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Torse DA, Khanai R, Pai K, Iyer S, Mavinkattimath S, Kallimani R, Shahpur S. Optimal feature selection for COVID-19 detection with CT images enabled by metaheuristic optimization and artificial intelligence. MULTIMEDIA TOOLS AND APPLICATIONS 2023:1-31. [PMID: 37362744 PMCID: PMC10025793 DOI: 10.1007/s11042-023-15031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/09/2022] [Accepted: 02/27/2023] [Indexed: 06/28/2023]
Abstract
There is a broad range of novel Coronaviruses (CoV) such as the common cold, cough, and severe lung infections. The mutation of this virus, which originally started as COVID-19 in Wuhan, China, has continued the rapid spread globally. As the mutated form of this virus spreads across the world, testing and screening procedures of patients have become tedious for healthcare departments in largely populated countries such as India. To diagnose COVID-19 pneumonia by radiological methods, high-resolution computed tomography (CT) of the chest has been considered the most precise method of examination. The use of modern artificial intelligence (AI) techniques on chest high-resolution computed tomography (HRCT) images can help to detect the disease, especially in remote areas with a lack of specialized physicians. This article presents a novel metaheuristic algorithm for automatic COVID-19 detection using a least square support vector machine (LSSVM) classifier for three classes namely normal, COVID, and pneumonia. The proposed model results in a classification accuracy of 87.2% and an F1-score of 86.3% for multiclass classifications from simulations. The analysis of information transfer rate (ITR) revealed that the modified quantum-based marine predators algorithm (Mq-MPA) feature selection algorithm reduces the classification time of LSSVM by 23% when compared to the deep learning models.
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Affiliation(s)
- Dattaprasad A. Torse
- Department of ECE, KLE Dr. M.S. Sheshgiri College of Engineering and Technology, Udyambag, Belagavi, KA 590008 India
| | - Rajashri Khanai
- Department of CSE, KLE Dr. M.S. Sheshgiri College of Engineering and Technology, Udyambag, Belagavi, KA 590008 India
| | - Krishna Pai
- Department of ECE, KLE Dr. M.S. Sheshgiri College of Engineering and Technology, Udyambag, Belagavi, KA 590008 India
| | - Sridhar Iyer
- Department of ECE, KLE Dr. M.S. Sheshgiri College of Engineering and Technology, Udyambag, Belagavi, KA 590008 India
| | - Swati Mavinkattimath
- Department of ECE, KLE Dr. M.S. Sheshgiri College of Engineering and Technology, Udyambag, Belagavi, KA 590008 India
| | - Rakhee Kallimani
- Department of EEE, KLE Dr. M.S. Sheshgiri College of Engineering and Technology, Udyambag, Belagavi, KA 590008 India
| | - Salma Shahpur
- Department of ECE, Jain College of Engineering, Belagavi, KA 590008 India
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2
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Chrysostomou AC, Aristokleous A, Rodosthenous JH, Christodoulou C, Stathi G, Kostrikis LG. Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay. Life (Basel) 2023; 13:life13020304. [PMID: 36836661 PMCID: PMC9960118 DOI: 10.3390/life13020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health.
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Affiliation(s)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | | | | | - Georgia Stathi
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
- Correspondence: ; Tel.: +35-72-289-2885
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3
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Shankar P, Singh J, Joshi A, Malhotra AG, Shrivas A, Goel G, Gupta P, Yadav J, Saigal S, Singh S, Purwar S. Organ Involvement in COVID-19: A Molecular Investigation of Autopsied Patients. Microorganisms 2022; 10:microorganisms10071333. [PMID: 35889052 PMCID: PMC9318581 DOI: 10.3390/microorganisms10071333] [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: 04/22/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 02/07/2023] Open
Abstract
Precise reasons for severe manifestation of SARS-CoV-2 remain unanswered, and efforts have been focused on respiratory system management. Demonstration of unequivocal presence of SARS-CoV-2 in vital body organs by cadaver autopsy was the only way to prove multi-organ involvement. Hence, the primary objective of the study was to determine presence of the SARS-CoV-2 in various organs of patients succumbing to SARS-CoV-2 infection. A total of 246 samples from different organs of 21 patients who died due to severe COVID-19 illness were investigated by qRT-PCR, and SARS-CoV-2 was detected in 181 (73.57%) samples and highest positivity of SARS-CoV-2 being (expectedly) found in nasopharynx (90.4%) followed by bilateral lungs (87.30%), peritoneal fluid (80%), pancreas (72.72%), bilateral kidneys (68.42%), liver (65%) and even in brain (47.2%). The deceased patients were categorized to three subgroups based upon the extent of organs in which SARS-CoV-2 was detected by qRT-PCR (high intensity ≥80%, intermediate intensity = 65-80% and low intensity ≤65% organs involvement). It was conclusively established that SARS-CoV-2 has the property of invasion beyond lungs and even crosses the blood-brain barrier, resulting in multi-system disease; this is probably the reason behind cytokine storm, though it is not clear whether organ damage is due to direct injury caused by the virus or result of inflammatory assault. Significant inverse correlation was found between the Ct value of lung samples and number of organs involved, implying that higher viral load in lungs is directly proportionate to involvement of extrapulmonary organs and patients with higher viral load in respiratory secretions should be monitored more closely for any warning signs and the treatment strategies should also address involvement of other organs for better outcome, because lungs, though the primary site of infection, are not the only organ system responsible for pathogenesis of systemic illness.
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Affiliation(s)
- Prem Shankar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Ankur Joshi
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Anvita Gupta Malhotra
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Arti Shrivas
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Garima Goel
- Department of Pathology & Laboratory Medicine, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Priyal Gupta
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Jayanthi Yadav
- Department of Forensic Medicine, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Saurabh Saigal
- Anaesthesia and Critical Care, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
- Department of Biomedical Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Shashank Purwar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
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4
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Wang Y, Xu H, Dong Z, Wang Z, Yang Z, Yu X, Chang L. Micro/nano biomedical devices for point-of-care diagnosis of infectious respiratory diseases. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022; 14:100116. [PMID: 35187465 PMCID: PMC8837495 DOI: 10.1016/j.medntd.2022.100116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/14/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
Corona Virus Disease 2019 (COVID-19) has developed into a global pandemic in the last two years, causing significant impacts on our daily life in many countries. Rapid and accurate detection of COVID-19 is of great importance to both treatments and pandemic management. Till now, a variety of point-of-care testing (POCT) approaches devices, including nucleic acid-based test and immunological detection, have been developed and some of them has been rapidly ruled out for clinical diagnosis of COVID-19 due to the requirement of mass testing. In this review, we provide a summary and commentary on the methods and biomedical devices innovated or renovated for the quick and early diagnosis of COVID-19. In particular, some of micro and nano devices with miniaturized structures, showing outstanding analytical performances such as ultra-sensitivity, rapidness, accuracy and low cost, are discussed in this paper. We also provide our insights on the further implementation of biomedical devices using advanced micro and nano technologies to meet the demand of point-of-care diagnosis and home testing to facilitate pandemic management. In general, our paper provides a comprehensive overview of the latest advances on the POCT device for diagnosis of COVID-19, which may provide insightful knowledge for researcher to further develop novel diagnostic technologies for rapid and on-site detection of pathogens including SARS-CoV-2.
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Affiliation(s)
- Yang Wang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Huiren Xu
- School of Biomedical Information and Engineering, Hainan Medical University, Haikou, 471100, China
| | - Zaizai Dong
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhiying Wang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, United Kingdom,Corresponding author
| | - Xinge Yu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China,Corresponding author.
| | - Lingqian Chang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China,Corresponding author.
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5
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Entesari M, Zamani M, Heidarizadeh M, Moradi R, Khakdan F, Rafiei F. An Insight Into Detection Pathways/Biosensors of Highly Infectious Coronaviruses. Mol Biotechnol 2022; 64:339-354. [PMID: 34655396 PMCID: PMC8520350 DOI: 10.1007/s12033-021-00417-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/07/2021] [Indexed: 01/12/2023]
Abstract
The outbreak of COVID-19 pandemic and its consequences have inflicted a substantial damage on the world. In this study, it was attempted to review the recent coronaviruses appeared among the human being and their epidemic/pandemic spread throughout the world. Currently, there is an inevitable need for the establishment of a quick and easily available biosensor for tracing COVID-19 in all countries. It has been known that the incubation time of COVID-19 lasts about 14 days and 25% of the infected individuals are asymptomatic. To improve the ability to determine SARS-CoV-2 precisely and reduce the risk of eliciting false-negative results produced by mutating nature of coronaviruses, many researchers have established a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay using mismatch-tolerant molecular beacons as multiplex real-time RT-PCR to distinguish between pathogenic and non-pathogenic strains of coronaviruses. The possible mechanisms and pathways for the detection of coronaviruses by biosensors have been reviewed in this study.
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Affiliation(s)
- Mehrnaz Entesari
- Department of Genetic Engineering and Molecular Genetics, Zanjan University, Zanjan, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Heidarizadeh
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Rasoul Moradi
- Department of Chemical Engineering, School of Engineering & Applied Science, Khazar University, Baku, Azerbaijan
| | | | - Fariba Rafiei
- Department of Agronomy & Plant Breeding, Collage of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
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6
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Chrysostomou AC, Hezka Rodosthenous J, Topcu C, Papa C, Aristokleous A, Stathi G, Christodoulou C, Eleftheriou C, Stylianou DC, Kostrikis LG. A Multiallelic Molecular Beacon-Based Real-Time RT-PCR Assay for the Detection of SARS-CoV-2. Life (Basel) 2021; 11:life11111146. [PMID: 34833022 PMCID: PMC8619337 DOI: 10.3390/life11111146] [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: 10/04/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
Emerging infectious viruses have led to global advances in the development of specific and sensitive detection techniques. Viruses have an inherent potential to easily mutate, presenting major hurdles for diagnostics and requiring methods capable of detecting genetically diverse viral strains. One such infectious agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in December 2019 and has resulted in the global coronavirus disease 2019 (COVID-19) pandemic. This study presents a real-time reverse transcription PCR (RT-PCR) detection assay for SARS-CoV-2, taking into account its intrinsic polymorphic nature that arises due to genetic drift and recombination, as well as the possibility of continuous and multiple introductions of genetically nonidentical strains into the human population. This advance was achieved by using mismatch-tolerant molecular beacons designed to specifically detect the SARS-CoV-2 S, E, M, and N genes. These were applied to create a simple and reproducible real-time RT-PCR assay, which was validated using external quality control panels (QCMD: CVOP20, WHO: SARS-CoV-2-EQAP-01) and clinical samples. This assay was designed for high target detection accuracy and specificity and can also be readily adapted for the detection of other emerging and rapidly mutating pathogens.
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Affiliation(s)
- Andreas C. Chrysostomou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Johana Hezka Rodosthenous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Cicek Topcu
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Christina Papa
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Georgia Stathi
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Christina Christodoulou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Christina Eleftheriou
- Department of Health and Safety, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus;
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (J.H.R.); (C.T.); (C.P.); (A.A.); (G.S.); (C.C.); (D.C.S.)
- Correspondence: ; Tel.: +357-2289-2885
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7
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Carvalho J, Lopes-Nunes J, Figueiredo J, Santos T, Miranda A, Riscado M, Sousa F, Duarte AP, Socorro S, Tomaz CT, Felgueiras M, Teixeira R, Faria C, Cruz C. Molecular Beacon Assay Development for Severe Acute Respiratory Syndrome Coronavirus 2 Detection. SENSORS (BASEL, SWITZERLAND) 2021; 21:7015. [PMID: 34770321 PMCID: PMC8587319 DOI: 10.3390/s21217015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/23/2022]
Abstract
The fast spread of SARS-CoV-2 has led to a global pandemic, calling for fast and accurate assays to allow infection diagnosis and prevention of transmission. We aimed to develop a molecular beacon (MB)-based detection assay for SARS-CoV-2, designed to detect the ORF1ab and S genes, proposing a two-stage COVID-19 testing strategy. The novelty of this work lies in the design and optimization of two MBs for detection of SARS-CoV-2, namely, concentration, fluorescence plateaus of hybridization, reaction temperature and real-time results. We also identify putative G-quadruplex (G4) regions in the genome of SARS-CoV-2. A total of 458 nasopharyngeal and throat swab samples (426 positive and 32 negative) were tested with the MB assay and the fluorescence levels compared with the cycle threshold (Ct) values obtained from a commercial RT-PCR test in terms of test duration, sensitivity, and specificity. Our results show that the samples with higher fluorescence levels correspond to those with low Ct values, suggesting a correlation between viral load and increased MB fluorescence. The proposed assay represents a fast (total duration of 2 h 20 min including amplification and fluorescence reading stages) and simple way of detecting SARS-CoV-2 in clinical samples from the upper respiratory tract.
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Affiliation(s)
- Josué Carvalho
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Jéssica Lopes-Nunes
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Joana Figueiredo
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - André Miranda
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Micaela Riscado
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Fani Sousa
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
- C4—Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Ana Paula Duarte
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
- C4—Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Sílvia Socorro
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Cândida Teixeira Tomaz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
- C4—Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Mafalda Felgueiras
- Serviço de Patologia Clínica do Centro Hospitalar Universitário Cova da Beira (CHUCB), 6200-251 Covilhã, Portugal; (M.F.); (R.T.); (C.F.)
| | - Rui Teixeira
- Serviço de Patologia Clínica do Centro Hospitalar Universitário Cova da Beira (CHUCB), 6200-251 Covilhã, Portugal; (M.F.); (R.T.); (C.F.)
| | - Conceição Faria
- Serviço de Patologia Clínica do Centro Hospitalar Universitário Cova da Beira (CHUCB), 6200-251 Covilhã, Portugal; (M.F.); (R.T.); (C.F.)
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
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8
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Bukkitgar SD, Shetti NP, Aminabhavi TM. Electrochemical investigations for COVID-19 detection-A comparison with other viral detection methods. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 420:127575. [PMID: 33162783 PMCID: PMC7605744 DOI: 10.1016/j.cej.2020.127575] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/07/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
Virus-induced infection such as SARS-CoV-2 is a serious threat to human health and the economic setback of the world. Continued advances in the development of technologies are required before the viruses undergo mutation. The low concentration of viruses in environmental samples makes the detection extremely challenging; simple, accurate and rapid detection methods are in urgent need. Of all the analytical techniques, electrochemical methods have the established capabilities to address the issues. Particularly, the integration of nanotechnology would allow miniature devices to be made available at the point-of-care. This review outlines the capabilities of electrochemical methods in conjunction with nanotechnology for the detection of SARS-CoV-2. Future directions and challenges of the electrochemical biosensors for pathogen detection are covered including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, and reusable biosensors for on-site monitoring, thereby providing low-cost and disposable biosensors.
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Key Words
- AIV H5N1, Avian influenza
- AIV, Avian influenza virus
- ASFV, African swine fever virus
- BVDV, Bovine viral diarrhea virus
- CGV, Chikungunya viruses
- CMV, Cucumber mosaic virus
- COVID-19
- CSFV, Classic swine fever virus
- CV, Cyclic voltammetry
- DAstV-1, Duck astrovirus 1
- DAstV-2, Duck astrovirus 2
- DENV, Dengue virus
- DEV, Duck enteritis virus
- DHAV-1, Duck hepatitis A virus 1
- DHAV-3, Duck hepatitis A virus 3
- DPV, Differential pulse voltammetry
- DRV-1, Duck reovirus 1
- DRV-2, Duck reovirus 2
- Detection
- EBV, Epstein-Barr virus
- EIS, Electric impedance spectroscopy
- EPC, External positive controls
- EV, Human enterovirus
- EV71, Human enterovirus 71
- Electrochemical sensor
- FMI SMOF, Fluorescence molecularly imprinted sensor based on a metal–organic framework
- GCE, Glassy carbon electrode
- GCFaV-1, Ginger chlorotic fleck associated virus 1
- GCFaV-2, Ginger chlorotic fleck-associated virus 2
- GEV VN-96, Gastroenteritis virus VN-96
- GPV, Goose parvovirus
- HHV, Human herpes virus 6
- HIAV, Human influenza A viruses
- HPB19, Human parvovirus B19
- HSV, Herpes simplex
- IAV, influenza A virus
- IEA, Interdigitated electrode array
- IMA, Interdigitated microelectrode array
- INAA, Isothermal nucleic acid amplification-based
- JEV, Japanese encephalitis virus
- LAMP, Loop-Mediated Isothermal Amplification
- LSV, Linear sweep voltammetry
- MERS, Middle East respiratory syndrome
- MIEC, Molecularly imprinted electrochemiluminescence
- MNV, Murine norovirus
- MeV, Measles virus
- NNV, Nervous necrosis virus
- Nanotechnology
- PBoV, Porcine bocavirus
- PCNAME, Pt-coated nanostructured alumina membrane electrode
- PCR
- PCRLFS, Polymerase Chain Reaction with a lateral flow strip with a lateral flow strip
- PCV, Porcine circovirus 3
- PEDV, Porcine epidemic diarrhoea virus
- PRRSV, porcine reproductive and respiratory syndrome virus
- PSV, Pseudorabies virus
- RCA, Rolling circle amplification
- RGO, Reduced graphene oxide
- RT-LAMP-VF, RT-LAMP and a vertical flow visualization strip
- RV, Rubella virus
- SARS, Severe acute respiratory syndrome
- SIVH1N1, Swine influenza virus
- SWV, Square wave voltammetry
- TGEV, transmissible gastroenteritis coronavirus
- TMUV, Tembusu virus
- USEGFET, Ultra-sensitive electrolyte-gated field-effect transistor
- VZV, Varicella-zoster virus
- VZV, varicella-Zoster virus
- Viruses
- ZV, Zika virus
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Affiliation(s)
- Shikandar D Bukkitgar
- Centre for Electrochemical Science and Materials, Department of Chemistry, K.L.E. Institute of Technology, Gokul, Hubballi 580030, Karnataka, India
| | - Nagaraj P Shetti
- Centre for Electrochemical Science and Materials, Department of Chemistry, K.L.E. Institute of Technology, Gokul, Hubballi 580030, Karnataka, India
| | - Tejraj M Aminabhavi
- Pharmaceutical Engineering, Soniya College of Pharmacy, Dharwad 580-007, India
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9
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Cuong HQ, Hai ND, Linh HT, Hieu NT, Anh NH, Ton T, Dong TC, Thao VT, Tuoi DTH, Tuan ND, Loan HTK, Long NT, Thang CM, Thao NTT, Lan PT. The Production of Standardized Samples with Known Concentrations for Severe Acute Respiratory Syndrome Coronavirus 2 RT-qPCR Testing Validation for Developing Countries in the Period of the Pandemic Era. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5516344. [PMID: 34368349 PMCID: PMC8337105 DOI: 10.1155/2021/5516344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic of pneumonia spreading around the world, leading to serious threats to public health and attracting enormous attention. There is an urgent need for sensitive diagnostic testing implementation to control and manage SARS-CoV-2 in public health laboratories. The quantitative reverse transcription PCR (RT-qPCR) assay is the gold standard method, but the sensitivity and specificity of SARS-CoV-2 testing are dependent on a number of factors. METHODS We synthesized RNA based on the genes published to estimate the concentration of inactivated virus samples in a biosafety level 3 laboratory. The limit of detection (LOD), linearity, accuracy, and precision were evaluated according to the bioanalytical method validation guidelines. RESULTS We found that the LOD reached around 3 copies/reaction. Furthermore, intra-assay precision, accuracy, and linearity met the accepted criterion with an RSD for copies of less than 25%, and linear regression met the accepted R 2 of 0.98. CONCLUSIONS We suggest that synthesized RNA based on the database of the NCBI gene bank for estimating the concentration of inactivated virus samples provides a potential opportunity for reliable testing to diagnose coronavirus disease 2019 (COVID-19) as well as limit the spread of the disease. This method may be relatively quick and inexpensive, and it may be useful for developing countries during the pandemic era. In the long term, it is also applicable for evaluation, verification, validation, and external quality assessment.
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Affiliation(s)
- Hoang Quoc Cuong
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Nguyen Duc Hai
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Hoang Thuy Linh
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Nguyen Trung Hieu
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Nguyen Hoang Anh
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Tran Ton
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Tran Cat Dong
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Vietnam
| | - Vu Thanh Thao
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Vietnam
| | - Do Thi Hong Tuoi
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Vietnam
| | - Nguyen Duc Tuan
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Vietnam
| | - Huynh Thi Kim Loan
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Long
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Cao Minh Thang
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Nguyen Thi Thanh Thao
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
| | - Phan Trong Lan
- Microbiology and Immunology Department, Planning Division, Medical Testing and Calibration Centers, Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam
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10
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Barth RF, Buja LM, Barth AL, Carpenter DE, Parwani AV. A Comparison of the Clinical, Viral, Pathologic, and Immunologic Features of Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Coronavirus 2019 (COVID-19) Diseases. Arch Pathol Lab Med 2021; 145:1194-1211. [PMID: 34232978 DOI: 10.5858/arpa.2020-0820-sa] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT -The purpose of this review is to compare three coronavirus diseases: severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) caused by SARS-CoV, MERS-CoV, and SARS-CoV-2 viruses, respectively. OBJECTIVE -To cover the following topics: clinical considerations, viral characteristics, pathology, immune response, pathogenesis, and the prognosis associated with each coronavirus human disease in humans. DATA SOURCES -Clinically, flu-like symptoms are usual at the time of presentation for all 3 diseases, but these vary from asymptomatic to severe multi-system involvement. The pathology associated with symptomatic SARS and COVID-19 has been well described, the most prominent of which is diffuse alveolar damage (DAD). The immune response to each of these viruses is highly complex and includes both humoral and cellular components that can have a significant impact on prognosis. In severe cases of COVID-19, a dysregulated innate host immune system can initiate a hyperinflammatory syndrome dominated by endothelial dysfunction that can lead to a hypercoagulable state with microthrombi, resulting in a systemic micro- and macro-vascular disease. CONCLUSIONS -The SARS and MERS epidemics have been limited, involving 7,500 and 2,500 individuals, respectively. In contrast, COVID-19 has resulted in a worldwide pandemic with over 177 million cases and 3.9 million deaths as of June 15, 2021, and fatality rates ranging from <0.1% to ~10% depending upon the country. Ending on a positive note, the development of a number of vaccines, at least six of which now are in clinical use, should mitigate and eventually control the devastating COVID-19 pandemic.
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Affiliation(s)
- Rolf F Barth
- Department of Pathology (RF Barth, Parwani), S.P. Technical Editor (Retired) Departments of Neurosurgery and Radiation Oncology (Carpenter), The Ohio State University Columbus, Ohio
| | - L Maximillian Buja
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas (Buja)
| | - Alison L Barth
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA (AL Barth)
| | - David E Carpenter
- Department of Pathology (RF Barth, Parwani), S.P. Technical Editor (Retired) Departments of Neurosurgery and Radiation Oncology (Carpenter), The Ohio State University Columbus, Ohio
| | - Anil V Parwani
- Department of Pathology (RF Barth, Parwani), S.P. Technical Editor (Retired) Departments of Neurosurgery and Radiation Oncology (Carpenter), The Ohio State University Columbus, Ohio
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11
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Ezhilan M, Suresh I, Nesakumar N. SARS-CoV, MERS-CoV and SARS-CoV-2: A Diagnostic Challenge. MEASUREMENT : JOURNAL OF THE INTERNATIONAL MEASUREMENT CONFEDERATION 2021; 168:108335. [PMID: 33519010 PMCID: PMC7833337 DOI: 10.1016/j.measurement.2020.108335] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/20/2020] [Accepted: 08/01/2020] [Indexed: 05/15/2023]
Abstract
The highly pathogenic MERS-CoV, SARS-CoV and SARS-CoV-2 cause acute respiratory syndrome and are often fatal. These new viruses pose major problems to global health in general and primarily to infection control and public health services. Accurate and selective assessment of MERS-CoV, SARS-CoV and SARS-CoV-2 would assist in the effective diagnosis of infected individual, offer clinical guidance and aid in assessing clinical outcomes. In this mini-review, we review the literature on various aspects, including the history and diversity of SARS-CoV-2, SARS-CoV and MERS-CoV, their detection methods in effective clinical diagnosis, clinical assessment of COVID-19, safety guidelines recommended by World Health Organization and legal regulations. This review article also deals with existing challenges and difficulties in the clinical diagnosis of SARS-CoV-2. Developing alternative diagnostic platforms by spotting the shortcomings of the existing point-of-care diagnostic devices would be useful in preventing future outbreaks.
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Affiliation(s)
- Madeshwari Ezhilan
- School of Electrical and Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Indhu Suresh
- School of Electrical and Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Noel Nesakumar
- School of Chemical and Biotechnology, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
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12
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Krishna E, Pathak VK, Prasad R, Jose H, Kumar MM. COVID-19 reinfection: Linked Possibilities and future outlook. J Family Med Prim Care 2020; 9:5445-5449. [PMID: 33532377 PMCID: PMC7842419 DOI: 10.4103/jfmpc.jfmpc_1672_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 12/28/2022] Open
Abstract
SARS-CoV-2 is the third major coronavirus epidemic to affect humans. There had been multiple instances of patients turning positive after recovering from SARS-2-CoV infection. Though many different theories emerge, false positive RT-PCR is logically the foremost cause and there is a general consensus that during quarantine re-infection from outside seems unlikely when strictly adhered to. As many new strains emerge worldwide during the course of on-going pandemic, the chances of re-infection cannot be ignored as it may contribute to false negative RT-PCR test results. SARS-2-CoV though a novel virus, is phylogenetically similar to SARS-like CoV with around 79% similarity. Studies on immunological response to these infections suggest that antibodies formed after infection confers immunity only for a short period of time before it starts to wane. Also studies on SARS-CoV-2 suggest that antibody formation and longevity of immunity in an individual is dependent on the strain of coronavirus, its severity and age of the person infected. All these considerations demand reviewing the treatment duration, discharge criteria, appropriate use of imaging techniques and importance of risk communication and health education to those recovered.
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Affiliation(s)
- Ekta Krishna
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Vineet Kumar Pathak
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Reshma Prasad
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Hannah Jose
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - M Mohan Kumar
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
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13
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Javalkote VS, Kancharla N, Bhadra B, Shukla M, Soni B, Goodin M, Bandyopadhyay A, Dasgupta S. CRISPR-based assays for rapid detection of SARS-CoV-2. Methods 2020; 203:594-603. [PMID: 33045362 PMCID: PMC7546951 DOI: 10.1016/j.ymeth.2020.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
COVID-19 pandemic posed an unprecedented threat to global public health and economies. There is no effective treatment of the disease, hence, scaling up testing for rapid diagnosis of SARS-CoV-2 infected patients and quarantine them from healthy individuals is one the best strategies to curb the pandemic. Establishing globally accepted easy-to-access diagnostic tests is extremely important to understanding the epidemiology of the present pandemic. While nucleic acid based tests are considered to be more sensitive with respect to serological tests but present gold standard qRT-PCR-based assays possess limitations such as low sample throughput, requirement for sophisticated reagents and instrumentation. To overcome these shortcomings, recent efforts of incorporating LAMP-based isothermal detection, and minimizing the number of reagents required are on rise. CRISPR based novel techniques, when merge with isothermal and allied technologies, promises to provide sensitive and rapid detection of SARS-CoV-2 nucleic acids. Here, we discuss and present compilation of state-of-the-art detection techniques for COVID-19 using CRISPR technology which has tremendous potential to transform diagnostics and epidemiology.
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Affiliation(s)
- Vivek S Javalkote
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Nagesh Kancharla
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Bhaskar Bhadra
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Manish Shukla
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Badrish Soni
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India
| | - Michael Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA
| | - Anindya Bandyopadhyay
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India.
| | - Santanu Dasgupta
- Reliance Industries Ltd, R&D-Synthetic Biology group, Reliance Corporate park, Navi Mumbai, India.
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14
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Prabhakar PK, Lakhanpal J. Recent advances in the nucleic acid-based diagnostic tool for coronavirus. Mol Biol Rep 2020; 47:9033-9041. [PMID: 33025503 PMCID: PMC7538041 DOI: 10.1007/s11033-020-05889-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
Abstract Recently in China, a novel coronavirus outbreak took place which caused pneumonia-like symptoms. This coronavirus belongs to the family of SARS and MERS and causes respiratory system disease known as COVID-19. At present we use polymerase chain reaction (PCR) based molecular biology methods for the detection of coronavirus. Other than these PCR based methods, some improved methods also exist such as microarray-based techniques, Real time-quantitative PCR, CRISPR-Cas13 based tools but almost all of the available methods have advantages and disadvantages. There are many limitations associated with this method and hence there is a need for a fast, more sensitive, and specific diagnostic tool which can detect a greater number of samples in less time. Here we have summarised currently available nucleic acid-based diagnostic methods for the detection of coronavirus and the need for developing a better technique for a fast and sensitive detection of coronavirus infections. Graphic abstract
Nucleic acid based detection tool for SARS-CoV-2.![]()
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Affiliation(s)
- Pranav Kumar Prabhakar
- Department of Medical Laboratory Sciences, Lovely Professional University, Punjab, 144411, India.
| | - Jyoti Lakhanpal
- Department of Medical Laboratory Sciences, Lovely Professional University, Punjab, 144411, India
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15
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Venter M, Richter K. Towards effective diagnostic assays for COVID-19: a review. J Clin Pathol 2020; 73:370-377. [PMID: 32404473 DOI: 10.1136/jclinpath-2020-206685] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/04/2022]
Abstract
Countries globally are affected by the COVID-19 pandemic, with nearly two million cases and 120 000 deaths occurring within 4 months of the discovery of the severe acute respiratory syndrome coronavirus-2 in December 2019 in China. Accurate diagnoses of cases is key in managing the pandemic by identification, isolation and treatment of patients and defining the epidemiology of the virus. By mid-January 2020, a scientist from China published the full genome of the virus, which facilitated the development of accurate molecular diagnostic assays. By the end of January 2020, the WHO, in collaboration with laboratories in Asia, Europe and the USA, published several real-time reverse transcriptase PCR (rtRT-PCR) protocols that allowed identification of cases and development of commercial assays. Clinical investigations facilitated development of accurate case definition and guidance for laboratories on the optimum specimens and procedures for diagnoses. Currently, laboratory-based rtRT-PCR is the recommended test for diagnoses of acute cases to ensure patients can be identified and isolated and to facilitate the public health response. However, due to delays in diagnoses, severe shortage of tests and laboratory capacity, point-of-care molecular or antigen tests are becoming more attractive. Although serological tests are not suitable for diagnoses of acute cases, they are important to define epidemiological questions, including attack rate in the population, and to identify immune individuals. This review aimed to summarise the current available information for diagnoses of cases and to aid laboratories and healthcare workers to select the best assays and procedures.
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Affiliation(s)
- Marietjie Venter
- Medical Virology, University of Pretoria, Pretoria, South Africa .,Zoonotic Arbo- and Respiratory Virus Research Program, Centre for Viral Zoonosis, University of Pretoria, Pretoria, South Africa
| | - Karin Richter
- Medical Virology, University of Pretoria, Pretoria, South Africa.,Lancet Laboratories, Pretoria, South Africa
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16
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Shen M, Zhou Y, Ye J, Abdullah Al-Maskri AA, Kang Y, Zeng S, Cai S. Recent advances and perspectives of nucleic acid detection for coronavirus. J Pharm Anal 2020; 10:97-101. [PMID: 32292623 PMCID: PMC7102540 DOI: 10.1016/j.jpha.2020.02.010] [Citation(s) in RCA: 285] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
The recent pneumonia outbreak caused by a novel coronavirus (SARS-CoV-2) is posing a great threat to global public health. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people’s lives and preventing epidemics. It is important to establish a quick standard diagnostic test for the detection of the infectious disease (COVID-19) to prevent subsequent secondary spread. Polymerase chain reaction (PCR) is regarded as a gold standard test for the molecular diagnosis of viral and bacterial infections with high sensitivity and specificity. Isothermal nucleic acid amplification is considered to be a highly promising candidate method due to its fundamental advantage in quick procedure time at constant temperature without thermocycler operation. A variety of improved or new approaches also have been developed. This review summarizes the currently available detection methods for coronavirus nucleic acid. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. This review summarizes the currently available detection methods for coronavirus nucleic acid. It will assist researchers in developing better techniques for timely and effective detection of coronavirus infection. It will help the establishment of SARS-CoV-2 RNA detection method which is useful for the early diagnosis of COVID-19.
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Affiliation(s)
- Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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17
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Reusken CBEM, Broberg EK, Haagmans B, Meijer A, Corman VM, Papa A, Charrel R, Drosten C, Koopmans M, Leitmeyer K. Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020. Euro Surveill 2020; 25:2000082. [PMID: 32046815 PMCID: PMC7029448 DOI: 10.2807/1560-7917.es.2020.25.6.2000082] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 12/29/2022] Open
Abstract
Timely detection of novel coronavirus (2019-nCoV) infection cases is crucial to interrupt the spread of this virus. We assessed the required expertise and capacity for molecular detection of 2019-nCoV in specialised laboratories in 30 European Union/European Economic Area (EU/EEA) countries. Thirty-eight laboratories in 24 EU/EEA countries had diagnostic tests available by 29 January 2020. A coverage of all EU/EEA countries was expected by mid-February. Availability of primers/probes, positive controls and personnel were main implementation barriers.
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Affiliation(s)
- Chantal B E M Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Viroscience department, Erasmus MC, Rotterdam, the Netherlands
| | - Eeva K Broberg
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Bart Haagmans
- Viroscience department, Erasmus MC, Rotterdam, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Remi Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marion Koopmans
- Viroscience department, Erasmus MC, Rotterdam, the Netherlands
| | - Katrin Leitmeyer
- European Centre for Disease Prevention and Control, Solna, Sweden
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18
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Abstract
The human coronaviruses have been shown to be a major player in clinical microbiology and frequently occur as pathogens responsible for mild to severe respiratory infections. Moreover, two of the most dangerous viral respiratory infections are caused by novel coronaviruses, namely, the SARS and the MERS coronavirus. This chapter briefly summarizes the most important facts and knowledge required for the appropriate laboratory diagnostics of infections caused by the human coronaviruses.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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19
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Noh JY, Yoon SW, Kim DJ, Lee MS, Kim JH, Na W, Song D, Jeong DG, Kim HK. Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR. Arch Virol 2017; 162:1617-1623. [PMID: 28220326 PMCID: PMC7086956 DOI: 10.1007/s00705-017-3281-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/02/2017] [Indexed: 12/31/2022]
Abstract
Since severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) share similar characteristics with respect to clinical signs, etiology, and transmission, methods for a rapid and accurate differential diagnosis are important. Therefore, the aim of this study was to develop a duplex real-time reverse transcription (RT)-PCR method for the simultaneous detection of these viruses. Primers and probes that target the conserved spike S2 region of human SARS-CoV, MERS-CoV, and their related bat CoVs were designed. The results of real-time RT-PCR showed specific reactions for each virus with adequate detection limits of 50–100 copies/mL and 5–100 copies/mL using pUC57-SARS-pS2 (a template for SARS-CoV) and pGEM-MERS-S2 (a template for MERS-CoV), respectively. In addition, this real-time RT-PCR system was able to detect the target viruses SARS-like bat CoV and MERS-CoV in bat fecal samples and sputum of MERS patients, respectively. Therefore, this newly developed real-time RT-PCR method is expected to detect not only SARS-CoV and MERS-CoV in humans but also several bat CoVs that are closely related to these viruses in bats.
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Affiliation(s)
- Ji Yeong Noh
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sun-Woo Yoon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Doo-Jin Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Moo-Seung Lee
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Ji-Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Woonsung Na
- Department of Pharmacy, College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Daesub Song
- Department of Pharmacy, College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Dae Gwin Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea. .,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Hye Kwon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
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20
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Abstract
It was widely believed in the late 1960s that infectious diseases had been conquered by vaccines and antibiotics and humans were no longer under threat by microbial pathogens. Yet, since that time more than 60 pathogens have been discovered that can cause serious emerging infectious diseases. Molecular methods have played critical roles in the discovery, monitoring, and clinical diagnostics of emerging pathogens. In this chapter, we present well-recognized emerging pathogens. We provide examples of the utility of molecular assays in research and clinical care of emerging infectious diseases. We also discuss some theoretical and practical limitations of molecular tests and the future prospects of expanding molecular diagnostics for emerging pathogens based on new advances of knowledge and technologies.
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21
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Structurally responsive oligonucleotide-based single-probe lateral-flow test for detection of miRNA-21 mimics. Anal Bioanal Chem 2015; 408:1475-85. [DOI: 10.1007/s00216-015-9250-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
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22
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Abstract
Real-time PCR or quantitative PCR (QPCR) is a powerful technique that allows measurement of PCR product while the amplification reaction proceeds. It incorporates the fluorescent element into conventional PCR as the calculation standard to provide a quantitative result. In this sense, fluorescent chemistry is the key component in QPCR. Till now, two types of fluorescent chemistries have been adopted in the QPCR systems: one is nonspecific probe and the other is specific. As a brilliant invention by Kramer et al. in 1996, molecular beacon is naturally suited as the reporting element in real-time PCR and has been adapted for many molecular biology applications. In this chapter, we briefly introduce the working principle of QPCR and overview different fluorescent chemistries, and then we focus on the applications of molecular beacons-like gene expression study, single-nucleotide polymorphisms and mutation detection, and pathogenic detection.
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Affiliation(s)
- Chaoyong James Yang
- Department of Chemical Biology College of Chemistry and Chemical Xiamen University, Xiamen, Fujian China, People's Republic
| | - Weihong Tan
- Department of Biomedical Engineering and Department of Chemistry Hunan University, Changsha, China, People's Republic
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23
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Han SX, Jia X, Ma JL, Zhu Q. Molecular beacons: a novel optical diagnostic tool. Arch Immunol Ther Exp (Warsz) 2013; 61:139-48. [PMID: 23292078 PMCID: PMC7079750 DOI: 10.1007/s00005-012-0209-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/20/2012] [Indexed: 12/31/2022]
Abstract
As a result of the efforts of the Human Genome Project and the rise in demand for molecular diagnostic assays, the development and optimization of novel hybridization probes have focused on speed, reliability, and accuracy in the identification of nucleic acids. Molecular beacons (MBs) are single-stranded, fluorophore-labeled nucleic acid probes that are capable of generating a fluorescent signal in the presence of target, but are dark in the absence of target. Because of the high specificity and sensitivity characteristics, MBs have been used in variety of fields. In this review, MBs are introduced and discussed as diagnostic tools in four sections: several technologies of MBs will be illustrated primarily; the limitation of MBs next; the third part is new fashions of MBs; and the last one is to present the application of MBs in disease diagnosis.
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Affiliation(s)
- Su-Xia Han
- Department of Oncology, The First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi 710061, People's Republic of China
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