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Chhipa AS, Radadiya E, Patel S. CRISPR-Cas based diagnostic tools: Bringing diagnosis out of labs. Diagn Microbiol Infect Dis 2024; 109:116252. [PMID: 38479094 DOI: 10.1016/j.diagmicrobio.2024.116252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/30/2024]
Abstract
Timely detection is important for the effective management of infectious diseases. Reverse Transcription Polymerase Chain Reaction (RT-PCR) stands as the prime nucleic acid based test that is employed for the detection of infectious diseases. The method ensures sensitivity and specificity. However, RT-PCR is a relatively expensive technique due to the requirement of costly equipment and reagents. Further, it requires skilled personnel and established laboratories that are usually inaccessible in underdeveloped areas. On the other hand, rapid antigen based techniques are cost effective and easily accessible, but are less effective in terms of sensitivity and specificity. CRISPR-Cas systems are advanced diagnostic tools that combine the advantages of both PCR and antigen based detection techniques, and allows the rapid detection with high sensitivity/specificity. The present review aims to discuss the applicability of CRISPR-Cas based diagnostic tools for the infectious disease detection. The review further attempts to highlight the current limitations and future research directions to improve the CRISPR based diagnostic tools for rapid and effective disease detection.
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Affiliation(s)
- Abu Sufiyan Chhipa
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India
| | - Ekta Radadiya
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India
| | - Snehal Patel
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India.
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Krause E, Michel J, Puyskens A, Hofmann N, Rinner T, Biere B, Dorner BG, Skiba M, Schaade L, Nitsche A. Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic. Virol J 2023; 20:139. [PMID: 37408040 DOI: 10.1186/s12985-023-02088-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed. METHODS We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing. RESULTS All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing. CONCLUSION Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.
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Affiliation(s)
- Eva Krause
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany.
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Puyskens
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Natalie Hofmann
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Thomas Rinner
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Barbara Biere
- Department for Infectious Diseases, Unit Influenza and Other Respiratory Viruses (FG 17), Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Brigitte G Dorner
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Martin Skiba
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
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Sagoe KO, Kyama MC, Maina N, Kamita M, Njokah M, Thiong'o K, Kanoi BN, Wandera EA, Ndegwa D, Kinyua DM, Gitaka J. Application of Hybridization Chain Reaction/CRISPR-Cas12a for the Detection of SARS-CoV-2 Infection. Diagnostics (Basel) 2023; 13:diagnostics13091644. [PMID: 37175035 PMCID: PMC10178590 DOI: 10.3390/diagnostics13091644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Globally, the emergence of the coronavirus disease (COVID-19) has had a significant impact on life. The need for ongoing SARS-CoV-2 screening employing inexpensive and quick diagnostic approaches is undeniable, given the ongoing pandemic and variations in vaccine administration in resource-constrained regions. This study presents results as proof of concept to use hybridization chain reaction (HCR) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a complex for detecting SARS-CoV-2. HCR hairpin probes were designed using the NUPACK web-based program and further used to amplify the SARS-CoV-2 N gene in archived nasopharyngeal samples. The results were visualized using agarose gels and CRISPR Cas12a-based lateral flow strips. The assay was evaluated using the gold standard, real-time polymerase chain reaction (RT-PCR), as recommended by the World Health Organization (WHO). The results show the comparative efficiency of HCR to RT-PCR. This study shows that HCR and CRISPR are viable alternatives for diagnosing SARS-CoV-2 in samples.
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Affiliation(s)
- Kate Obaayaa Sagoe
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation (PAUSTI), Nairobi P.O. Box 62000-00200, Kenya
| | - Mutinda Cleophas Kyama
- Department of Medical Laboratory Science, College of Health Sciences, Jomo Kenyatta University of Agriculture & Technology, Nairobi P.O. Box 62000-00200, Kenya
| | - Naomi Maina
- Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture & Technology, Nairobi P.O. Box 62000-00200, Kenya
| | - Moses Kamita
- Directorate of Research and Innovation, Mount Kenya University, Thika P.O. Box 342-01000, Kenya
| | - Muturi Njokah
- Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture & Technology, Nairobi P.O. Box 62000-00200, Kenya
| | - Kelvin Thiong'o
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | - Bernard N Kanoi
- Directorate of Research and Innovation, Mount Kenya University, Thika P.O. Box 342-01000, Kenya
| | - Ernest Apondi Wandera
- Directorate of Research and Innovation, Mount Kenya University, Thika P.O. Box 342-01000, Kenya
- Center for Virus Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | - Davies Ndegwa
- Department of Medical Laboratory Sciences, Kenya Medical Training College, Nairobi P.O. Box 30195-00100, Kenya
| | - Dickson Mwenda Kinyua
- Department of Physical Sciences, Meru University of Science & Technology, Meru P.O. Box 972-60200, Kenya
- Department of Pure and Applied Sciences, Kirinyaga University, Kerugoya P.O. Box 143-10300, Kenya
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika P.O. Box 342-01000, Kenya
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Sakhabutdinova AR, Gazizov RR, Chemeris AV, Garafutdinov RR. Reverse transcriptase-free detection of viral RNA using Hemo Klentaq DNA polymerase. Anal Biochem 2022; 659:114960. [PMID: 36306819 PMCID: PMC9597527 DOI: 10.1016/j.ab.2022.114960] [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: 08/19/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
COVID-19 pandemic highlighted the demand for the fast and reliable detection of viral RNA. Although various methods for RNA amplification and detection have been proposed, some limitations, including those caused by reverse transcription (RT), need to be overcome. Here, we report on the direct detection of specific RNA by conventional polymerase chain reaction (PCR) requiring no prior RT step. It was found that Hemo KlenTaq (HKTaq), which is posed as DNA-dependent DNA polymerase, possesses reverse transcriptase activity and provides reproducible amplification of RNA targets with an efficiency comparable to common RT-PCR. Using nasopharyngeal swab extracts from COVID-19-positive patients, the high reliability of SARS-CoV-2 detection based on HKTaq was demonstrated. The most accurate detection of specific targets are provided by nearby primers, which allow to determine RNA in solutions affected to multiple freeze-thaw cycles. HKTaq can be used for elaboration of simplified amplification techniques intended for the analysis of any specific RNA and requiring only one DNA polymerase.
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Ang GY, Chan KG, Yean CY, Yu CY. Lateral Flow Immunoassays for SARS-CoV-2. Diagnostics (Basel) 2022; 12:diagnostics12112854. [PMID: 36428918 PMCID: PMC9689684 DOI: 10.3390/diagnostics12112854] [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: 10/15/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
The continued circulation of SARS-CoV-2 virus in different parts of the world opens up the possibility for more virulent variants to evolve even as the coronavirus disease 2019 transitions from pandemic to endemic. Highly transmissible and virulent variants may seed new disruptive epidemic waves that can easily put the healthcare system under tremendous pressure. Despite various nucleic acid-based diagnostic tests that are now commercially available, the wide applications of these tests are largely hampered by specialized equipment requirements that may not be readily available, accessible and affordable in less developed countries or in low resource settings. Hence, the availability of lateral flow immunoassays (LFIs), which can serve as a diagnostic tool by detecting SARS-CoV-2 antigen or as a serological tool by measuring host immune response, is highly appealing. LFI is rapid, low cost, equipment-free, scalable for mass production and ideal for point-of-care settings. In this review, we first summarize the principle and assay format of these LFIs with emphasis on those that were granted emergency use authorization by the US Food and Drug Administration followed by discussion on the specimen type, marker selection and assay performance. We conclude with an overview of challenges and future perspective of LFI applications.
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Affiliation(s)
- Geik Yong Ang
- Faculty of Sports Science and Recreation, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
- Correspondence: (G.Y.A.); (C.Y.Y.)
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Malaysia
| | - Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: (G.Y.A.); (C.Y.Y.)
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Zhang L, Jiang H, Zhu Z, Liu J, Li B. Integrating CRISPR/Cas within isothermal amplification for point-of-Care Assay of nucleic acid. Talanta 2022; 243:123388. [DOI: 10.1016/j.talanta.2022.123388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/03/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022]
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Hussein M, Andrade dos Ramos Z, Berkhout B, Herrera-Carrillo E. In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack. Viruses 2022; 14:v14020385. [PMID: 35215977 PMCID: PMC8880226 DOI: 10.3390/v14020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.
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Affiliation(s)
| | | | - Ben Berkhout
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
| | - Elena Herrera-Carrillo
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
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