Mosquera MM, Soriano A, Martínez A, Marcos MA, Vila J, Casals-Pascual C. Lack of Prognostic Value of SARS-CoV2 RT-PCR Cycle Threshold in the Community. Infect Dis Ther 2021; 11:587-593. [PMID: 34762246 PMCID: PMC8582337 DOI: 10.1007/s40121-021-00561-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022] Open
Abstract
The immense impact of the COVID-19 pandemic on health systems has motivated the scientific community to search for clinical prognostic factors for SARS-CoV-2 infection. Low cycle threshold values (Ct) of diagnostic real-time RT-PCR assays in hospitalized patients have been associated with a poor prognosis in several studies, whereas other studies did not find this association. We explored whether SARS-CoV-2 Ct values at diagnosis were associated with a poor outcome (admission to hospital and death) in 604 community patients diagnosed at primary health centers. Although lower Ct values were found in patients who died of COVID-19, the Ct value was not significantly associated with a worse outcome in a multivariate analysis, while age remained an independent prognostic factor. We did not find evidence to support the role of Ct values as a prognostic factor of COVID-19 in community cases.
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Affiliation(s)
- Miguel J Martínez
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Luca Basile
- Public Health Agency of Catalonia, Generalitat of Catalonia, Barcelona, Spain
| | - Antoni Sisó-Almirall
- Consorci d'Atenció Primària de Salut Barcelona Esquerra (CAPSBE), Barcelona, Spain
| | - Victor Cristino
- Public Health Agency of Catalonia, Generalitat of Catalonia, Barcelona, Spain
| | - Genoveva Cuesta
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Juan Carlos Hurtado
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | | | - María Mar Mosquera
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clinic of Barcelona-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ana Martínez
- Public Health Agency of Catalonia, Generalitat of Catalonia, Barcelona, Spain
| | - Mª Angeles Marcos
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Jordi Vila
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Climent Casals-Pascual
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain. .,Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.
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14
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Bivins A, Kaya D, Bibby K, Simpson SL, Bustin SA, Shanks OC, Ahmed W. Variability in RT-qPCR assay parameters indicates unreliable SARS-CoV-2 RNA quantification for wastewater surveillance. WATER RESEARCH 2021; 203:117516. [PMID: 34412018 DOI: 10.20944/preprints202106.0320.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 05/19/2023]
Abstract
Due to the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) has been used to generate large datasets aimed at detecting and quantifying SARS-CoV-2 RNA in wastewater. Although RT-qPCR is rapid and sensitive, there is no standard method yet, there are no certified quantification standards, and experiments are conducted using different assays, reagents, instruments, and data analysis protocols. These variations can induce errors in quantitative data reports, thereby potentially misleading interpretations, and conclusions. We review the SARS-CoV-2 wastewater surveillance literature focusing on variability of RT-qPCR data as revealed by inconsistent standard curves and associated parameters. We find that variation in these parameters and deviations from best practices, as described in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines suggest a frequent lack of reproducibility and reliability in quantitative measurements of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Devrim Kaya
- School of Chemical, Biological, & Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Stephen A Bustin
- Medical Technology Research Center, Faculty of Health, Education and Social Care, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK
| | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH, 45268, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park 4102, QLD, Australia.
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15
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Bivins A, Kaya D, Bibby K, Simpson SL, Bustin SA, Shanks OC, Ahmed W. Variability in RT-qPCR assay parameters indicates unreliable SARS-CoV-2 RNA quantification for wastewater surveillance. WATER RESEARCH 2021; 203:117516. [PMID: 34412018 PMCID: PMC8341816 DOI: 10.1016/j.watres.2021.117516] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
Due to the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) has been used to generate large datasets aimed at detecting and quantifying SARS-CoV-2 RNA in wastewater. Although RT-qPCR is rapid and sensitive, there is no standard method yet, there are no certified quantification standards, and experiments are conducted using different assays, reagents, instruments, and data analysis protocols. These variations can induce errors in quantitative data reports, thereby potentially misleading interpretations, and conclusions. We review the SARS-CoV-2 wastewater surveillance literature focusing on variability of RT-qPCR data as revealed by inconsistent standard curves and associated parameters. We find that variation in these parameters and deviations from best practices, as described in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines suggest a frequent lack of reproducibility and reliability in quantitative measurements of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Devrim Kaya
- School of Chemical, Biological, & Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Stephen A Bustin
- Medical Technology Research Center, Faculty of Health, Education and Social Care, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK
| | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH, 45268, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park 4102, QLD, Australia.
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16
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Whale AS, von der Heide EK, Kohlenberg M, Brinckmann A, Baedker S, Karalay O, Fernandez-Gonzalez A, Busby EJ, Bustin SA, Hauser H, Missel A, O'Sullivan DM, Huggett JF, Pfaffl MW, Nolan T. Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics. Methods 2021; 201:5-14. [PMID: 34454016 PMCID: PMC8387146 DOI: 10.1016/j.ymeth.2021.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious, acute respiratory disease caused mainly by person-to-person transmission of the coronavirus SARS-CoV-2. Its emergence has caused a world-wide acute health crisis, intensified by the challenge of reliably identifying individuals likely to transmit the disease. Diagnosis is hampered by the many unknowns surrounding this disease, including those relating to infectious viral burden. This uncertainty is exacerbated by disagreement surrounding the clinical relevance of molecular testing using reverse transcription quantitative PCR (RT-qPCR) for the presence of viral RNA, most often based on the reporting of quantification cycles (Cq), which is also termed the cycle threshold (Ct) or crossing point (Cp). Despite it being common knowledge that Cqs are relative values varying according to a wide range of different parameters, there have been efforts to use them as though they were absolute units, with Cqs below an arbitrarily determined value, deemed to signify a positive result and those above, a negative one. Our results investigated the effects of a range of common variables on Cq values. These data include a detailed analysis of the effect of different carrier molecules on RNA extraction. The impact of sample matrix of buccal swabs and saliva on RNA extraction efficiency was demonstrated in RT-qPCR and the impact of potentially inhibiting compounds in urine along with bile salts were investigated in RT-digital PCR (RT-dPCR). The latter studies were performed such that the impact on the RT step could be separated from the PCR step. In this way, the RT was shown to be more susceptible to inhibitors than the PCR. Together, these studies demonstrate that the consequent variability of test results makes subjective Cq cut-off values unsuitable for the identification of infectious individuals. We also discuss the importance of using reliable control materials for accurate quantification and highlight the substantial role played by dPCR as a method for their development.
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Affiliation(s)
- Alexandra S Whale
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Eva K von der Heide
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Max Kohlenberg
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Anja Brinckmann
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Silke Baedker
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | - Oezlem Karalay
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | | | - Eloise J Busby
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Stephen A Bustin
- Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK.
| | - Heiko Hauser
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Andreas Missel
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | - Denise M O'Sullivan
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
| | - Tania Nolan
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany; Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK.
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17
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Evaluation of a PlexZyme-Based PCR Assay and Assessment of COVID-19 Surge Testing Throughput Compared to Cobas SARS-CoV-2. Pathogens 2021; 10:pathogens10091088. [PMID: 34578121 PMCID: PMC8465568 DOI: 10.3390/pathogens10091088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
Reliable high-throughput methods are required for the detection of severe acute respiratory coronavirus 2 (SARS-CoV-2). We evaluated the new research use only (RUO) SpeeDx PlexZyme SARS-CoV-2 components (Plex) compared to the Roche cobas SARS-CoV-2 assay (cobas). A collection of positive (n = 214) and negative samples (n = 201) was tested in parallel comparing Plex with cobas. The overall agreement comparing the qualitative outcomes was 96.9%. Using an in-house quantitative PCR method, correlation comparing Plex ORF1ab to cobas ORF1a was r2 = 0.95. The median Plex ORF1ab change in target copy number compared to cobas ORF1a was +0.48 log10 copies/mL respectively. Inter- and intra-assay reproducibility of each assay was compared, including a limit-of-detection study. Reproducibility was comparable; however cobas was more sensitive than Plex by 1-log dilution. Throughput was evaluated during a COVID-19 testing surge of 4324 samples in a 30-h period. Plex demonstrated less hands-on time per reportable result (19% decrease) and increased throughput (155% increase of 102 results/hour) compared to cobas (40 results/hour). Our study demonstrates good qualitative and quantitative correlation of Plex compared to cobas and that Plex is well-suited for high throughput testing.
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18
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Bustin S, Kirvell S, Huggett JF, Nolan T. RT-qPCR Diagnostics: The "Drosten" SARS-CoV-2 Assay Paradigm. Int J Mol Sci 2021; 22:ijms22168702. [PMID: 34445406 PMCID: PMC8395416 DOI: 10.3390/ijms22168702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an established tool for the diagnosis of RNA pathogens. Its potential for automation has caused it to be used as a presence/absence diagnostic tool even when RNA quantification is not required. This technology has been pushed to the forefront of public awareness by the COVID-19 pandemic, as its global application has enabled rapid and analytically sensitive mass testing, with the first assays targeting three viral genes published within days of the publication of the SARS-CoV-2 genomic sequence. One of those, targeting the RNA-dependent RNA polymerase gene, has been heavily criticised for supposed scientific flaws at the molecular and methodological level, and this criticism has been extrapolated to doubts about the validity of RT-qPCR for COVID-19 testing in general. We have analysed this assay in detail, and our findings reveal some limitations but also highlight the robustness of the RT-qPCR methodology for SARS-CoV-2 detection. Nevertheless, whilst our data show that some errors can be tolerated, it is always prudent to confirm that the primer and probe sequences complement their intended target, since, when errors do occur, they may result in a reduction in the analytical sensitivity. However, in this case, it is unlikely that a mismatch will result in poor specificity or a significant number of false-positive SARS-CoV-2 diagnoses, especially as this is routinely checked by diagnostic laboratories as part of their quality assurance.
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Affiliation(s)
- Stephen Bustin
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
- Correspondence:
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Queens Rd, Teddington, London TW11 0LY, UK;
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
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19
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Brukner I, Resendes A, Eintracht S, Papadakis AI, Oughton M. Sample Adequacy Control (SAC) Lowers False Negatives and Increases the Quality of Screening: Introduction of "Non-Competitive" SAC for qPCR Assays. Diagnostics (Basel) 2021; 11:diagnostics11071133. [PMID: 34206413 PMCID: PMC8305439 DOI: 10.3390/diagnostics11071133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 01/15/2023] Open
Abstract
Sample Adequacy Control (SAC) has critical analytical, clinical and epidemiological value that increases confidence in a negative test result. The SAC is an integral qPCR assay control, which ensures that all pre-analytical and analytical steps are adequate for accurate testing and reporting. As such, a negative SAC with a negative result on pathogen screen specifies that the result should be reported as inconclusive instead of negative. Despite this, many regulatory approved tests do not incorporate SAC into their assay design. Herein, we emphasize the universal value of SAC and offer for the first time, a simple technical strategy to introduce non-competitive SAC which does not interfere with the limit of detection for the screened pathogen. Integration of SAC can provide key benefits towards identifying, isolating, quarantining and contact tracing infected individuals and in turn can improve worldwide efforts in infection control.
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Affiliation(s)
- Ivan Brukner
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
- Correspondence: (I.B.); (M.O.); Tel.: +1-514-8038782 (I.B.); +1-514-3408222 (ext. 22662) (M.O.)
| | - Alex Resendes
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
| | - Shaun Eintracht
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Andreas I. Papadakis
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
| | - Matthew Oughton
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
- Correspondence: (I.B.); (M.O.); Tel.: +1-514-8038782 (I.B.); +1-514-3408222 (ext. 22662) (M.O.)
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