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Venugopal DC, Viswanathan P, Ravindran S, Punnoose AM, Yasasve M, Dicky John DG, Prabhakar L, Ramanathan G, Sankarapandian S, Ramshankar V. Antifibrotic effect of silymarin on arecoline-induced fibrosis in primary human buccal fibroblasts: an in silico and in vitro analysis. Mol Biol Rep 2024; 51:303. [PMID: 38356030 DOI: 10.1007/s11033-023-09177-8] [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: 10/19/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024]
Abstract
BACKGROUND This study aimed to assess silymarin's anticancer and antifibrotic potential through in silico analysis and investigate its impact on in vitro arecoline-induced fibrosis in primary human buccal fibroblasts (HBF). METHODS & RESULTS The study utilized iGEMDOCK for molecular docking, evaluating nine bioflavonoids, and identified silymarin and baicalein as the top two compounds with the highest target affinity, followed by subsequent validation through a 100ns Molecular Dynamic Simulation demonstrating silymarin's stable behavior with Transforming Growth Factor Beta. HBF cell lines were developed from tissue samples obtained from patients undergoing third molar extraction. Arecoline, a known etiological factor in oral submucous fibrosis (OSMF), was employed to induce fibrogenesis in these HBFs. The inhibitory concentration (IC50) of arecoline was determined using the MTT assay, revealing dose-dependent cytotoxicity of HBFs to arecoline, with notable cytotoxicity observed at concentrations exceeding 50µM. Subsequently, the cytotoxicity of silymarin was assessed at 24 and 72 h, spanning concentrations from 5µM to 200µM, and an IC50 value of 143µM was determined. Real-time polymerase chain reaction (qPCR) was used to analyze the significant downregulation of key markers including collagen, epithelial-mesenchymal transition (EMT), stem cell, hypoxia, angiogenesis and stress markers in silymarin-treated arecoline-induced primary buccal fibroblast cells. CONCLUSION Silymarin effectively inhibited fibroblast proliferation and downregulated genes associated with cancer progression and EMT pathway, both of which are implicated in malignant transformation. To our knowledge, this study represents the first exploration of silymarin's potential as a novel therapeutic agent in an in vitro model of OSMF.
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Affiliation(s)
- Divyambika Catakapatri Venugopal
- Department of Oral Medicine and Radiology, Sri Ramachandra Dental College & Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, 600 116, India.
| | - Paramesh Viswanathan
- Stem Cell & Regenerative Biology Laboratory, Faculty of Clinical Research, Sri Ramachandra Institute of Higher Education & Research (DU), Porur, Chennai, 600 116, India
| | - Soundharya Ravindran
- Department of Preventive Oncology (Research), Cancer Institute (WIA), Adyar, Chennai, 600020, India
| | - Alan Mathew Punnoose
- Stem Cell & Regenerative Biology Laboratory, Faculty of Clinical Research, Sri Ramachandra Institute of Higher Education & Research (DU), Porur, Chennai, 600 116, India
| | - Madhavan Yasasve
- Department of Oral Medicine and Radiology, Sri Ramachandra Dental College & Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, 600 116, India
| | - Davis G Dicky John
- Department of Bioinformatics, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, 600 116, India
| | - Lavanya Prabhakar
- Department of Bioinformatics, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, 600 116, India
| | - Gnanasambandan Ramanathan
- Department of Biomedical Science, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Sathasivasubramanian Sankarapandian
- Department of Oral Medicine and Radiology, Sri Ramachandra Dental College & Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, 600 116, India
| | - Vijayalakshmi Ramshankar
- Department of Preventive Oncology (Research), Cancer Institute (WIA), Adyar, Chennai, 600020, India.
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Nakhaie M, Ghoreshi ZAS, Rukerd MRZ, Askarpour H, Arefinia N. Novel Mutations in the Non-Structure Protein 2 of SARS-CoV-2. Mediterr J Hematol Infect Dis 2023; 15:e2023059. [PMID: 38028396 PMCID: PMC10631707 DOI: 10.4084/mjhid.2023.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Mutation in the genome of SARS-CoV-2 may play a role in immune evasion, pathogenicity, and speed of its transmission. Our investigation aimed to evaluate the mutations that exist in the NSP2. Materials and Method RNA was extracted from nasopharyngeal swabs from 100 COVID-19 patients. RT-PCR was performed on all samples using NSP2-specific primers. Following gel electrophoresis, the bands were cut, purified, and sequenced using the Sanger method. After sequencing, 90 sequences could be used for further analysis. Bioinformatics analysis was conducted to investigate the effect of mutations on protein structure, stability, prediction of homology models, and phylogeny tree. Results The patients' mean age was 51.08. The results revealed that 8 of the 17 NSP2 mutations (R207C, T224I, G262V, T265I, K337D, N348S, G392D, and I431M) were missense. One deletion was also found in NSP2. Among NSP2 missense mutations studied, K337D and G392D increased structural stability while the others decreased it. The homology-designed models demonstrated that the homologies were comparable to the sequences of the Wuhan-HU-1 virus. Conclusion Our study suggested that the mutations K337D and G392D modulate the stability of NSP2, and tracking viral evolution should be implemented and vaccine development updated.
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Affiliation(s)
- Mohsen Nakhaie
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Zohreh-al-sadat Ghoreshi
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
- Student Research Committee Jiroft University of Medical Sciences, Jiroft, Iran
| | - Mohammad Rezaei Zadeh Rukerd
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hedyeh Askarpour
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Nasir Arefinia
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
- Bio Environmental Health Hazard Research Center, Jiroft University of Medical Sciences, Jiroft, Iran
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Venugopal DC, Caleb CL, Kirupakaran NP, Shyamsundar V, Ravindran S, Yasasve M, Krishnamurthy A, Harikrishnan T, Sankarapandian S, Ramshankar V. Clinicopathological Significance of Cancer Stem Cell Markers (OCT-3/4 and SOX-2) in Oral Submucous Fibrosis and Oral Squamous Cell Carcinoma. Biomedicines 2023; 11:biomedicines11041040. [PMID: 37189658 DOI: 10.3390/biomedicines11041040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Oral submucous fibrosis (OSMF) is highly prevalent in South East Asia with higher rates of malignant transformation in Indian subcontinent. Numerous biomarkers are now being studied to predict disease prognosis and detect malignant alterations at an early stage. Patients with clinically and biopsy-proven oral submucous fibrosis and oral squamous cell carcinoma were included in the study as the experimental group, while patients without a tobacco or betel nut habit who had their third molars surgically removed were included as the healthy control group. For the immunohistochemistry (IHC) investigation, 5-μm slices from formalin-fixed, paraffin-embedded tissue blocks (FFPE) were obtained. Fresh tissues (n = 45) from all three groups were collected and gene expression was studied using relative quantitation-based qPCR. The protein expression of octamer-binding transcription factor 3/4 (OCT 3/4) and sex-determining region Y-box 2 (SOX 2) was evaluated in the experimental group and compared with healthy controls. The IHC results showed a significant correlation with the expression of OCT 3/4 (p value = 0.000; χ2 = 20.244) and SOX 2 (p value = 0.006; χ2 = 10.101) among OSCC and OSMF patients in comparison to healthy controls. Both OCT 3/4 and SOX 2 showed overexpression of four-fold and three-fold in OSMF when compared to OSCC and healthy controls, respectively. This study shows the significant importance of cancer stem cell markers OCT 3/4 and SOX 2 to assess the disease prognosis in OSMF.
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Yip CCY, Sridhar S, Chan WM, Ip JD, Chu AWH, Leung KH, Cheng VCC, Yuen KY, To KKW. Development and Validation of a Novel COVID-19 nsp8 One-Tube RT-LAMP-CRISPR Assay for SARS-CoV-2 Diagnosis. Microbiol Spectr 2022; 10:e0196222. [PMID: 36445095 PMCID: PMC9769742 DOI: 10.1128/spectrum.01962-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
Accurate and simple diagnostic tests for coronavirus disease 2019 (COVID-19) are essential components of the pandemic response. In this study, we evaluated a one-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay coupled with clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-mediated endpoint detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical samples. RT-LAMP-CRISPR is fast and affordable, does not require bulky thermocyclers, and minimizes carryover contamination risk. Results can be read either visually or with a fluorometer. RT-LAMP-CRISPR assays using primers targeting a highly expressed nsp8 gene and previously described nucleocapsid (N) gene primers were designed. The analytical characteristics and diagnostic performance of RT-LAMP-CRISPR assays were compared to those of a commercial real-time RT-PCR E gene assay. The limits of detection (LODs) of the nsp8 and N RT-LAMP-CRISPR assays were 750 and 2,000 copies/mL, which were higher than that of the commercial real-time RT-PCR assay (31.3 copies/mL). Despite the higher LOD, RT-LAMP-CRISPR assays showed diagnostic sensitivity and specificity of 98.6% and 100%, respectively, equivalent to those of the real-time RT-PCR assay (P = 0.5). The median fluorescence reading from the nsp8 assay (378.3 raw fluorescence unit [RFU] [range, 215.6 to 592.6]) was significantly higher than that of the N gene assay (342.0 RFU [range, 143.0 to 576.6]) (P < 0.0001). In conclusion, we demonstrate that RT-LAMP-CRISPR assays using primers rationally designed from highly expressed gene targets are highly sensitive, specific, and easy to perform. Such assays are a valuable asset in resource-limited settings. IMPORTANCE Accurate tests for the diagnosis of SARS-CoV-2, the virus causing coronavirus disease 2019 (COVID-19), are important for timely treatment and infection control decisions. Conventional tests such as real-time reverse transcription-PCR (RT-PCR) require specialized equipment and are expensive. On the other hand, rapid antigen tests suffer from a lack of sensitivity. In this study, we describe a novel assay format for the diagnosis of COVID-19 that is based on principles of loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas chemistry. A major advantage of this assay format is that it does not require expensive equipment to perform, and results can be read visually. This method proved to be fast, easy to perform, and inexpensive. The test compared well against an RT-PCR assay in terms of the ability to detect SARS-CoV-2 RNA in clinical samples. No false-positive test results were observed. The new assay format is ideal for SARS-CoV-2 diagnosis in resource-limited settings.
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Grants
- Health@InnoHK, Innovation and Technology Commission of Hong Kong
- Donations from Richard Yu and Carol Yu, the Shaw Foundation Hong Kong, Michael Seak-Kan Tong, The Hui Ming, Chan Yin Chuen Memorial Charitable Foundation
- Donations from Marina Man-Wai Lee, the Jessie & George Ho Charitable Foundation, Kai Chong Tong, Tse Kam Ming Laurence, Foo Oi Foundation Limited, Betty Hing-Chu Lee, and Ping Cham So
- Hui Hoy and Chow Sin Lan Charity Fund (許海周倩蘭慈善基金有限公司)
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
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Hossain MAM, Uddin SMK, Hashem A, Mamun MA, Sagadevan S, Johan MR, Johan MR. Advancements in Detection Approaches of Severe Acute Respiratory Syndrome Coronavirus 2. Malays J Med Sci 2022; 29:15-33. [PMID: 36818907 PMCID: PMC9910375 DOI: 10.21315/mjms2022.29.6.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/30/2021] [Indexed: 12/24/2022] Open
Abstract
Diagnostic testing to identify individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in selecting appropriate treatments, saving people's lives and preventing the global pandemic of COVID-19. By testing on a massive scale, some countries could successfully contain the disease spread. Since early viral detection may provide the best approach to curb the disease outbreak, the rapid and reliable detection of coronavirus (CoV) is therefore becoming increasingly important. Nucleic acid detection methods, especially real-time reverse transcription polymerase chain reaction (RT-PCR)-based assays are considered the gold standard for COVID-19 diagnostics. Some non-PCR-based molecular methods without thermocycler operation, such as isothermal nucleic acid amplification have been proved promising. Serologic immunoassays are also available. A variety of novel and improved methods based on biosensors, Clustered-Regularly Interspaced Short Palindromic Repeats (CRISPR) technology, lateral flow assay (LFA), microarray, aptamer etc. have also been developed. Several integrated, random-access, point-of-care (POC) molecular devices are rapidly emerging for quick and accurate detection of SARS-CoV-2 that can be used in the local hospitals and clinics. This review intends to summarize the currently available detection approaches of SARS-CoV-2, highlight gaps in existing diagnostic capacity, and propose potential solutions and thus may assist clinicians and researchers develop better technologies for rapid and authentic diagnosis of CoV infection.
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Affiliation(s)
- M. A. Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Syed Muhammad Kamal Uddin
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Abu Hashem
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia,Microbial Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Mohammad Al Mamun
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia,Department of Chemistry, Jagannath University, Dhaka, Bangladesh
| | - Suresh Sagadevan
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
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Identification of mutations in SARS-CoV-2 PCR primer regions. Sci Rep 2022; 12:18651. [PMID: 36333366 PMCID: PMC9636223 DOI: 10.1038/s41598-022-21953-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as "prone to misclassification" vs. "likely to be correctly detected" by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.
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Moorthy A, Venugopal DC, Shyamsundar V, Madhavan Y, Ravindran S, Kuppuloganathan M, Krishnamurthy A, Sankarapandian S, Ganapathy V, Ramshankar V. Identification of EGFR as a Biomarker in Saliva and Buccal Cells from Oral Submucous Fibrosis Patients—A Baseline Study. Diagnostics (Basel) 2022; 12:diagnostics12081935. [PMID: 36010285 PMCID: PMC9406318 DOI: 10.3390/diagnostics12081935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Oral Submucous Fibrosis (OSMF) is a chronic debilitating disease more frequently encountered in the South-East Asian population. This disease represents a public health priority as it is grouped within oral potentially malignant disorders, with malignant transformation rates of around 7–19%. Hence, early identification of high-risk OSMF patients is of the utmost importance to prevent malignant transformation. Among various biomarkers, EGFR overexpression has an unfavorable clinical outcome, poor prognosis, and low survival rates in Oral Squamous Cell Carcinoma (OSCC). The current study aimed to evaluate the expression of EGFR in saliva and exfoliated buccal cells of OSMF. Immunoexpression of EGFR was observed in healthy controls (n = 11), OSCC (n = 106), and OPMD with dysplasia (n = 56), which showed significant expression with increasing grades of dysplasia and OSCC. EGFR expression was evaluated in saliva and exfoliated buccal cells of healthy controls (n = 15), OSMF (n = 24), and OSCC (n = 10) patients using ELISA, which revealed significant expression in OSMF and OSCC. Validation studies were also performed using real-time PCR (RT-PCR) to compare gene expression in healthy controls (n = 9), OSMF (n = 9), and OSCC (n = 25), which showed significant 18-fold upregulation in OSCC and three-fold upregulation in OSMF when compared to healthy controls. Hence, saliva and exfoliated buccal cells could be considered as potential non-invasive diagnostic samples for the evaluation of high-risk patients of OSMF using EGFR as a biomarker.
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Affiliation(s)
- Abirami Moorthy
- Department of Oral Medicine and Radiology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai 600116, India
| | - Divyambika Catakapatri Venugopal
- Department of Oral Medicine and Radiology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai 600116, India
- Correspondence: (D.C.V.); (V.R.)
| | - Vidyarani Shyamsundar
- Centre for Oral Cancer Prevention and Research, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai 600100, India
| | - Yasasve Madhavan
- Department of Oral Medicine and Radiology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai 600116, India
| | - Soundharya Ravindran
- Department of Preventive Oncology (Research), Cancer Institute (WIA), Adyar, Chennai 600020, India
| | | | - Arvind Krishnamurthy
- Department of Surgical Oncology, Cancer Institute (WIA), Adyar, Chennai 600020, India
| | | | - Vani Ganapathy
- Department of Biochemistry, University of Madras, Chennai 600025, India
| | - Vijayalakshmi Ramshankar
- Department of Preventive Oncology (Research), Cancer Institute (WIA), Adyar, Chennai 600020, India
- Correspondence: (D.C.V.); (V.R.)
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8
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Jeong H, Lee S, Ko J, Ko M, Seo HW. Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design. Genes Genomics 2022; 44:899-912. [PMID: 35653026 PMCID: PMC9160177 DOI: 10.1007/s13258-022-01264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/03/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND As the rapidly evolving characteristic of SARS-CoV-2 could result in false negative diagnosis, the use of as much sequence data as possible is key to the identification of conserved viral sequences. However, multiple alignment of massive genome sequences is computationally intensive. OBJECTIVE To extract conserved sequences from SARS-CoV-2 genomes for the design of diagnostic PCR primers using a bioinformatics approach that can handle massive genomic sequences efficiently. METHODS A total of 230,163 full-length viral genomes were retrieved from the NCBI SARS-CoV-2 Resources and GISAID EpiCoV database. This number was reduced to 14.11% following removal of 5'-/3'-untranslated regions and sequence dereplication. Fast, reference-based, multiple sequence alignments identified conserved sequences and specific primer sets were designed against these regions using a conventional tool. Primer sets chosen among the candidates were evaluated by in silico PCR and RT-qPCR. RESULTS Out of 17 conserved sequences (totaling 4.3 kb), two primer sets targeting the nsp2 and ORF3a genes were picked that exhibited > 99.9% in silico amplification coverage against the original dataset (230,163 genomes) when a 5% mismatch between the primers and target was allowed. In addition, the primer sets successfully detected nine SARS-CoV-2 variant RNA samples (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Iota, and Kappa) in experimental RT-qPCR validations. CONCLUSION In addition to the RdRp, E, N, and S genes that are targeted commonly, our approach can be used to identify novel primer targets in SARS-CoV-2 and should be a priority strategy in the event of novel SARS-CoV-2 variants or other pandemic outbreaks.
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Affiliation(s)
- Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Siseok Lee
- NanoHelix Co., Ltd. 43-15, Daejeon, 34014, Republic of Korea
| | - Junsang Ko
- NanoHelix Co., Ltd. 43-15, Daejeon, 34014, Republic of Korea
| | - Minsu Ko
- NanoHelix Co., Ltd. 43-15, Daejeon, 34014, Republic of Korea
| | - Hwi Won Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
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9
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Negrón DA, Kang J, Mitchell S, Holland MY, Wist S, Voss J, Brinkac L, Jennings K, Guertin S, Goodwin BG, Sozhamannan S. Impact of SARS-CoV-2 Mutations on PCR Assay Sequence Alignment. Front Public Health 2022; 10:889973. [PMID: 35570946 PMCID: PMC9096222 DOI: 10.3389/fpubh.2022.889973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022] Open
Abstract
Real-time reverse transcription polymerase chain reaction (RT-PCR) assays are the most widely used molecular tests for the detection of SARS-CoV-2 and diagnosis of COVID-19 in clinical samples. PCR assays target unique genomic RNA regions to identify SARS-CoV-2 with high sensitivity and specificity. In general, assay development incorporates the whole genome sequences available at design time to be inclusive of all target species and exclusive of near neighbors. However, rapid accumulation of mutations in viral genomes during sustained growth in the population can result in signature erosion and assay failures, creating situational blind spots during a pandemic. In this study, we analyzed the signatures of 43 PCR assays distributed across the genome against over 1.6 million SARS-CoV-2 sequences. We present evidence of significant signature erosion emerging in just two assays due to mutations, while adequate sequence identity was preserved in the other 41 assays. Failure of more than one assay against a given variant sequence was rare and mostly occurred in the two assays noted to have signature erosion. Assays tended to be designed in regions with statistically higher mutations rates. in silico analyses over time can provide insights into mutation trends and alert users to the emergence of novel variants that are present in the population at low proportions before they become dominant. Such routine assessment can also potentially highlight false negatives in test samples that may be indicative of mutations having functional consequences in the form of vaccine and therapeutic failures. This study highlights the importance of whole genome sequencing and expanded real-time monitoring of diagnostic PCR assays during a pandemic.
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Affiliation(s)
| | - June Kang
- Noblis, Inc., Reston, VA, United States
| | | | | | | | - Jameson Voss
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States
| | | | | | | | - Bruce G Goodwin
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States
| | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States.,Logistics Management Institute, Tysons, VA, United States
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10
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CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants. Viruses 2022; 14:v14030561. [PMID: 35336968 PMCID: PMC8955889 DOI: 10.3390/v14030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022] Open
Abstract
The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.
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Amara U, Rashid S, Mahmood K, Nawaz MH, Hayat A, Hassan M. Insight into prognostics, diagnostics, and management strategies for SARS CoV-2. RSC Adv 2022; 12:8059-8094. [PMID: 35424750 PMCID: PMC8982343 DOI: 10.1039/d1ra07988c] [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: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 01/08/2023] Open
Abstract
The foremost challenge in countering infectious diseases is the shortage of effective therapeutics. The emergence of coronavirus disease (COVID-19) outbreak has posed a great menace to the public health system globally, prompting unprecedented endeavors to contain the virus. Many countries have organized research programs for therapeutics and management development. However, the longstanding process has forced authorities to implement widespread infrastructures for detailed prognostic and diagnostics study of severe acute respiratory syndrome (SARS CoV-2). This review discussed nearly all the globally developed diagnostic methodologies reported for SARS CoV-2 detection. We have highlighted in detail the approaches for evaluating COVID-19 biomarkers along with the most employed nucleic acid- and protein-based detection methodologies and the causes of their severe downfall and rejection. As the variable variants of SARS CoV-2 came into the picture, we captured the breadth of newly integrated digital sensing prototypes comprised of plasmonic and field-effect transistor-based sensors along with commercially available food and drug administration (FDA) approved detection kits. However, more efforts are required to exploit the available resources to manufacture cheap and robust diagnostic methodologies. Likewise, the visualization and characterization tools along with the current challenges associated with waste-water surveillance, food security, contact tracing, and their role during this intense period of the pandemic have also been discussed. We expect that the integrated data will be supportive and aid in the evaluation of sensing technologies not only in current but also future pandemics.
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Affiliation(s)
- Umay Amara
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Sidra Rashid
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Khalid Mahmood
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
| | - Mian Hasnain Nawaz
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Akhtar Hayat
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Maria Hassan
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
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12
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Le TB, Kim HK, Ahn MJ, Zanin M, Lo VT, Ling S, Jiang Z, Kang JA, Bae PK, Kim YS, Kim S, Wong SS, Jeong DG, Yoon SW. Diagnostic performance and clinical feasibility of a novel one-step RT-qPCR assay for simultaneous detection of multiple severe acute respiratory syndrome coronaviruses. Arch Virol 2022; 167:871-879. [PMID: 35137250 PMCID: PMC8885489 DOI: 10.1007/s00705-022-05383-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Other coronaviruses (CoVs) can also infect humans, although the majority cause only mild respiratory symptoms. Because early diagnosis of SARS-CoV-2 is critical for preventing further transmission events and improving clinical outcomes, it is important to be able to distinguish SARS-CoV-2 from other SARS-related CoVs in respiratory samples. Therefore, we developed and evaluated a novel reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the genes encoding the spike (S) and membrane (M) proteins to enable the rapid identification of SARS-CoV-2, including several new circulating variants and other emerging SARS-like CoVs. By analysis of in vitro-transcribed mRNA, we established multiplex RT-qPCR assays capable of detecting 5 × 10° copies/reaction. Using RNA extracted from cell culture supernatants, our multiple simultaneous SARS-CoV-2 assays had a limit of detection of 1 × 10° TCID50/mL and showed no cross-reaction with human CoVs or other respiratory viruses. We also validated our method using human clinical samples from patients with COVID-19 and healthy individuals, including nasal swab and sputum samples. This novel one-step multiplex RT-qPCR assay can be used to improve the laboratory diagnosis of human-pathogenic CoVs, including SARS-CoV-2, and may be useful for the identification of other SARS-like CoVs of zoonotic origin.
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Affiliation(s)
- Tran Bac Le
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea
| | - Hye Kwon Kim
- Chungbuk National University, Cheongju, South Korea
| | - Min-Ju Ahn
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea
| | - Mark Zanin
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China.,School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Van Thi Lo
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea
| | - Shiman Ling
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhanpeng Jiang
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Jung-Ah Kang
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Pan Kee Bae
- BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yeon-Sook Kim
- Chungnam National University School of Medicine, Daejeon, South Korea
| | | | - Sook-San Wong
- State Key Laboratory for Respiratory Diseases, Guangzhou Medical University, Guangzhou, Guangdong Province, China. .,School of Public Health, The University of Hong Kong, Hong Kong, China.
| | - Dae Gwin Jeong
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea. .,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea.
| | - Sun-Woo Yoon
- Bio-nanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea. .,Bio-Analytical Science Division, University of Science and Technology, Daejeon, South Korea.
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13
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Ilkhani H, Hedayat N, Farhad S. Novel approaches for rapid detection of COVID-19 during the pandemic: A review. Anal Biochem 2021; 634:114362. [PMID: 34478703 PMCID: PMC8406551 DOI: 10.1016/j.ab.2021.114362] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 02/03/2023]
Abstract
The rapid spread of the SARS-CoV-2 virus that caused the COVID-19 disease, has highlighted our urgent need for sensitive, fast and accurate diagnostic technologies. In fact, one of the main challenges for flatting COVID-19 spread charts is the ability to accurately and rapidly identify asymptomatic cases that result in spreading the virus to close contacts. SARS-CoV-2 virus mutation is also relatively rapid, which makes the detection of COVID-19 diseases still crucial even after the vaccination. Conventional techniques, which are commercially available have focused on clinical manifestation, along with molecular and serological detection tools that can identify the SARS-CoV-2 virus however, owing to various disadvantages including low specificity and sensitivity, a quick, low cost and easy approach is needed for diagnosis of COVID-19. Scientists are now showing extensive interest in an effective portable and simple detection method to diagnose COVID-19. There are several novel methods and approaches that are considered viable advanced systems that can meet the demands. This study reviews the new approaches and sensing technologies that work on COVID-19 diagnosis for easy and successful detection of SARS-CoV-2 virus.
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Affiliation(s)
- Hoda Ilkhani
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, 87144, United States,Corresponding author
| | - Nader Hedayat
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, United States
| | - Siamak Farhad
- Advanced Energy & Sensor Lab, Department of Mechanical Engineering, The University of Akron, Akron, OH, 44325, United States,Corresponding author
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14
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Hassani Nejad Z, Fatemi F, Ranaei Siadat SE. An outlook on coronavirus disease 2019 detection methods. J Pharm Anal 2021; 12:205-214. [PMID: 34777894 PMCID: PMC8578030 DOI: 10.1016/j.jpha.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/22/2021] [Accepted: 11/07/2021] [Indexed: 12/15/2022] Open
Abstract
Diagnostic testing plays a fundamental role in the mitigation and containment of coronavirus disease 2019 (COVID-19), as it enables immediate quarantine of those who are infected and contagious and is essential for the epidemiological characterization of the virus and estimating the number of infected cases worldwide. Confirmation of viral infections, such as COVID-19, can be achieved through two general approaches: nucleic acid amplification tests (NAATs) or molecular tests, and serological or antibody-based tests. The genetic material of the pathogen is detected in NAAT, and in serological tests, host antibodies produced in response to the pathogen are identified. Other methods of diagnosing COVID-19 include radiological imaging of the lungs and in vitro detection of viral antigens. This review covers different approaches available to diagnosing COVID-19 by outlining their advantages and shortcomings, as well as appropriate indications for more accurate testing. Diagnostic tests to detect coronavirus disease 2019 (COVID-19). Advantages and disadvantages associated with each detection method. Implications for a more accurate and rapid testing of COVID-19 or other similar future emergent viruses.
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Affiliation(s)
- Zahra Hassani Nejad
- Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, 1417935840, Iran
| | - Fataneh Fatemi
- Department of Protein Research, Protein Research Center, Shahid Beheshti University, Tehran, 1983969411, Iran
- Corresponding author.
| | - Seyed Ehsan Ranaei Siadat
- Sobhan Recombinant Protein Company, Research and Development Department, Tehran, 1654120871, Iran
- Corresponding author.
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15
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Asif M, Xu Y, Xiao F, Sun Y. Diagnosis of COVID-19, vitality of emerging technologies and preventive measures. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 423:130189. [PMID: 33994842 PMCID: PMC8103773 DOI: 10.1016/j.cej.2021.130189] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 05/18/2023]
Abstract
Coronavirus diseases-2019 (COVID-19) is becoming increasing serious and major threat to public health concerns. As a matter of fact, timely testing enhances the life-saving judgments on treatment and isolation of COVID-19 infected individuals at possible earliest stage which ultimately suppresses spread of infectious diseases. Many government and private research institutes and manufacturing companies are striving to develop reliable tests for prompt quantification of SARS-CoV-2. In this review, we summarize existing diagnostic methods as manual laboratory-based nucleic acid assays for COVID-19 and their limitations. Moreover, vitality of rapid and point of care serological tests together with emerging biosensing technologies has been discussed in details. Point of care tests with characteristics of rapidity, accurateness, portability, low cost and requiring non-specific devices possess great suitability in COVID-19 diagnosis and detection. Besides, this review also sheds light on several preventive measures to track and manage disease spread in current and future outbreaks of diseases.
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Affiliation(s)
- Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yun Xu
- Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430205, China
| | - Fei Xiao
- Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430205, China
| | - Yimin Sun
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
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16
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CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers. Genomics 2021; 113:3174-3184. [PMID: 34293476 PMCID: PMC8289724 DOI: 10.1016/j.ygeno.2021.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/30/2021] [Accepted: 07/17/2021] [Indexed: 01/17/2023]
Abstract
As mutations in SARS-CoV-2 virus accumulate rapidly, novel primers that amplify this virus sensitively and specifically are in demand. We have developed a webserver named CoVrimer by which users can search for and align existing or newly designed conserved/degenerate primer pair sequences against the viral genome and assess the mutation load of both primers and amplicons. CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations, from which potential primer pairs are designed and provided to the user for filtering based on generalized and SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation. Consequently, CoVrimer is likely to help researchers with the challenges posed by viral evolution and is freely available at http://konulabapps.bilkent.edu.tr:3838/CoVrimer/.
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17
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Zheng YX, Wang L, Kong WS, Chen H, Wang XN, Meng Q, Zhang HN, Guo SJ, Jiang HW, Tao SC. Nsp2 has the potential to be a drug target revealed by global identification of SARS-CoV-2 Nsp2-interacting proteins. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1134-1141. [PMID: 34159380 DOI: 10.1093/abbs/gmab088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health threat since December 2019, and there is still no highly effective drug to control the pandemic. To facilitate drug target identification for drug development, studies on molecular mechanisms, such as SARS-CoV-2 protein interactions, are urgently needed. In this study, we focused on Nsp2, a non-structural protein with largely unknown function and mechanism. The interactome of Nsp2 was revealed through the combination of affinity purification mass spectrometry (AP-MS) and stable isotope labeling by amino acids in cell culture (SILAC), and 84 proteins of high-confidence were identified. Gene ontology analysis demonstrated that Nsp2-interacting proteins are involved in several biological processes such as endosome transport and translation. Network analysis generated two clusters, including ribosome assembly and vesicular transport. Bio-layer interferometry (BLI) assay confirmed the bindings between Nsp2- and 4-interacting proteins, i.e. STAU2 (Staufen2), HNRNPLL, ATP6V1B2, and RAP1GDS1 (SmgGDS), which were randomly selected from the list of 84 proteins. Our findings provide insights into the Nsp2-host interplay and indicate that Nsp2 may play important roles in SARS-CoV-2 infection and serve as a potential drug target for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Sha Kong
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Meng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
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18
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Ma J, Chen Y, Wu W, Chen Z. Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2. Virol Sin 2021; 36:1104-1112. [PMID: 34398430 PMCID: PMC8365134 DOI: 10.1007/s12250-021-00431-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 has become a global pandemic threatening human health and safety. It is urgent to find effective therapeutic agents and targets with the continuous emergence of novel mutant strains. The knowledge of the molecular basis and pathogenesis of SARS-CoV-2 in host cells requires to be understood comprehensively. The unknown structure and function of nsp2 have hindered our understanding of its role in SARS-CoV-2 infection. Here, we report the crystal structure of the N-terminal of SARS-CoV-2 nsp2 to a high resolution of 1.96 Å. This novel structure contains three zinc fingers, belonging to the C2H2, C4, and C2HC types, respectively. Structure analysis suggests that nsp2 may be involved in binding nucleic acids and regulating intracellular signaling pathways. The binding to single or double-stranded nucleic acids was mainly through the large positively charged region on the surface of nsp2, and K111, K112, K113 were key residues. Our findings lay the foundation for a better understanding of the relationship between structure and function for nsp2. It is helpful to make full use of nsp2 as further research and development of antiviral targets and drug design.
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Affiliation(s)
- Jun Ma
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yiyun Chen
- Cherry Creek High School, 9300 East Union Avenue, Greenwood Village, 80111, USA
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Qasem A, Shaw AM, Elkamel E, Naser SA. Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations. Curr Issues Mol Biol 2021; 43:728-748. [PMID: 34287238 PMCID: PMC8929116 DOI: 10.3390/cimb43020053] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
The ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a severe threat to human health and the global economy and has resulted in overwhelming stress on health care systems worldwide. Despite the global health catastrophe, especially in the number of infections and fatalities, the COVID-19 pandemic has also revolutionized research and discovery with remarkable success in diagnostics, treatments, and vaccine development. The use of many diagnostic methods has helped establish public health guidelines to mitigate the spread of COVID-19. However, limited information has been shared about these methods, and there is a need for the scientific community to learn about these technologies, in addition to their sensitivity, specificity, and limitations. This review article is focused on providing insights into the major methods used for SARS-CoV-2 detection. We describe in detail the core principle of each method, including molecular and serological approaches, along with reported claims about the rates of false negatives and false positives, the types of specimens needed, and the level of technology and the time required to perform each test. Although this study will not rank or prioritize these methods, the information will help in the development of guidelines and diagnostic protocols in clinical settings and reference laboratories.
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Affiliation(s)
| | | | | | - Saleh A. Naser
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA; (A.Q.); (A.M.S.); (E.E.)
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20
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Abdul Bari AB, Samuel PJ. Road toward universal COVID-19 testing method - A review. J Immunoassay Immunochem 2021; 42:335-346. [PMID: 33689569 DOI: 10.1080/15321819.2021.1895214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Patients infected with novel coronavirus exhibit a wide range of symptoms from common cold to pneumonia. Furthermore, several cases have been reported as asymptomatic across the globe. Since there are no conclusive clinical manifestations, clinicians have to rely more on laboratory diagnostic methods for confirmation of coronavirus disease. Hematological and biochemical tests are found to be of more prognostic value. Genetic assays by means of rRT-PCR technique is time-consuming but seems to be a more sensitive and specific test among the available testing methods for diagnosis of the coronavirus disease. Radiological imaging of the CT chest of the confirmed positive patients taken during the initial few days doesn't show any significant changes. However, from the second week onward a ground glass lesion pattern is observed. The immunological tests which are being used as a rapid testing method are found to be more false test negative. Hence, based on the effectiveness of various testing methods, it can be concluded that either rRT-PCR or mass antibody testing has to be done, and it has to be compared with CT chest in order to avoid false negatives across the globe which may help in the prevention of community spread of the disease.
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21
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Yip CCY, Leung KH, Ng ACK, Chan KH, To KKW, Chan JFW, Hung IFN, Cheng VCC, Sridhar S. Comparative evaluation of a dual-target real-time RT-PCR assay for COVID-19 diagnosis and assessment of performance in pooled saliva and nasopharyngeal swab samples. Expert Rev Mol Diagn 2021; 21:741-747. [PMID: 34014785 PMCID: PMC8182820 DOI: 10.1080/14737159.2021.1933445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 05/19/2021] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Sensitive molecular diagnostic assays are essential for COVID-19 diagnosis. We evaluated the Hecin Scientific SARS-CoV-2 nucleic acid test kit, a dual-target real-time RT-PCR assay targeting the SARS-CoV-2 N and ORF1ab genes. METHODS The Hecin test kit's diagnostic performance in detecting SARS-CoV-2 RNA was compared to the LightMix Modular SARS and Wuhan CoV E-gene kit (TIB Molbiol) and an in-house single-tube nested real-time RT-PCR using 296 clinical specimens, 11 proficiency testing samples, and 30 low-positive deep throat saliva and nasopharyngeal swab (NPS) samples pooled into negative samples in ratios of 1:5, 1:10, and 1:30. RESULTS The limit-of-detection of the Hecin test kit was around 500 dC/mL for the N and ORF1ab targets. Sensitivity and specificity of the Hecin test kit were 98.1% (95% CI: 93.4-99.8%) and 100% (98.1-100%), respectively, when measured against the reference method. The Hecin test kit showed fair sensitivity (80%) in low-positive NPS samples pooled in ratios of 1:5 and 1:10. Its performance in pooled samples could be dramatically improved by adjusting the assay Ct cutoff. CONCLUSION The Hecin test kit enables sensitive and specific detection of SARS-CoV-2 in clinical samples and pooled samples.
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Affiliation(s)
- Cyril C. Y. Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Anthony C. K. Ng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kelvin K. W. To
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jasper F. W Chan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ivan F. N. Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Vincent C. C. Cheng
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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22
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Gadkar VJ, Goldfarb DM, Young V, Watson N, Al-Rawahi GN, Srigley JA, Tilley P. Development and validation of a new triplex real-time quantitative reverse Transcriptase-PCR assay for the clinical detection of SARS-CoV-2. Mol Cell Probes 2021; 58:101744. [PMID: 34089805 PMCID: PMC8176879 DOI: 10.1016/j.mcp.2021.101744] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/19/2021] [Accepted: 05/27/2021] [Indexed: 12/03/2022]
Abstract
To increase the repertoire of PCR based laboratory developed tests (LDTs) for the detection of SARS-CoV-2, we describe a new multiplex assay (SORP), targeting the SARS-CoV-2's, Spike and ORF8 genes. The widely used human RNaseP internal control was modified to specifically co-amplify the RNaseP mRNA. The SORP triplex assay was tested on a cohort (n = 372; POS = 144/NEG = 228) of nasopharyngeal flocked swab (NPFS) specimens, previously tested for the presence of SARS-CoV-2 using a PCR assay targeting E and RdRp genes. The overall sensitivity and specificity of the SORP assay was: 99.31% (95% CI: 96.22–99.98%), 100.0% (95% CI: 98.4–100%) respectively. The SORP assay could also detect a panel of variants of concern (VOC) from the B1.1.7 (UK) and B1.351 (SA) lineage. In summary, access to a repertoire of new SARS-CoV-2 LDT's would assist diagnostic laboratories in developing strategies to overcome some of the testing issues encountered during high-throughput SARS-CoV-2 testing.
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Affiliation(s)
- Vijay J Gadkar
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada; Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
| | - David M Goldfarb
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada; Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Virginia Young
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Nicole Watson
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Ghada N Al-Rawahi
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada; Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Jocelyn A Srigley
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada; Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter Tilley
- Department of Pathology & Laboratory Medicine, Division of Microbiology, Virology & Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada; Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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23
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Melo-Vallès A, Ballesté-Delpierre C, Vila J. Review of the Microbiological Diagnostic Approaches of COVID-19. Front Public Health 2021; 9:592500. [PMID: 33987157 PMCID: PMC8110909 DOI: 10.3389/fpubh.2021.592500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
On March 12, the World Health Organization declared a pandemic following the exponential increase of SARS-CoV-2 cases. The rapid spread of the virus is due to both its high infectivity and the free circulation of unrecognized infectious cases. Thus, diagnostic testing is a key element to prevent further dissemination of the virus. Urged by WHO's call, laboratories worldwide have been working on nucleic acid tests protocols and immunoassays that became available, albeit poorly validated, within a comparatively short time. Since then, external studies evaluating these diagnostic tests have been published. The present study is a review of the COVID-19 diagnostic approaches, discussing both direct and indirect microbiological diagnoses. A compendium of the literature on commercial assays kits available to date is provided together with the conclusions drawn as well as RT-PCR protocols published by the WHO. Briefly, diagnostic accuracy varies according to time elapsed since symptom onset and evolves together with understanding of the COVID-19 disease. Taking into account all these variables will allow determining the most adequate diagnostic test to use and how to optimize diagnostic testing for COVID-19.
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Affiliation(s)
- Ada Melo-Vallès
- Bachelor of Human Biology, Fourth Grade Student, Life and Health Sciences Faculty, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Jordi Vila
- ISGlobal Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Centre for Biomedical Diagnosis, Hospital Clínic, Barcelona, Spain
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24
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Chu AWH, Yip CCY, Chan WM, Ng ACK, Chan DLS, Siu RHP, Chung CYT, Ng JPL, Kittur H, Mosley GL, Poon RWS, Chiu RYT, To KKW. Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR. Viruses 2021; 13:v13040615. [PMID: 33918447 PMCID: PMC8067048 DOI: 10.3390/v13040615] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFY™) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs. 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.
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Affiliation(s)
- Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (A.W.-H.C.); (W.-M.C.); (A.C.-K.N.)
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pok Fu Lam, Hong Kong; (C.C.-Y.Y.); (R.W.-S.P.)
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (A.W.-H.C.); (W.-M.C.); (A.C.-K.N.)
| | - Anthony Chin-Ki Ng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (A.W.-H.C.); (W.-M.C.); (A.C.-K.N.)
| | - Dream Lok-Sze Chan
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Ryan Ho-Ping Siu
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Cheuk Yiu Tenny Chung
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Jessica Pui-Ling Ng
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Harsha Kittur
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Garrett Lee Mosley
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Rosana Wing-Shan Poon
- Department of Microbiology, Queen Mary Hospital, Pok Fu Lam, Hong Kong; (C.C.-Y.Y.); (R.W.-S.P.)
| | - Ricky Yin-To Chiu
- PHASE Scientific International Limited, Kowloon, Hong Kong; (D.L.-S.C.); (R.H.-P.S.); (C.Y.T.C.); (J.P.-L.N.); (H.K.); (G.L.M.); (R.Y.-T.C.)
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (A.W.-H.C.); (W.-M.C.); (A.C.-K.N.)
- Department of Microbiology, Queen Mary Hospital, Pok Fu Lam, Hong Kong; (C.C.-Y.Y.); (R.W.-S.P.)
- Correspondence: ; Tel.: +(852)-2255-2413; Fax: +(852)-2855-1241
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25
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Abstract
COVID-19, caused by the SARS-CoV-2 virus, has developed into a global health crisis, causing over 2 million deaths and changing people's daily life the world over. Current main-stream diagnostic methods in the laboratory include nucleic acid PCR tests and direct viral antigen tests for detecting active infections, and indirect human antibody tests specific to SARS-CoV-2 to detect prior exposure. In this Perspective, we briefly describe the PCR and antigen tests and then focus mainly on existing antibody tests and their limitations including inaccuracies and possible causes of unreliability. False negatives in antibody immunoassays can arise from assay formats, selection of viral antigens and antibody types, diagnostic testing windows, individual variance, and fluctuation in antibody levels. Reasons for false positives in antibody immunoassays mainly involve antibody cross-reactivity from other viruses, as well as autoimmune disease. The spectrum bias has an effect on both the false negatives and false positives. For assay developers, not only improvement of assay formats but also selection of viral antigens and isotopes of human antibodies need to be carefully considered to improve sensitivity and specificity. For clinicians, the factors influencing the accuracy of assays must be kept in mind to test patients using currently imperfect but available tests with smart tactics and realistic interpretation of the test results.
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Affiliation(s)
- Guoqiang Liu
- Medical College, Jiaxing
University, 118 Jiahang Road, Jiaxing, Zhejiang Province,
China
- Department of Chemistry, University of
Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269,
United States
| | - James F. Rusling
- Department of Chemistry, University of
Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269,
United States
- Department of Surgery and Neag Cancer Center,
UConn Health, Farmington, Connecticut 06232, United
States
- Institute of Materials Science,
University of Connecticut, 97 North Eagleville Road, Storrs,
Connecticut 0626, United States
- School of Chemistry, National University
of Ireland Galway, University Road, Galway,
Ireland
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26
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Elaswad A, Fawzy M. Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays. Pathogens 2021; 10:371. [PMID: 33808783 PMCID: PMC8003424 DOI: 10.3390/pathogens10030371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.
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Affiliation(s)
- Ahmed Elaswad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
- Middle East for Vaccines (ME VAC®), Sharquia 44813, Egypt
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27
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Oishee MJ, Ali T, Jahan N, Khandker SS, Haq MA, Khondoker MU, Sil BK, Lugova H, Krishnapillai A, Abubakar AR, Kumar S, Haque M, Jamiruddin MR, Adnan N. COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools. Infect Drug Resist 2021; 14:1049-1082. [PMID: 33762831 PMCID: PMC7982560 DOI: 10.2147/idr.s289629] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.
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Affiliation(s)
| | - Tamanna Ali
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | - Nowshin Jahan
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | - Md Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | | | - Halyna Lugova
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Ambigga Krishnapillai
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, Kano, 700233, Kano, Nigeria
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati University, Gandhinagar, 382422, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
| | | | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
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28
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Miranda P, Weber G. Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes. Mol Cell Probes 2021; 56:101707. [PMID: 33609730 PMCID: PMC7888997 DOI: 10.1016/j.mcp.2021.101707] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 11/28/2022]
Abstract
Background DNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primer or probe regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed. Methods We calculate the hybridization temperatures of primer/probe sets after aligning to SARS-CoV-2, SARS-CoV-1 and non-SARS genomes, considering all possible combinations of single, double and triple consecutive mismatches. We consider the mismatched hybridization temperature within a range of 5 ∘C to the fully matched reference temperature. Results We obtained the alignments of 19 PCR primers sets that were recently reported for the detection of SARS-CoV-2 and to 21665 SARS-CoV-2 genomes as well as 323 genomes of other viruses of the coronavirus family of which 10 are SARS-CoV-1. We find that many incompletely aligned primers become fully aligned to most of the SARS-CoV-2 when mismatches are considered. However, we also found that many cross-align to SARS-CoV-1 and non-SARS genomes. Conclusions Some primer/probe sets only align substantially to most SARS-CoV-2 genomes if mismatches are taken into account. Unfortunately, by the same mechanism, almost 75% of these sets also align to some SARS-CoV-1 and non-SARS viruses. It is therefore recommended to consider mismatch hybridization for the design of primers whenever possible, especially to avoid undesired cross-reactivity.
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Affiliation(s)
- Pâmella Miranda
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil; Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil.
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29
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Shetti NP, Mishra A, Bukkitgar SD, Basu S, Narang J, Raghava Reddy K, Aminabhavi TM. Conventional and Nanotechnology-Based Sensing Methods for SARS Coronavirus (2019-nCoV). ACS APPLIED BIO MATERIALS 2021; 4:1178-1190. [PMID: 34192244 PMCID: PMC7874501 DOI: 10.1021/acsabm.0c01545] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/28/2021] [Indexed: 12/16/2022]
Abstract
Ongoing pandemic coronavirus (COVID-19) has affected over 218 countries and infected 88,512,243 and 1,906,853 deaths reported by Jan. 8, 2021. At present, vaccines are being developed in Europe, Russia, USA, and China, although some of these are in phase III of trials, which are waiting to be available for the general public. The only option available now is by vigorous testing, isolation of the infected cases, and maintaining physical and social distances. Numerous methods are now available or being developed for testing the suspected cases, which may act as carriers of the virus. In this review, efforts have been made to discuss the conventional as well as fast, rapid, and efficient testing methods developed for the diagnosis of 2019-nCoV.Testing methods can be based on the sensing of targets, which include RNA, spike proteins and antibodies such as IgG and IgM. Apart from the development of RNA targeted PCR, antibody and VSV pseudovirus neutralization assay along with several other diagnostic techniques have been developed. Additionally, nanotechnology-based sensors are being developed for the diagnosis of the virus, and these are also discussed.
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Affiliation(s)
- Nagaraj P. Shetti
- Center
for Electrochemical Science and Materials, Department of Chemistry, K.L.E. Institute of Technology, Hubballi 580 027, Karnataka, India
| | - Amit Mishra
- Department
of Chemical Engineering, Inha University, Incheon 22212,South Korea
| | - Shikandar D. Bukkitgar
- Center
for Electrochemical Science and Materials, Department of Chemistry, K.L.E. Institute of Technology, Hubballi 580 027, Karnataka, India
| | - Soumen Basu
- School
of Chemistry and Biochemistry, Thapar Institute
of Engineering & Technology, Patiala 147004, Punjab, India
| | - Jagriti Narang
- Department
of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard
Nagar, New Delhi 110062, India
| | - Kakarla Raghava Reddy
- School
of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tejraj M. Aminabhavi
- Department
of Pharmaceutical Engineering, SET’s
College of Pharmacy, Dharwad, Karnataka 580 002, India
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30
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Zhang Z, Zhang L, Zhu A, Wang Y, Guan W, Zeng Z, Sun J, Li F, Zhao J, Yang Z, Zhao J, Zhong N. Narrative review of the novel coronavirus SARS-CoV-2: update on genomic characteristics, transmissions and animal model. J Thorac Dis 2021; 12:7454-7466. [PMID: 33447433 PMCID: PMC7797876 DOI: 10.21037/jtd-20-2084] [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] [Indexed: 01/08/2023]
Abstract
Two outbreaks of severe respiratory infection caused by severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) caused global pandemics and highlighted the importance of preparedness for respiratory CoVs. Recently, a third highly pathogenic CoV, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, Hubei, China and posed a public health crisis worldwide. Here, we focus on the recent advances of the novel CoV, and discuss its genomic similarity with other CoVs, transmission, animal model and clinical treatment of coronavirus disease 2019 (COVID-19) induced by SARS-CoV-2, which help epidemic prevention and control, and guide treatment strategies.
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Affiliation(s)
- Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lu Zhang
- Technology Center, Guangzhou Custom, Guangzhou, China.,Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenda Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiqi Zeng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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31
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Huergo MAC, Thanh NTK. Current advances in the detection of COVID-19 and evaluation of the humoral response. Analyst 2021; 146:382-402. [PMID: 33410826 DOI: 10.1039/d0an01686a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The new outbreak caused by coronavirus SARS-CoV-2 started at the end of 2019 and was declared a pandemic in March 2020. Since then, several diagnostic approaches have been re-adapted, and also improved from the previous detections of SARS and MERS coronavirus. The best strategy to handle this situation seems to rely on a triad of detection methods: (i) highly sensitive and specific techniques as the gold standard method, (ii) easier and faster point of care tests accessible for large population screening, and (iii) serology assays to complement the direct detection and to use for surveillance. In this study, we assessed the techniques and tests described in the literature, their advantages and disadvantages, and the interpretation of the results. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is undoubtedly the gold standard technique utilized not only for diagnostics, but also as a standard for comparison and validation of newer approaches. Other nucleic acid amplification methods have been shown to be adequate as point of care (POC) diagnostic tests with similar performance as RT-qPCR. The analysis of seroconversion with immunotests shows the complexity of the immune response to COVID-19. The detection of anti-SARS-CoV-2 antibodies can also help to detect previously infected asymptomatic individuals with negative RT-qPCR tests. Nevertheless, more controlled serology cohort studies should be performed as soon as possible to understand the immune response to SARS-CoV-2.
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Affiliation(s)
- Maria Ana Cristina Huergo
- Theoretical and Applied Physical Chemical Research Institute (INIFTA), National Univesity of La Plata (UNLP), CONICET. Sucursal 4 Casilla de Correo 16, 1900 La Plata, Argentina.
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32
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Tsai SC, Lu CC, Bau DT, Chiu YJ, Yen YT, Hsu YM, Fu CW, Kuo SC, Lo YS, Chiu HY, Juan YN, Tsai FJ, Yang JS. Approaches towards fighting the COVID‑19 pandemic (Review). Int J Mol Med 2021; 47:3-22. [PMID: 33236131 PMCID: PMC7723515 DOI: 10.3892/ijmm.2020.4794] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/04/2020] [Indexed: 11/05/2022] Open
Abstract
The coronavirus disease 2019 (COVID‑19) outbreak, which has caused >46 millions confirmed infections and >1.2 million coronavirus related deaths, is one of the most devastating worldwide crises in recent years. Infection with COVID‑19 results in a fever, dry cough, general fatigue, respiratory symptoms, diarrhoea and a sore throat, similar to those of acute respiratory distress syndrome. The causative agent of COVID‑19, SARS‑CoV‑2, is a novel coronavirus strain. To date, remdesivir has been granted emergency use authorization for use in the management of infection. Additionally, several efficient diagnostic tools are being actively developed, and novel drugs and vaccines are being evaluated for their efficacy as therapeutic agents against COVID‑19, or in the prevention of infection. The present review highlights the prevalent clinical manifestations of COVID‑19, characterizes the SARS‑CoV‑2 viral genome sequence and life cycle, highlights the optimal methods for preventing viral transmission, and discusses possible molecular pharmacological mechanisms and approaches in the development of anti‑SARS‑CoV‑2 therapeutic agents. In addition, the use of traditional Chinese medicines for management of COVID‑19 is discussed. It is expected that novel anti‑viral agents, vaccines or an effective combination therapy for treatment/management of SARS‑CoV‑2 infection and spread therapy will be developed and implemented in 2021, and we would like to extend our best regards to the frontline health workers across the world in their fight against COVID‑19.
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Affiliation(s)
- Shih-Chang Tsai
- Department of Biological Science and Technology, China Medical University
| | - Chi-Cheng Lu
- Department of Sport Performance, National Taiwan University of Sport
| | - Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354
| | - Yu-Jen Chiu
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Taipei Veteran General Hospital
- Department of Surgery, School of Medicine, National Yang Ming University, Taipei 11217
| | - Yu-Ting Yen
- Drug Development Center, Institute of New Drug Development, China Medical University, Taichung 40402
| | - Yuan-Man Hsu
- Department of Biological Science and Technology, China Medical University
| | - Chih-Wei Fu
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu 310401
| | - Sheng-Chu Kuo
- School of Pharmacy, China Medical University, Taichung 40402
| | - Yu-Shiang Lo
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40447
| | - Hong-Yi Chiu
- Department of Pharmacy, Buddhist Tzu Chi General Hospital, Hualien 97002
- Master and PhD Program in Pharmacology and Toxicology, School of Medicine, Tzu Chi University, Hualien 97004
- General Education Center, Tzu Chi University of Science and Technology, Hualien 97005
| | - Yu-Ning Juan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40447
| | - Fuu-Jen Tsai
- School of Chinese Medicine, College of Chinese Medicine, China Medical University
- China Medical University Children's Hospital, China Medical University, Taichung 40402, Taiwan, R.O.C
| | - Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40447
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Andryukov BG, Lyapun IN. COVID-19 diagnostic laboratory strategies: modern technologies and development trends (review of literature). ACTA ACUST UNITED AC 2020; 65:757-766. [DOI: 10.18821/0869-2084-2020-65-12-757-766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic, associated with the new coronavirus SARS-CoV-2, has caused a surge in incidence worldwide, as well as a severe crisis in global health and economy. Therefore, fast and accurate diagnosis of infection is key to timely treatment and elimination of the spread of the virus. Currently, the standard method for detecting coronavirus is reverse transcription polymerase chain reaction (RT-PCR). However, this method requires expensive equipment and trained personnel, which limits the conduct of mass testing and lengthens the time to obtain a research result. Serological tests for antibodies against SARS-CoV-2 and the determination of protective immunity in various populations are used to retrospectively identify patients with asymptomatic and mild forms of infection, monitor the course of infection in hospitalized patients, and also track contacts and epidemiological surveillance. The use of standard methods for diagnosing COVID-19 in conditions of mass morbidity, especially in conditions of insufficient resources and lack of appropriate infrastructure, is associated with a number of limitations. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. The review examines new laboratory technologies for diagnosing a new infection - loop isothermal amplification (LAMP) and immunochromatographic analysis (ICA), which can become a real alternative to the used molecular and enzyme immunoassay methods. The dynamic development of these methods in recent years expands the prospects for their use both for diagnosing COVID-19 and monitoring a pandemic.
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Affiliation(s)
- Boris Georgievich Andryukov
- Somov Research Institute of Epidemiology and Microbiology, Russian Ministry of Education and Science; Far Eastern Federal University of the Ministry of Education and Science of Russia
| | - I. N. Lyapun
- Somov Research Institute of Epidemiology and Microbiology, Russian Ministry of Education and Science
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Mattioli IA, Hassan A, Oliveira ON, Crespilho FN. On the Challenges for the Diagnosis of SARS-CoV-2 Based on a Review of Current Methodologies. ACS Sens 2020; 5:3655-3677. [PMID: 33267587 PMCID: PMC7724986 DOI: 10.1021/acssensors.0c01382] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022]
Abstract
Diagnosis of COVID-19 has been challenging owing to the need for mass testing and for combining distinct types of detection to cover the different stages of the infection. In this review, we have surveyed the most used methodologies for diagnosis of COVID-19, which can be basically categorized into genetic-material detection and immunoassays. Detection of genetic material with real-time polymerase chain reaction (RT-PCR) and similar techniques has been achieved with high accuracy, but these methods are expensive and require time-consuming protocols which are not widely available, especially in less developed countries. Immunoassays for detecting a few antibodies, on the other hand, have been used for rapid, less expensive tests, but their accuracy in diagnosing infected individuals has been limited. We have therefore discussed the strengths and limitations of all of these methodologies, particularly in light of the required combination of tests owing to the long incubation periods. We identified the bottlenecks that prevented mass testing in many countries, and proposed strategies for further action, which are mostly associated with materials science and chemistry. Of special relevance are the methodologies which can be integrated into point-of-care (POC) devices and the use of artificial intelligence that do not require products from a well-developed biotech industry.
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Affiliation(s)
- Isabela A. Mattioli
- São Carlos Institute of
Chemistry, University of São Paulo,
São Carlos 13560-970, São Paulo,
Brazil
| | - Ayaz Hassan
- São Carlos Institute of
Chemistry, University of São Paulo,
São Carlos 13560-970, São Paulo,
Brazil
| | - Osvaldo N. Oliveira
- São Carlos Institute of
Physics, University of São Paulo,
São Carlos 13560-590, São Paulo,
Brazil
| | - Frank N. Crespilho
- São Carlos Institute of
Chemistry, University of São Paulo,
São Carlos 13560-970, São Paulo,
Brazil
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Lan R, Sujanto R, Lu K, He Z, Zhang CJP, Ming WK. Perceived Effectiveness, Safety, and Attitudes Toward the Use of Nucleic Tests of SARS-CoV-2 Among Clinicians and General Public in China. Front Public Health 2020; 8:599862. [PMID: 33392138 PMCID: PMC7773769 DOI: 10.3389/fpubh.2020.599862] [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: 08/28/2020] [Accepted: 11/02/2020] [Indexed: 11/13/2022] Open
Abstract
Objective: To assess whether there is a knowledge gap about the use of test kits for residents and to explore the knowledge, attitudes, and practices of using test kits in China during the coronavirus disease 2019 (COVID-19) epidemic. Method: An online-based, nationwide, and cross-sectional study was conducted. A total of 1,167 respondents were recruited from June 19 to July 2, 2020. All participants completed a validated questionnaire written in Chinese. Electronic consent was obtained from all participants upon their agreement to commence the questionnaire. Perceived efficacy, safety, and their attitudes toward the use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing kits were measured. Result: The majority of the study respondents were female [749 (64.2%)], aged 31-40 years old [372 (31.9%)], and located in mainland China [1,137 (97.4%)]. The majority of the respondents held a positive view toward the introduction of the fast-track approval policy for novel coronavirus testing products (6.16 ± 1.30) as well as toward putting more investment in scientific research and biomedicine to improve the detection accuracy of detection kits (5.94 ± 1.55) in China. The respondents valued the detection accuracy more as opposed to the detection time of the testing kits (4.66 ± 2.00), whereas few participants agreed that in the research and development process, detection accuracy could be sacrificed to speed up production and coverage capacity (3.02 ± 2.04). Conclusion: The majority of the participants have a basic knowledge of the detection methods of the SARS-CoV-2 virus and the types of test kits, as well as great confidence in China's domestic production of test kits and decisions. However, how basic knowledge, high compliance, and positive attitudes play a role in easing the tension of the pandemic still remains unknown.
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Affiliation(s)
- Ruirui Lan
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Robin Sujanto
- International School, Jinan University, Guangzhou, China
| | - Kengbo Lu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Zonglin He
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China.,International School, Jinan University, Guangzhou, China
| | - Casper J P Zhang
- LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Wai-Kit Ming
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China.,International School, Jinan University, Guangzhou, China
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Torrente-Rodríguez RM, Lukas H, Tu J, Min J, Yang Y, Xu C, Rossiter HB, Gao W. SARS-CoV-2 RapidPlex: A Graphene-Based Multiplexed Telemedicine Platform for Rapid and Low-Cost COVID-19 Diagnosis and Monitoring. MATTER 2020; 3:1981-1998. [PMID: 33043291 PMCID: PMC7535803 DOI: 10.1016/j.matt.2020.09.027] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/20/2020] [Accepted: 09/29/2020] [Indexed: 05/15/2023]
Abstract
The COVID-19 pandemic is an ongoing global challenge for public health systems. Ultrasensitive and early identification of infection is critical in preventing widespread COVID-19 infection by presymptomatic and asymptomatic individuals, especially in the community and in-home settings. We demonstrate a multiplexed, portable, wireless electrochemical platform for ultra-rapid detection of COVID-19: the SARS-CoV-2 RapidPlex. It detects viral antigen nucleocapsid protein, IgM and IgG antibodies, as well as the inflammatory biomarker C-reactive protein, based on our mass-producible laser-engraved graphene electrodes. We demonstrate ultrasensitive, highly selective, and rapid electrochemical detection in the physiologically relevant ranges. We successfully evaluated the applicability of our SARS-CoV-2 RapidPlex platform with COVID-19-positive and COVID-19-negative blood and saliva samples. Based on this pilot study, our multiplexed immunosensor platform may allow for high-frequency at-home testing for COVID-19 telemedicine diagnosis and monitoring.
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Affiliation(s)
- Rebeca M Torrente-Rodríguez
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Heather Lukas
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jiaobing Tu
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jihong Min
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yiran Yang
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Changhao Xu
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry B Rossiter
- Rehabilitation Clinical Trials Center, Division of Respiratory and Critical Care Physiology and Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Bezier C, Anthoine G, Charki A. Reliability of real-time RT-PCR tests to detect SARS-Cov-2: A literature review. INTERNATIONAL JOURNAL OF METROLOGY AND QUALITY ENGINEERING 2020. [DOI: 10.1051/ijmqe/2020014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the face of the COVID-19 (Coronavirus Disease 2019) pandemic, the World Health Organization (WHO) has urged countries to test the population more widely. Clinical laboratories have been confronted with a huge demand for testing and have had to make urgent preparations for staff training, to establish new analytical processes, reorganize the workspace, and stock up on specific equipment and diagnostic test kits. The reliability of SARS-Cov-2 test results is of critical importance, given the impact it has on patient care and the management of the health crisis. A review of the literature available for the period leading up to and including June 2020 on the reliability of SARS-Cov-2 (Severe Acute Respiratory Syndrome Coronavirus) detection methods using real-time RT PCR (Reverse Transcription - Polymerase Chain Reaction) brings together the primary factors teams of scientists claim or demonstrate to affect the reliability of results. A description is given of the RT-PCR testing method, followed by a presentation of the characteristics and validation techniques used. A summary of data from the literature on the reliability of tests and commercial kits for SARS-Cov-2 detection, including current uncertainties with regard to the molecular targets selected and genetic diversity of SARS-Cov-2 is provided. The limitations and perspectives are then discussed in detail in the light of the bibliographic data available. Many questions have been asked that still remain unanswered. The lack of knowledge about this novel virus, which appeared at the end of 2019, has a significant impact on the technical capacity to develop reliable, rapid and practical tools for its detection.
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Contribution of CT Features in the Diagnosis of COVID-19. Can Respir J 2020; 2020:1237418. [PMID: 33224361 PMCID: PMC7670585 DOI: 10.1155/2020/1237418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/19/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
The outbreak of novel coronavirus disease 2019 (COVID-19) first occurred in Wuhan, Hubei Province, China, and spread across the country and worldwide quickly. It has been defined as a major global health emergency by the World Health Organization (WHO). As this is a novel virus, its diagnosis is crucial to clinical treatment and management. To date, real-time reverse transcription-polymerase chain reaction (RT-PCR) has been recognized as the diagnostic criterion for COVID-19. However, the results of RT-PCR can be complemented by the features obtained in chest computed tomography (CT). In this review, we aim to discuss the diagnosis and main CT features of patients with COVID-19 based on the results of the published literature, in order to enhance the understanding of COVID-19 and provide more detailed information regarding treatment.
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Varlamov DA, Blagodatskikh KA, Smirnova EV, Kramarov VM, Ignatov KB. Combinations of PCR and Isothermal Amplification Techniques Are Suitable for Fast and Sensitive Detection of SARS-CoV-2 Viral RNA. Front Bioeng Biotechnol 2020; 8:604793. [PMID: 33251206 PMCID: PMC7672014 DOI: 10.3389/fbioe.2020.604793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
The newly identified coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes coronavirus disease 2019 (COVID-19) and has affected over 25 million people worldwide as of August 31, 2020. To aid in the development of diagnostic kits for rapid and sensitive detection of the virus, we evaluated a combination of polymerase chain reaction (PCR) and isothermal nucleic acid amplification techniques. Here, we compared conventional PCR and loop-mediated isothermal amplification (LAMP) methods with hybrid techniques such as polymerase chain displacement reaction (PCDR) and a newly developed PCR-LAMP method. We found that the hybrid methods demonstrated higher sensitivity and assay reaction rates than those of the classic LAMP and PCR techniques and can be used to for SARS-CoV-2 detection. The proposed methods based on the modern hybrid amplification techniques markedly improve virus detection and, therefore, can be extremely useful in the development of new diagnostic kits.
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Affiliation(s)
| | | | - Evgenia V. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M. Kramarov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin B. Ignatov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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Liu HL, Yeh IJ, Phan NN, Wu YH, Yen MC, Hung JH, Chiao CC, Chen CF, Sun Z, Jiang JZ, Hsu HP, Wang CY, Lai MD. Gene signatures of SARS-CoV/SARS-CoV-2-infected ferret lungs in short- and long-term models. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104438. [PMID: 32615317 PMCID: PMC7832673 DOI: 10.1016/j.meegid.2020.104438] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/11/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
Coronaviruses (CoVs) consist of six strains, and the severe acute respiratory syndrome coronavirus (SARS-CoV), newly found coronavirus (SARS-CoV-2) has rapidly spread leading to a global outbreak. The ferret (Mustela putorius furo) serves as a useful animal model for studying SARS-CoV/SARS-CoV-2 infection and developing therapeutic strategies. A holistic approach for distinguishing differences in gene signatures during disease progression is lacking. The present study discovered gene expression profiles of short-term (3 days) and long-term (14 days) ferret models after SARS-CoV/SARS-CoV-2 infection using a bioinformatics approach. Through Gene Ontology (GO) and MetaCore analyses, we found that the development of stemness signaling was related to short-term SARS-CoV/SARS-CoV-2 infection. In contrast, pathways involving extracellular matrix and immune responses were associated with long-term SARS-CoV/SARS-CoV-2 infection. Some highly expressed genes in both short- and long-term models played a crucial role in the progression of SARS-CoV/SARS-CoV-2 infection, including DPP4, BMP2, NFIA, AXIN2, DAAM1, ZNF608, ME1, MGLL, LGR4, ABHD6, and ACADM. Meanwhile, we revealed that metabolic, glucocorticoid, and reactive oxygen species-associated networks were enriched in both short- and long-term infection models. The present study showed alterations in gene expressions from short-term to long-term SARS-CoV/SARS-CoV-2 infection. The current result provides an explanation of the pathophysiology for post-infectious sequelae and potential targets for treatment.
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Affiliation(s)
- Hsin-Liang Liu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Nam Nhut Phan
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Yen-Hung Wu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Jui-Hsiang Hung
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Chung-Chieh Chiao
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 82445, Taiwan
| | - Chien-Fu Chen
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung 82445, Taiwan
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, 1725 Eastshore Hwy, Berkeley, CA 94710, USA
| | - Jia-Zhen Jiang
- Emergency Department, Huashan Hospital North, Fudan University, Shanghai 201508, People's Republic of China
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, National Cheng Kung University, Tainan 70101, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
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Bordea IR, Xhajanka E, Candrea S, Bran S, Onișor F, Inchingolo AD, Malcangi G, Pham VH, Inchingolo AM, Scarano A, Lorusso F, Isacco CG, Aityan SK, Ballini A, Dipalma G, Inchingolo F. Coronavirus (SARS-CoV-2) Pandemic: Future Challenges for Dental Practitioners. Microorganisms 2020; 8:E1704. [PMID: 33142764 PMCID: PMC7694165 DOI: 10.3390/microorganisms8111704] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022] Open
Abstract
In the context of the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) pandemic, the medical system has been subjected to many changes. Face-to-face treatments have been suspended for a period of time. After the lockdown, dentists have to be aware of the modalities to protect themselves and their patients in order not to get infected. Dental practitioners are potentially exposed to a high degree of contamination with SARS-CoV-2 while performing dental procedures that produce aerosols. It should also be noted that the airways, namely the oral cavity and nostrils, are the access pathways for SARS-CoV-2. In order to protect themselves and their patients, they have to use full personal protective equipment. Relevant data regarding this pandemic are under evaluation and are still under test. In this article, we made a synthesis about the way in which SARS-CoV-2 spreads, how to diagnose a novel corona virus infection, what the possible treatments are, and which protective personal equipment we can use to stop its spreading.
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Affiliation(s)
- Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Edit Xhajanka
- President of Dental School, Medical University of Tirana, Rruga e Dibrës, 1001 Tirana, Albania;
| | - Sebastian Candrea
- Department of Pedodontics, County Hospital Cluj-Napoca, 400000 Cluj-Napoca, Romania
| | - Simion Bran
- Department of Maxilofacial Surgery and Implantology, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (S.B.); (F.O.)
| | - Florin Onișor
- Department of Maxilofacial Surgery and Implantology, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (S.B.); (F.O.)
| | - Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine (D.I.M.), University of Medicine Aldo Moro, 70121 Bari, Italy; (A.D.I.); (G.M.); (A.M.I.); (G.D.); (F.I.)
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine (D.I.M.), University of Medicine Aldo Moro, 70121 Bari, Italy; (A.D.I.); (G.M.); (A.M.I.); (G.D.); (F.I.)
| | - Van H Pham
- Nam Khoa Laboratories and Pham Chau Trinh University of Medicine, Hoi An 70000, Vietnam;
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine (D.I.M.), University of Medicine Aldo Moro, 70121 Bari, Italy; (A.D.I.); (G.M.); (A.M.I.); (G.D.); (F.I.)
| | - Antonio Scarano
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, 66100 Chieti, Italy; (A.S.); (F.L.)
| | - Felice Lorusso
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, 66100 Chieti, Italy; (A.S.); (F.L.)
| | - Ciro Gargiulo Isacco
- Director of Research at Human Stem Cells Research Center HSC, Ho Chi Minh 70000, Vietnam;
- Associate Professor of Embryology and Regenerative Medicine and Immunology at Pham Chau Trinh University of Medicine, Hoi An 70000, Vietnam
- Visiting Professor of Regenerative Medicine and Metabolic Disorders at Department of Interdisciplinary Medicine (D.I.M.), University of Medicine Aldo Moro, 70121 Bari, Italy
| | - Sergey K Aityan
- Director of Multidisciplinary Research Center, Lincoln University, Oakland, CA 94102, USA;
| | - Andrea Ballini
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Campus Universitario “Ernesto Quagliariello” University of Bari “Aldo Moro”, 70125 Bari, Italy;
- Department of Precision Medicine, University of Campania“Luigi Vanvitelli”, 80138 Naples, Italy
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine (D.I.M.), University of Medicine Aldo Moro, 70121 Bari, Italy; (A.D.I.); (G.M.); (A.M.I.); (G.D.); (F.I.)
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine (D.I.M.), University of Medicine Aldo Moro, 70121 Bari, Italy; (A.D.I.); (G.M.); (A.M.I.); (G.D.); (F.I.)
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Manghisi VM, Fiorentino M, Boccaccio A, Gattullo M, Cascella GL, Toschi N, Pietroiusti A, Uva AE. A Body Tracking-Based Low-Cost Solution for Monitoring Workers' Hygiene Best Practices during Pandemics. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6149. [PMID: 33138092 PMCID: PMC7663493 DOI: 10.3390/s20216149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Since its beginning at the end of 2019, the pandemic spread of the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) caused more than one million deaths in only nine months. The threat of emerging and re-emerging infectious diseases exists as an imminent threat to human health. It is essential to implement adequate hygiene best practices to break the contagion chain and enhance society preparedness for such critical scenarios and understand the relevance of each disease transmission route. As the unconscious hand-face contact gesture constitutes a potential pathway of contagion, in this paper, the authors present a prototype system based on low-cost depth sensors able to monitor in real-time the attitude towards such a habit. The system records people's behavior to enhance their awareness by providing real-time warnings, providing for statistical reports for designing proper hygiene solutions, and better understanding the role of such route of contagion. A preliminary validation study measured an overall accuracy of 91%. A Cohen's Kappa equal to 0.876 supports rejecting the hypothesis that such accuracy is accidental. Low-cost body tracking technologies can effectively support monitoring compliance with hygiene best practices and training people in real-time. By collecting data and analyzing them with respect to people categories and contagion statistics, it could be possible to understand the importance of this contagion pathway and identify for which people category such a behavioral attitude constitutes a significant risk.
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Affiliation(s)
- Vito M. Manghisi
- Department of Mechanics, Mathematics, and Management, Polytechnic University of Bari, via Oraboba 4, 70125 Bari, Italy; (M.F.); (A.B.); (M.G.); (A.E.U.)
| | - Michele Fiorentino
- Department of Mechanics, Mathematics, and Management, Polytechnic University of Bari, via Oraboba 4, 70125 Bari, Italy; (M.F.); (A.B.); (M.G.); (A.E.U.)
| | - Antonio Boccaccio
- Department of Mechanics, Mathematics, and Management, Polytechnic University of Bari, via Oraboba 4, 70125 Bari, Italy; (M.F.); (A.B.); (M.G.); (A.E.U.)
| | - Michele Gattullo
- Department of Mechanics, Mathematics, and Management, Polytechnic University of Bari, via Oraboba 4, 70125 Bari, Italy; (M.F.); (A.B.); (M.G.); (A.E.U.)
| | - Giuseppe L. Cascella
- Department of Electrical Engineering and Information Technology, Polytechnic University of Bari, via Oraboba 4, 70125 Bari, Italy;
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome ‘Tor Vergata’ Facoltà di Medicina e Chirurgia Viale Montpellier, 1, 00133 Rome, Italy; (N.T.); (A.P.)
| | - Antonio Pietroiusti
- Department of Biomedicine and Prevention, University of Rome ‘Tor Vergata’ Facoltà di Medicina e Chirurgia Viale Montpellier, 1, 00133 Rome, Italy; (N.T.); (A.P.)
| | - Antonio E. Uva
- Department of Mechanics, Mathematics, and Management, Polytechnic University of Bari, via Oraboba 4, 70125 Bari, Italy; (M.F.); (A.B.); (M.G.); (A.E.U.)
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Ji T, Liu Z, Wang G, Guo X, Akbar Khan S, Lai C, Chen H, Huang S, Xia S, Chen B, Jia H, Chen Y, Zhou Q. Detection of COVID-19: A review of the current literature and future perspectives. Biosens Bioelectron 2020; 166:112455. [PMID: 32739797 PMCID: PMC7371595 DOI: 10.1016/j.bios.2020.112455] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) worldwide pandemic. This unprecedented situation has garnered worldwide attention. An effective strategy for controlling the COVID-19 pandemic is to develop highly accurate methods for the rapid identification and isolation of SARS-CoV-2 infected patients. Many companies and institutes are therefore striving to develop effective methods for the rapid detection of SARS-CoV-2 ribonucleic acid (RNA), antibodies, antigens, and the virus. In this review, we summarize the structure of the SARS-CoV-2 virus, its genome and gene expression characteristics, and the current progression of SARS-CoV-2 RNA, antibodies, antigens, and virus detection. Further, we discuss the reasons for the observed false-negative and false-positive RNA and antibody detection results in practical clinical applications. Finally, we provide a review of the biosensors which hold promising potential for point-of-care detection of COVID-19 patients. This review thereby provides general guidelines for both scientists in the biosensing research community and for those in the biosensor industry to develop a highly sensitive and accurate point-of-care COVID-19 detection system, which would be of enormous benefit for controlling the current COVID-19 pandemic.
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Affiliation(s)
- Tianxing Ji
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China.
| | - Zhenwei Liu
- Guangzhou Institute of Respiratory Medicine Company Limited, Guangzhou, 510535, PR China
| | - GuoQiang Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Xuguang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, PR China
| | - Shahzad Akbar Khan
- Laboratory of Pathology, Department of Pathobiology, University of Poonch Rawalakot, Rawala Kot, 12350, Pakistan
| | - Changchun Lai
- Department of Clinical Laboratory, Maoming People's Hospital, Maoming, 525000, PR China
| | - Haoyu Chen
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Shiwen Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Shaomei Xia
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Bo Chen
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Hongyun Jia
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, HongKong, PR China.
| | - Qiang Zhou
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China.
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Mahendiratta S, Batra G, Sarma P, Kumar H, Bansal S, Kumar S, Prakash A, Sehgal R, Medhi B. Molecular diagnosis of COVID-19 in different biologic matrix, their diagnostic validity and clinical relevance: A systematic review. Life Sci 2020; 258:118207. [PMID: 32777301 PMCID: PMC7411381 DOI: 10.1016/j.lfs.2020.118207] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/18/2020] [Accepted: 08/02/2020] [Indexed: 12/14/2022]
Abstract
Due to COVID 19 outbreak many studies are being conducted for therapeutic strategies and vaccines but detection methods play an important role in the containment of the disease. Hence, this systematic review aims to evaluate the effectiveness of the molecular detection techniques in COVID-19. For framing the systematic review 6 literature databases (PubMed, EMBASE, OVID, Web of Science, Scopus and Google Scholar) were searched for relevant studies and articles were screened for relevant content till 25th April 2020. Observations from this systematic review reveal the utility of RT-PCR with serological testing as one such method cannot correlate with accurate results. Availability of point of care devices do not conform to sensitivity and specificity in comparison to the conventional methods due to lack of clinical investigations. Pivotal aim of molecular and serological research is the development of detection methods that can support the clinical decision making of patients suspected with SARS-CoV-2. However, none of the methods were 100% sensitive and specific; hence additional studies are required to overcome the challenges addressed here. We hope that the present article with its observations and suggestions will assist the researchers to realize this vision in future.
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Affiliation(s)
| | - Gitika Batra
- Department of Neurology, PGIMER, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Harish Kumar
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Seema Bansal
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Rakesh Sehgal
- Department of Parasitology, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India.
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Karthik K, Aravindh Babu RP, Dhama K, Chitra MA, Kalaiselvi G, Alagesan Senthilkumar TM, Raj GD. Biosafety Concerns During the Collection, Transportation, and Processing of COVID-19 Samples for Diagnosis. Arch Med Res 2020; 51:623-630. [PMID: 32948378 PMCID: PMC7486853 DOI: 10.1016/j.arcmed.2020.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/17/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, which started in China, has created a panic among the general public and health care/laboratory workers. Thus far, there is no medication or vaccine to prevent and control the spread of COVID-19. As the virus is airborne and transmitted through droplets, there has been significant demand for face masks and other personal protective equipment to prevent the spread of infection. Health care and laboratory workers who come in close contact with infected people or material are at a high risk of infection. Therefore, robust biosafety measures are required at hospitals and laboratories to prevent the spread of COVID-19. Various diagnostic platforms including of serological, molecular and other advanced tools and techniques have been designed and developed for rapid detection of SARS-CoV-2 and each has its own merits and demerits. Molecular assays such as real-time reverse transcriptase polymerase chain reaction (rRT-PCR) has been used worldwide for diagnosis of COVID-19. Samples such as nasal swabs or oropharyngeal swabs are used for rRT-PCR. Laboratory acquired infection has been a significant problem worldwide, which has gained importance during the current pandemic as the samples for rRT-PCR may contain intact virus with serious threat. COVID-19 can spread to workers during the sampling, transportation, processing, and disposal of tested samples. Here, we present an overview on advances in diagnosis of COVID-19 and details the issues associated with biosafety procedures and potential safety precautions to be followed during collection, transportation, and processing of COVID-19 samples for laboratory diagnosis so as to avoid virus infection.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.
| | | | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute, Bareilly, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Govindan Kalaiselvi
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | | | - Gopal Dhinakar Raj
- Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
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Falcão LF, da Silva Pontes L, Afonso da Silva BG, Vieira da Silva Franco KM, Costa LA, Barbosa Rocha RS, Simões Quaresma JA. The complexity of respiratory disease associated with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection: From immunopathogenesis to respiratory therapy. Rev Med Virol 2020. [DOI: 10.1002/rmv.2167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Luiz Fábio Falcão
- Center for Biological and Health Sciences State University of Pará Belém Pará Brazil
| | | | | | | | - Luiz Adriano Costa
- Center for Biological and Health Sciences State University of Pará Belém Pará Brazil
| | | | - Juarez Antônio Simões Quaresma
- Center for Biological and Health Sciences State University of Pará Belém Pará Brazil
- Evandro Chagas Institute Ministry of Health Ananindeua Pará Brazil
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Wu SY, Yau HS, Yu MY, Tsang HF, Chan LWC, Cho WCS, Shing Yu AC, Yuen Yim AK, Li MJW, Wong YKE, Pei XM, Cesar Wong SC. The diagnostic methods in the COVID-19 pandemic, today and in the future. Expert Rev Mol Diagn 2020; 20:985-993. [PMID: 32845192 DOI: 10.1080/14737159.2020.1816171] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The emergence of anovel coronavirus identified in patients with unknown cause of acute respiratory disease in Wuhan, China at the end of 2019 has caused aglobal outbreak. The causative coronavirus was later named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease caused by SARS-CoV-2 was named as Coronavirus Disease-2019 (COVID-19). As of 10 August 2020, more than 19,718,030 confirmed cases and 728,013 deaths have been reported. COVID-19 is spread via respiratory droplets which are inhaled into the lungs. AREAS COVERED In this article, we summarized the knowledge about the causative pathogen of COVID-19 and various diagnostic methods in this pandemic for better understanding of the limitations and the nuances of virus testing for COVID-19. EXPERT OPINION In this pandemic, rapid and accurate identification of COVID-19 patients are critical to break the chain of infection in the community. RT-PCR provides a rapid and reliable identification of SARS-CoV-2 infection. In the future, molecular diagnostics will still be the gold standard and next-generation sequencing can help us to understand more on the pathogenesis and detect novel mutations. It is believed that more sophisticated detection methods will be introduced to detect SARS-CoV-2 as earliest as possible.
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Affiliation(s)
- So Yat Wu
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - Hoi Shan Yau
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - Man Yee Yu
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - Lawrence Wing Chi Chan
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital , Hong Kong Special Administrative Region, China
| | | | | | - Marco J W Li
- Codex Genetics Limited , Hong Kong Special Administrative Region, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - Xiao Meng Pei
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Hong Kong Polytechnic University , Hong Kong Special Administrative Region, China
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Zou J, Zhi S, Chen M, Su X, Kang L, Li C, Su X, Zhang S, Ge S, Li W. Heat inactivation decreases the qualitative real-time RT-PCR detection rates of clinical samples with high cycle threshold values in COVID-19. Diagn Microbiol Infect Dis 2020; 98:115109. [PMID: 32593875 PMCID: PMC7289114 DOI: 10.1016/j.diagmicrobio.2020.115109] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 01/07/2023]
Abstract
SARS-CoV-2 has caused COVID-19 pandemic globally in the beginning of 2020, and qualitative real-time RT-PCR has become the gold standard in diagnosis. As SARSCoV-2 with strong transmissibility and pathogenicity, it has become a professional consensus that clinical samples from suspected patients should be heat inactivated at 56°C for 30 min before further processing. However, previous studies on the effect of inactivation on qualitative real-time RT-PCR were conducted with diluted samples rather than clinical samples. The aim of this study was to investigate whether heat inactivation on clinical samples before detection will affect the accuracy of qualitative real-time RT-PCR detection. All 46 throat swab samples from 46 confirmed inpatients were detected by qualitative real-time RT-PCR directly, as well as after heat inactivation. Heat-Inactivation has significantly influenced the qualitative detection results on clinical samples, especially weakly positive samples. The results indicate the urgency to establish a more suitable protocol for COVID-19 clinical sample's inactivation.
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Affiliation(s)
- Jingbo Zou
- Yongchuan District Center for Disease Control and Prevention of Chongqing, Changjiang Road, Yuzhong District, Chongqing, China.
| | - Shenshen Zhi
- Chongqing University Central Hospital, Chongqing Emergency Medical Center, Jiankang Road, Yuzhong District, Chongqing, China.
| | - Mengyuan Chen
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Xingyu Su
- Yongchuan Health Center for Women and Children, Renmin Avenue, Yongchuan District, Chongqing, China.
| | - Ling Kang
- Yongchuan District Hospital of traditional Chinese Medicine, Yingbin Avenue, Yongchuan District, Chongqing, China.
| | - Caiyu Li
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Xiaosong Su
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Shiyin Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Wei Li
- Chongqing University Central Hospital, Chongqing Emergency Medical Center, Jiankang Road, Yuzhong District, Chongqing, China.
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Andryukov BG. Six decades of lateral flow immunoassay: from determining metabolic markers to diagnosing COVID-19. AIMS Microbiol 2020; 6:280-304. [PMID: 33134745 PMCID: PMC7595842 DOI: 10.3934/microbiol.2020018] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
Technologies based on lateral flow immunoassay (LFIA), known in some countries of the world as immunochromatographic tests, have been successfully used for the last six decades in diagnostics of many diseases and conditions as they allow rapid detection of molecular ligands in biosubstrates. The popularity of these diagnostic platforms is constantly increasing in healthcare facilities, particularly those facing limited budgets and time, as well as in household use for individual health monitoring. The advantages of these low-cost devices over modern laboratory-based analyzers come from their availability, opportunity of rapid detection, and ease of use. The attractiveness of these portable diagnostic tools is associated primarily with their high analytical sensitivity and specificity, as well as with the easy visual readout of results. These qualities explain the growing popularity of LFIA in developing countries, when applied at small hospitals, in emergency situations where screening and monitoring health condition is crucially important, and as well as for self-testing of patients. These tools have passed the test of time, and now LFIA test systems are fully consistent with the world's modern concept of ‘point-of-care testing’, finding a wide range of applications not only in human medicine, but also in ecology, veterinary medicine, and agriculture. The extensive opportunities provided by LFIA contribute to the continuous development and improvement of this technology and to the creation of new-generation formats. This review will highlight the modern principles of design of the most widely used formats of test-systems for clinical laboratory diagnostics, summarize the main advantages and disadvantages of the method, as well as the current achievements and prospects of the LFIA technology. The latest innovations are aimed at improving the analytical performance of LFIA platforms for the diagnosis of bacterial and viral infections, including COVID-19.
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Affiliation(s)
- Boris G Andryukov
- Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russian Federation.,Far Eastern Federal University (FEFU), Vladivostok, Russian Federation
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50
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Yip CCY, Sridhar S, Leung KH, Ng ACK, Chan KH, Chan JFW, Tsang OTY, Hung IFN, Cheng VCC, Yuen KY, To KKW. Development and Evaluation of Novel and Highly Sensitive Single-Tube Nested Real-Time RT-PCR Assays for SARS-CoV-2 Detection. Int J Mol Sci 2020; 21:ijms21165674. [PMID: 32784770 PMCID: PMC7461039 DOI: 10.3390/ijms21165674] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China; (C.C.-Y.Y.); (V.C.-C.C.)
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kit-Hang Leung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
| | - Anthony Chin-Ki Ng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Owen Tak-Yin Tsang
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong, China;
| | | | | | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China; (C.C.-Y.Y.); (V.C.-C.C.)
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Correspondence: (K.-Y.Y.); (K.K.-W.T.); Tel.: +852-2255-2584 (K.-Y.Y. & K.K.-W.T.); Fax: +852-2855-1241 (K.-Y.Y. & K.K.-W.T.)
| | - Kelvin Kai-Wang To
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Correspondence: (K.-Y.Y.); (K.K.-W.T.); Tel.: +852-2255-2584 (K.-Y.Y. & K.K.-W.T.); Fax: +852-2855-1241 (K.-Y.Y. & K.K.-W.T.)
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