1
|
Sbruzzi RC, Feira MF, Cadore NA, Giudicelli GC, Kowalski TW, Gregianini TS, Chies JAB, Vianna FSL. An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium. Biopreserv Biobank 2024; 22:166-173. [PMID: 37579075 DOI: 10.1089/bio.2022.0188] [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] [Indexed: 08/16/2023] Open
Abstract
Introduction: During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. Objective: To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. Methods: In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. Results: The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink® method (0.14 μg, p < 0.001), but not from the QIAamp® method (0.47 μg, p = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan® assay. Conclusion: The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.
Collapse
Affiliation(s)
- Renan C Sbruzzi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Mariléa F Feira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Nathan A Cadore
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
| | - Thayne W Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual de Saúde do estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - José A B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| |
Collapse
|
2
|
Shahi F, Rasti M, Moradi M. Overview of the different methods for RNA preparation in COVID-19 diagnosis process during the pandemic. Anal Biochem 2024; 686:115410. [PMID: 38006951 DOI: 10.1016/j.ab.2023.115410] [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: 06/27/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
The COVID-19 pandemic brought to light the impact of a widespread disease on various aspects of human relationships, communities, and economies. One notable consequence was the increased demand for diagnostic kits, laboratory reagents, and personal health equipment. This surge in testing capacity worldwide led to shortages in the supply of essential items, including RNA extraction kits, which are crucial for detecting COVID-19 infections. To address this scarcity, researchers have proposed alternative and cost-effective strategies for RNA extraction, utilizing both chemical and physical solutions and extraction-free methods. These approaches aim to alleviate the challenges associated with the overwhelming number of tests being conducted in laboratories. The purpose of this review is intends to provide a comprehensive summary of the various kit-free RNA extraction methods available for COVID-19 diagnosis during the pandemic.
Collapse
Affiliation(s)
- Fatemeh Shahi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mojtaba Rasti
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Melika Moradi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| |
Collapse
|
3
|
Cerda A, Rivera M, Armijo G, Ibarra-Henriquez C, Reyes J, Blázquez-Sánchez P, Avilés J, Arce A, Seguel A, Brown AJ, Vásquez Y, Cortez-San Martín M, Cubillos FA, García P, Ferres M, Ramírez-Sarmiento CA, Federici F, Gutiérrez RA. An Open One-Step RT-qPCR for SARS-CoV-2 detection. PLoS One 2024; 19:e0297081. [PMID: 38271448 PMCID: PMC10810446 DOI: 10.1371/journal.pone.0297081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, demonstrating sensitivity comparable to a commercial kit routinely employed in clinical settings for patient diagnosis. Further evaluation on 40 clinical samples (20 positive and 20 negative) confirmed its comparable diagnostic accuracy. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.
Collapse
Affiliation(s)
- Ariel Cerda
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Grace Armijo
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Ibarra-Henriquez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Avilés
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aníbal Arce
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aldo Seguel
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alexander J. Brown
- Department of Biomedical Research, National Jewish Health, Denver, CO, United States of America
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Yesseny Vásquez
- Escuela de Ciencias Médicas, Facultad de Medicina, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Francisco A. Cubillos
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Patricia García
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferres
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Ramírez-Sarmiento
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A. Gutiérrez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
4
|
Bravo-González S, González-González E, Perales-Salinas V, Rodríguez-Sánchez IP, Ortiz-Castillo JE, Vargas-Martínez A, Perez-Gonzalez VH, Luna-Aguirre CM, Trujillo-de Santiago G, Alvarez MM. Self-Diagnosis of SARS-CoV-2 from Saliva Samples at Home: Isothermal Amplification Enabled by Do-It-Yourself Portable Incubators and Laminated Poly-ethyl Sulfonate Membranes. Diagnostics (Basel) 2024; 14:221. [PMID: 38275468 PMCID: PMC10814948 DOI: 10.3390/diagnostics14020221] [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: 11/08/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024] Open
Abstract
COVID-19 made explicit the need for rethinking the way in which we conduct testing for epidemic emergencies. During the COVID-19 pandemic, the dependence on centralized lab facilities and resource-intensive methodologies (e.g., RT-qPCR methods) greatly limited the deployment of widespread testing efforts in many developed and underdeveloped countries. Here, we illustrate the development of a simple and portable diagnostic kit that enables self-diagnosis of COVID-19 at home from saliva samples. We describe the development of a do-it-yourself (DIY) incubator for Eppendorf tubes that can be used to conduct SARS-CoV-2 detection with competitive sensitivity and selectivity from saliva at home. In a proof-of-concept experiment, we assembled Eppendorf-tube incubators at our home shop, prepared a single-tube mix of reagents and LAMP primers in our lab, and deployed these COVID-19 detection kits using urban delivery systems (i.e., Rappifavor or Uber) to more than 15 different locations in Monterrey, México. This straightforward strategy enabled rapid and cost-effective at-home molecular diagnostics of SARS-CoV-2 from real saliva samples with a high sensitivity (100%) and high selectivity (87%).
Collapse
Affiliation(s)
- Sergio Bravo-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Valeria Perales-Salinas
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Iram Pablo Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, NL, Mexico;
- Alfa Medical Center, Guadalupe 67100, NL, Mexico
| | - Jose E. Ortiz-Castillo
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Adriana Vargas-Martínez
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Victor H. Perez-Gonzalez
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Claudia Maribel Luna-Aguirre
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| |
Collapse
|
5
|
Moazami Goodarzi M, Taghizadeh Pirposhteh R, Ravan H, Vahidian F, Kheirkhah O, Fotouhi Ardakani R, Fotouhi F. A Comprehensive Comparison of Rapid RNA Extraction Methods for Detection of SARS-CoV-2 as the Infectious Agent of the Upper Respiratory Tract using Direct RT-LAMP Assay. Adv Biomed Res 2023; 12:261. [PMID: 38192891 PMCID: PMC10772793 DOI: 10.4103/abr.abr_63_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 01/10/2024] Open
Abstract
Background The current COVID-19 pandemic has highlighted the need for faster and more cost-effective diagnostic methods. The RNA extraction step in current diagnostic methods, such as real-time qPCR, increases the cost and time required for testing. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a promising technique for developing diagnostic tests with desired sensitivity and specificity without the need for RNA extraction. Materials and Methods An RT-LAMP assay was developed to detect SARS-CoV-2 with a sensitivity of 0.5 copies of positive control plasmid per microliter in 40 min. Several rapid RNA extraction protocols were evaluated using different reagents, including bovine serum albumin, Triton X-100, Tween 20, proteinase K, guanidine hydrochloride, guanidinium isothiocyanate (GITC), and thermal treatment. Finally, the sensitivity and specificity of the developed direct RT-LAMP were determined using 150 upper respiratory tract samples. Results Method 10 was selected as the most efficient protocol for the RNA extraction step. The sensitivity and specificity of the developed direct RT-LAMP assay with clinical samples were estimated at 98.4% and 88.8%, respectively. Conclusion These results suggest that the combination of GITC and Triton X-100 detergent is a highly efficient method for RNA extraction and direct RT-LAMP detection of SARS-CoV-2 in clinical samples, providing a valuable tool for the rapid and cost-effective diagnosis of COVID-19.
Collapse
Affiliation(s)
- Maryam Moazami Goodarzi
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, 3159915111 Karaj, Iran
| | | | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, 76169-14111 Kerman, Iran
| | - Farnaz Vahidian
- Department of Biology, Science and Arts University, Yazd, Iran
| | - Omolbani Kheirkhah
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Reza Fotouhi Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
6
|
Kang M, Jeong E, Kim JY, Yun SA, Jang MA, Jang JH, Kim TY, Huh HJ, Lee NY. Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay. Sci Rep 2023; 13:20364. [PMID: 37990045 PMCID: PMC10663557 DOI: 10.1038/s41598-023-47645-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
In the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
Collapse
Affiliation(s)
- Minhee Kang
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Eunjung Jeong
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji-Yeon Kim
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Sun Ae Yun
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| |
Collapse
|
7
|
Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
Collapse
Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| |
Collapse
|
8
|
Armenta-Leyva B, Munguía-Ramírez B, Giménez-Lirola LG, Lin X, Ye F, Zimmerman J. Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids. J Vet Diagn Invest 2023; 35:521-527. [PMID: 37337714 PMCID: PMC10467463 DOI: 10.1177/10406387231182102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Based on publications reporting improvements in real-time PCR (rtPCR) performance, we compared protocols based on heat treatment or dilution followed by direct rtPCR to standard extraction and amplification methods for the detection of porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus (IAV), porcine epidemic diarrhea virus (PEDV), or Mycoplasma hyopneumoniae (MHP) in swine oral fluids (OFs). In part A, we subjected aliquots of positive OF samples to 1 of 4 protocols: protocol 1: heat (95°C × 30 min) followed by direct rtPCR; protocol 2: heat and cool (25°C × 20 min) followed by direct rtPCR; protocol 3: heat, cool, extraction, and rtPCR; protocol 4 (control): extraction and then rtPCR. In part B, positive OF samples were split into 3, diluted (D1 = 1:2 with Tris-borate-EDTA (TBE); D2 = 1:2 with negative OF; D3 = not diluted), and then tested by rtPCR using the best-performing protocol from part A (protocol 4). In part A, with occasional exceptions, heat treatment resulted in marked reduction in the detection of target and internal sample control (ISC) nucleic acids. In part B, sample dilution with TBE or OF produced no improvement in the detection of targets and ISCs. Thus, standard extraction and amplification methods provided superior detection of PRRSV, IAV, PEDV, and MHP nucleic acids in OFs.
Collapse
Affiliation(s)
- Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Xue Lin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | - Jeffrey Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| |
Collapse
|
9
|
Allicock OM, Yolda-Carr D, Earnest R, Breban MI, Vega N, Ott IM, Kalinich C, Alpert T, Petrone ME, Wyllie AL. Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 182:103-108. [PMID: 37369293 PMCID: PMC10290768 DOI: 10.1016/j.pbiomolbio.2023.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/18/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Early in the pandemic, a simple, open-source, RNA extraction-free RT-qPCR protocol for SARS-CoV-2 detection in saliva was developed and made widely available. This simplified approach (SalivaDirect) requires only sample treatment with proteinase K prior to PCR testing. However, feedback from clinical laboratories highlighted a need for a flexible workflow that can be seamlessly integrated into their current health and safety requirements for the receiving and handling of potentially infectious samples. To address these varying needs, we explored additional pre-PCR workflows. We built upon the original SalivaDirect workflow to include an initial incubation step (95 °C for 30 min, 95 °C for 5 min or 65 °C for 15 min) with or without addition of proteinase K. The limit of detection for the workflows tested did not significantly differ from that of the original SalivaDirect workflow. When tested on de-identified saliva samples from confirmed COVID-19 individuals, these workflows also produced comparable virus detection and assay sensitivities, as determined by RT-qPCR analysis. Exclusion of proteinase K did not negatively affect the sensitivity of the assay. The addition of multiple heat pretreatment options to the SalivaDirect protocol increases the accessibility of this cost-effective SARS-CoV-2 test as it gives diagnostic laboratories the flexibility to implement the workflow which best suits their safety protocols.
Collapse
Affiliation(s)
- Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Noel Vega
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Chaney Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| |
Collapse
|
10
|
Khan MF, Roopa C. Dry Swab-Based Nucleic Acid Extraction vs. Spin Column-Based Nucleic Acid Extraction for COVID-19 RT-PCR Testing: A Comparative Study. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:6624932. [PMID: 37663452 PMCID: PMC10469701 DOI: 10.1155/2023/6624932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/30/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023]
Abstract
Conventional nucleic acid extraction involves usage of spin columns to isolate the RNA, but this is labor intensive. This study compares the spin column method with a dry swab-based method of extraction using a proteinase K buffer and subsequent heat inactivation. A total of 56 subjects were tested for COVID-19 by RT-PCR with probes targeting the E and RdRp genes by collecting two nasopharyngeal and two oropharyngeal swabs and subjecting one set to nucleic acid extraction by spin column and the other set to dry swab-based methods. Out of the 56 samples tested, 27 were positive for VTM-based extraction and 29 were negative. Dry swab-based extraction produced 22 positive results (sensitivity = 81.48%) and 34 negative results. The E gene was detectable in 25 samples by the dry swab method out of 27 samples that tested positive by the VTM-based method (sensitivity = 92.5%). The RdRp gene was detectable in 22 samples by the dry swab method out of 27 samples that tested positive by the VTM-based method (sensitivity = 81.48%). Concordance was 91% with discordance at 9% and a Kappa value of 0.82, indicating almost perfect agreement between the two methods. Our findings indicate that the dry swab method of nucleic acid extraction is a useful alternative to conventional spin column-based extraction with comparable sensitivity and specificity. The trial was registered with the Clinical Trials Registry of India (CTRI) with a CTRI registration number of CTRI/2021/12/038792.
Collapse
Affiliation(s)
- Mohammed Faraaz Khan
- Department of Microbiology, Kamineni Institute of Medical Sciences, Narketpally, Telangana, India
| | - C. Roopa
- Department of Microbiology, SVS Medical College, Mahabubnagar, Telangana, India
| |
Collapse
|
11
|
Ortiz-Cartagena C, Pablo-Marcos D, Fernández-García L, Blasco L, Pacios O, Bleriot I, Siller M, López M, Fernández J, Aracil B, Fraile-Ribot PA, García-Fernández S, Fernández-Cuenca F, Hernández-García M, Cantón R, Calvo-Montes J, Tomás M. CRISPR-Cas13a-Based Assay for Accurate Detection of OXA-48 and GES Carbapenemases. Microbiol Spectr 2023; 11:e0132923. [PMID: 37466441 PMCID: PMC10434040 DOI: 10.1128/spectrum.01329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
Carbapenem-resistant pathogens have been recognized as a health concern as they are both difficult to treat and detect in clinical microbiology laboratories. Researchers are making great efforts to develop highly specific, sensitive, accurate, and rapid diagnostic techniques, required to prevent the spread of these microorganisms and improve the prognosis of patients. In this context, CRISPR-Cas systems are proposed as promising tools for the development of diagnostic methods due to their high specificity; the Cas13a endonuclease can discriminate single nucleotide changes and displays collateral cleavage activity against single-stranded RNA molecules when activated. This technology is usually combined with isothermal pre-amplification reactions in order to increase its sensitivity. We have developed a new LAMP-CRISPR-Cas13a-based assay for the detection of OXA-48 and GES carbapenemases in clinical samples without the need for nucleic acid purification and concentration. To evaluate the assay, we used 68 OXA-48-like-producing Klebsiella pneumoniae clinical isolates as well as 64 Enterobacter cloacae complex GES-6, 14 Pseudomonas aeruginosa GES-5, 9 Serratia marcescens GES-6, 5 P. aeruginosa GES-6, and 3 P. aeruginosa (GES-15, GES-27, and GES-40) and 1 K. pneumoniae GES-2 isolates. The assay, which takes less than 2 h and costs approximately 10 € per reaction, exhibited 100% specificity and sensitivity (99% confidence interval [CI]) for both OXA-48 and all GES carbapenemases. IMPORTANCE Carbapenems are one of the last-resort antibiotics for defense against multidrug-resistant pathogens. Multiple nucleic acid amplification methods, including multiplex PCR, multiplex loop-mediated isothermal amplification (LAMP) and multiplex RPAs, can achieve rapid, accurate, and simultaneous detection of several resistance genes to carbapenems in a single reaction. However, these assays need thermal cycling steps and specialized instruments, giving them limited application in the field. In this work, we adapted with high specificity and sensitivity values, a new LAMP CRISPR-Cas13a-based assay for the detection of OXA-48 and GES carbapenemases in clinical samples without the need for RNA extraction.
Collapse
Affiliation(s)
- Concha Ortiz-Cartagena
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Daniel Pablo-Marcos
- Microbiology Service, University Hospital Marqués de Valdecilla – IDIVAL, Santander, Spain
| | - Laura Fernández-García
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Bleriot
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - María Siller
- Microbiology Service, University Hospital Marqués de Valdecilla – IDIVAL, Santander, Spain
| | - María López
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Javier Fernández
- Microbiology Service, University Hospital Central de Asturias. Translational Microbiology Group, ISPA, Oviedo, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Belén Aracil
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Arturo Fraile-Ribot
- Microbiology Service, University Hospital Son Espases and Health Research Institute Illes Balears (IdISBa), Palma de Mallorca, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Felipe Fernández-Cuenca
- Clinical Unit of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, Institute of Biomedicine of Sevilla (University Hospital Virgen Macarena/CSIC/University of Sevilla), Sevilla, Spain
| | - Marta Hernández-García
- Microbiology Service, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Microbiology Service, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Calvo-Montes
- Microbiology Service, University Hospital Marqués de Valdecilla – IDIVAL, Santander, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| |
Collapse
|
12
|
Chen X, Zhang P, Zhang Y, Fan S, Wei Y, Yang Z, Wang F, Peng X. Potential Effect of Glutamine in the Improvement of Intestinal Stem Cell Proliferation and the Alleviation of Burn-Induced Intestinal Injury via Activating YAP: A Preliminary Study. Nutrients 2023; 15:nu15071766. [PMID: 37049605 PMCID: PMC10097377 DOI: 10.3390/nu15071766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Burn injury is a common form of traumatic injury that leads to high mortality worldwide. A severe burn injury usually induces gut barrier dysfunction, partially resulting from the impairment in the proliferation and self-renewal of intestinal stem cells (ISCs) post burns. As a main energy substance of small intestinal enterocytes, glutamine (Gln) is important for intestinal cell viability and growth, while its roles in ISCs-induced regeneration after burns are still unclear. To demonstrate the potential effects of Gln in improving ISCs proliferation and alleviating burn-induced intestinal injury, in this study, we verified that Gln significantly alleviated small intestine injury in burned mice model. It showed that Gln could significantly decrease the ferroptosis of crypt cells in the ileum, promote the proliferation of ISCs, and repair the crypt. These effects of Gln were also confirmed in the mouse small intestine organoids model. Further research found that Yes-associated protein (YAP) is suppressed after burn injury, and Gln could improve cell proliferation and accelerate the renewal of the damaged intestinal mucosal barrier after burns by activating YAP. YAP is closely associated with the changes in intestinal stem cell proliferation after burn injury and could be served as a potential target for severe burns.
Collapse
Affiliation(s)
- Xia Chen
- Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Panyang Zhang
- Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yajuan Zhang
- Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Shijun Fan
- Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yan Wei
- Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zhifan Yang
- Institute of Combined Injury, State Key Laboratory of Trauma, Burns and Combined Injury, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Fengchao Wang
- Institute of Combined Injury, State Key Laboratory of Trauma, Burns and Combined Injury, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xi Peng
- Clinical Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| |
Collapse
|
13
|
Marano JM, Weger-Lucarelli J. Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness. Front Cell Infect Microbiol 2023; 13:1130749. [PMID: 36968111 PMCID: PMC10034770 DOI: 10.3389/fcimb.2023.1130749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionFlaviviruses like dengue virus (DENV) and Zika virus (ZIKV) are mosquito-borne viruses that cause febrile, hemorrhagic, and neurological diseases in humans, resulting in 400 million infections annually. Due to their co-circulation in many parts of the world, flaviviruses must replicate in the presence of pre-existing adaptive immune responses targeted at serologically closely related pathogens, which can provide protection or enhance disease. However, the impact of pre-existing cross-reactive immunity as a driver of flavivirus evolution, and subsequently the implications on the emergence of immune escape variants, is poorly understood. Therefore, we investigated how replication in the presence of convalescent dengue serum drives ZIKV evolution.MethodsWe used an in vitro directed evolution system, passaging ZIKV in the presence of serum from humans previously infected with DENV (anti-DENV) or serum from DENV-naïve patients (control serum). Following five passages in the presence of serum, we performed next-generation sequencing to identify mutations that arose during passaging. We studied two non-synonymous mutations found in the anti-DENV passaged population (E-V355I and NS1-T139A) by generating individual ZIKV mutants and assessing fitness in mammalian cells and live mosquitoes, as well as their sensitivity to antibody neutralization.Results and discussionBoth viruses had increased fitness in Vero cells with and without the addition of anti-DENV serum and in human lung epithelial and monocyte cells. In Aedes aegypti mosquitoes—using blood meals with and without anti-DENV serum—the mutant viruses had significantly reduced fitness compared to wild-type ZIKV. These results align with the trade-off hypothesis of constrained mosquito-borne virus evolution. Notably, only the NS1-T139A mutation escaped neutralization, while E-V335I demonstrated enhanced neutralization sensitivity to neutralization by anti-DENV serum, indicating that neutralization escape is not necessary for viruses passaged under cross-reactive immune pressures. Future studies are needed to assess cross-reactive immune selection in humans and relevant animal models or with different flaviviruses.
Collapse
Affiliation(s)
- Jeffrey M. Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: James Weger-Lucarelli,
| |
Collapse
|
14
|
Komu JG, Jamsransuren D, Matsuda S, Ogawa H, Takeda Y. Efficacy Validation of SARS-CoV-2-Inactivation and Viral Genome Stability in Saliva by a Guanidine Hydrochloride and Surfactant-Based Virus Lysis/Transport Buffer. Viruses 2023; 15:v15020509. [PMID: 36851723 PMCID: PMC9959814 DOI: 10.3390/v15020509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/29/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
To enhance biosafety and reliability in SARS-CoV-2 molecular diagnosis, virus lysis/transport buffers should inactivate the virus and preserve viral RNA under various conditions. Herein, we evaluated the SARS-CoV-2-inactivating activity of guanidine hydrochloride (GuHCl)- and surfactant (hexadecyltrimethylammonium chloride (Hexa-DTMC))-based buffer, Prep Buffer A, (Precision System Science Co., Ltd., Matsudo, Japan) and its efficacy in maintaining the stability of viral RNA at different temperatures using the traditional real-time one-step RT-PCR and geneLEAD VIII sample-to-result platform. Although Prep Buffer A successfully inactivated SARS-CoV-2 in solutions with high and low organic substance loading, there was considerable viral genome degradation at 35 °C compared with that at 4 °C. The individual roles of GuHCl and Hexa-DTMC in virus inactivation and virus genome stability at 35 °C were clarified. Hexa-DTMC alone (0.384%), but not 1.5 M GuHCl alone, exhibited considerable virucidal activity, suggesting that it was essential for potently inactivating SARS-CoV-2 using Prep Buffer A. GuHCl and Hexa-DTMC individually reduced the viral copy numbers to the same degree as Prep Buffer A. Although both components inhibited RNase activity, Hexa-DTMC, but not GuHCl, directly destroyed naked viral RNA. Our findings suggest that samples collected in Prep Buffer A should be stored at 4 °C when RT-PCR will not be performed for several days.
Collapse
Affiliation(s)
- James Gitau Komu
- Graduate School of Animal and Veterinary Sciences and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Hokkaido, Japan
- Department of Medical Laboratory Sciences, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya
| | - Dulamjav Jamsransuren
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Hokkaido, Japan
| | - Sachiko Matsuda
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Hokkaido, Japan
| | - Haruko Ogawa
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Hokkaido, Japan
| | - Yohei Takeda
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Hokkaido, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Hokkaido, Japan
- Correspondence: ; Tel.: +81-155-49-5896
| |
Collapse
|
15
|
Qiu S, Xu D, Dai J, Zhang L, Tian X, Li X, Chen D, Zhou R, Liu W. Improving the efficiency and biosafety of respiratory syncytial virus identification using a nucleic acid extraction-free reagent. J Med Virol 2023; 95:e28287. [PMID: 36345579 DOI: 10.1002/jmv.28287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/27/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Respiratory syncytial virus (RSV) is the most important virus that causes lower respiratory tract disease in children; efficient viral identification is an important component of disease prevention and treatment. Here, we developed and evaluated a ready-to-use (RTU) nucleic acid extraction-free direct reagent for identification of RSV (RTU-Direct test) in clinical samples. The limit of detection (LOD) of the RSV RTU-Direct test was consistent with the LOD of the standard test using extracted nucleic acids. The virus inactivation ability of RTU-Direct reagent was confirmed by viral infectivity assays involving RTU-Direct-treated samples containing RSV and human coronavirus OC43. RSV RNA stability was significantly better in RTU-Direct reagent than in conventional virus transport medium (VTM) at room temperature and 4°C (p < 0.05). The clinical performance of the RTU-Direct test was evaluated using 155 respiratory specimens from patients with suspected RSV infection. Positive agreement between the RTU-Direct test and the VTM standard test was 100% (42/42); negative agreement was 99.1% (112/113), and the kappa statistic was 0.968 (p < 0.001). The distributions of Ct values did not significantly differ between the RTU-Direct test and the standard test (p > 0.05). Overall, the RTU-Direct reagent can improve the efficiency and biosafety of RSV detection, while reducing the cost of detection.
Collapse
Affiliation(s)
- Shuyan Qiu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Dai
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Li Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Xiao Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Dehui Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China.,Guangzhou Laboratory, Guangzhou, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
16
|
Ortiz-Cartagena C, Fernández-García L, Blasco L, Pacios O, Bleriot I, López M, Cantón R, Tomás M. Reverse Transcription-Loop-Mediated Isothermal Amplification-CRISPR-Cas13a Technology as a Promising Diagnostic Tool for SARS-CoV-2. Microbiol Spectr 2022; 10:e0239822. [PMID: 36169448 PMCID: PMC9604158 DOI: 10.1128/spectrum.02398-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/07/2022] [Indexed: 01/04/2023] Open
Abstract
At the end of 2019, a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a pandemic that persists to date and has resulted in more than 6.2 million deaths. In the last couple of years, researchers have made great efforts to develop a diagnostic technique that maintains high levels of sensitivity and specificity, since an accurate and early diagnosis is required to minimize the prevalence of SARS-CoV-2 infection. In this context, CRISPR-Cas systems are proposed as promising tools for development as diagnostic techniques due to their high specificity, highlighting that Cas13 endonuclease discriminates single nucleotide changes and displays collateral activity against single-stranded RNA molecules. With the aim of improving the sensitivity of diagnosis, this technology is usually combined with isothermal preamplification reactions (SHERLOCK, DETECTR). Based on this, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP)-CRISPR-Cas13a method for SARS-CoV-2 virus detection in nasopharyngeal samples without using RNA extraction that exhibits 100% specificity and 83% sensitivity, as well as a positive predictive value (PPV) of 100% and negative predictive values (NPVs) of 100%, 81%, 79.1%, and 66.7% for cycle threshold (CT) values of <20, 20 to 30, >30 and overall, respectively. IMPORTANCE The coronavirus disease 2019 (COVID-19) crisis has driven the development of innovative molecular diagnosis methods, including CRISPR-Cas technology. In this work, we performed a protocol, working with RNA extraction kit-free samples and using RT-LAMP-CRISPR-Cas13a technology; our results place this method at the forefront of rapid and specific diagnostic methods for COVID-19 due to the high specificity (100%), sensitivity (83%), PPVs (100%), and NPVs (81% for high viral loads) obtained with clinical samples.
Collapse
Affiliation(s)
- Concha Ortiz-Cartagena
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Laura Fernández-García
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Lucia Blasco
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Olga Pacios
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Inés Bleriot
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María López
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - María Tomás
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
17
|
Chen H, Feng S, Zhou W, Li Z, Richard-Greenblatt M, Wang P. Pretreatment Methods for Human Nasopharyngeal Swabs to Increase the Signal to Noise Ratio of High Sensitivity Immunoassays. ACS MEASUREMENT SCIENCE AU 2022; 2:414-421. [PMID: 36785662 PMCID: PMC9885992 DOI: 10.1021/acsmeasuresciau.2c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Mucous samples collected through nasopharyngeal (NP) swabs are considered gold standard specimens for the detection of respiratory pathogens. Matrices of these highly viscous samples often cause significant background noises in immunoassays, especially immunoassays with high sensitivity. We demonstrated such nonspecific background signals in both a chemiluminescence enzyme-linked immunosorbent assay (ELISA) and a novel highly sensitive immunoassay called Microbubbling SARS-CoV-2 Antigen Assay (MSAA). We developed and demonstrated the effectiveness of two quick sample pretreatment methods, filtration and preadsorption, to decrease nonspecific signals and increase the signal-to-noise ratio (SNR). Using these pretreatment methods, the SNR (at 3.6 × 104 copies/mL of inactivated SARS-CoV-2) was increased by 42.4-fold (95% CI 41.0-43.8) and 67.1-fold (95% CI 57.9-76.3) in the MSAA, and 1.3-fold (95% CI 0.9-1.7) and 1.8-fold (95% CI 1.6-2.0) in the chemiluminescence ELISA assay. Sample pretreatment methods developed in this study are broadly adaptable for the development of immunoassays for highly viscous samples.
Collapse
|
18
|
Chelsky ZL, Dittmann D, Blanke T, Chang M, Vormittag-Nocito E, Jennings LJ. Validation Study of a Direct Real-Time PCR Protocol for Detection of Monkeypox Virus. J Mol Diagn 2022; 24:1155-1159. [PMID: 36113759 PMCID: PMC9534136 DOI: 10.1016/j.jmoldx.2022.09.001] [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: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/04/2022] Open
Abstract
Monkeypox has recently been described as a public health emergency of international concern by the World Health Organization and a public health emergency by the United States. If the outbreak continues to grow, rapid scalability of laboratory testing will be imperative. During the early days of the coronavirus disease 2019 (COVID-19) pandemic, laboratories improved the scalability of testing by using a direct-to-PCR approach. To improve the scalability of monkeypox testing, a direct real-time PCR protocol for the detection of monkeypox virus was validated. The assay retains the sensitivity and accuracy of the indirect assay while eliminating the need for nucleic acid extraction kits, reducing laboratory technologist time per sample and decreasing exposure to an infectious agent. The direct method will make it easier for laboratories across the world to rapidly develop, validate, and scale testing for monkeypox virus.
Collapse
Affiliation(s)
- Zachary L Chelsky
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - David Dittmann
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Timothy Blanke
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Michael Chang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Erica Vormittag-Nocito
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Lawrence J Jennings
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
| |
Collapse
|
19
|
Zai Y, Min C, Wang Z, Ding Y, Zhao H, Su E, He N. A sample-to-answer, quantitative real-time PCR system with low-cost, gravity-driven microfluidic cartridge for rapid detection of SARS-CoV-2, influenza A/B, and human papillomavirus 16/18. LAB ON A CHIP 2022; 22:3436-3452. [PMID: 35972195 DOI: 10.1039/d2lc00434h] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19), due to the novel coronavirus (SARS-CoV-2), has created an unprecedented threat to the global health system, especially in resource-limited areas. This challenge shines a spotlight on the urgent need for a point-of-care (POC) quantitative real-time PCR (qPCR) test for sensitive and rapid diagnosis of viral infections. In a POC system, a closed, single-use, microfluidic cartridge is commonly utilized for integration of nucleic acid preparation, PCR amplification and florescence detection. But, most current cartridge systems often involve complicated nucleic acid extraction via active pumping that relies on cumbersome external hardware, causing increases in system complexity and cost. In this work, we demonstrate a gravity-driven cartridge design for an integrated viral RNA/DNA diagnostic test that does not require auxiliary hardware for fluid pumping due to adopted extraction-free amplification. This microfluidic cartridge only contains two reaction chambers for nucleic acid lysis and amplification respectively, enabling a fast qPCR test in less than 30 min. This gravity-driven pumping strategy can help simplify and minimize the microfluidic cartridge, thus enabling high-throughput (up to 12 test cartridges per test) molecular detection via a small cartridge readout system. Thus, this work addresses the scalability limitation of POC molecular testing and can be run in any settings. We verified the analytical sensitivity and specificity of the cartridge testing for respiratory pathogens and sexually transmitted diseases using SARS-CoV-2, influenza A/B RNA samples, and human papillomavirus 16/18 DNA samples. Our cartridge system exhibited a comparable detection performance to the current gold standard qPCR instrument ABI 7500. Moreover, our system showed very high diagnostic accuracy for viral RNA/DNA detection that was well validated by ROC curve analysis. The sample-to-answer molecular testing system reported in this work has the advantages of simplicity, rapidity, and low cost, making it highly promising for prevention and control of infectious diseases in poor-resource areas.
Collapse
Affiliation(s)
- Yunfeng Zai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Chao Min
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Zunliang Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
| | - Yongjun Ding
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Huan Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Enben Su
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
| |
Collapse
|
20
|
High-Throughput COVID-19 Testing of Naso-Oropharyngeal Swabs Using a Sensitive Extraction-Free Sample Preparation Method. Microbiol Spectr 2022; 10:e0135822. [PMID: 35950846 PMCID: PMC9430511 DOI: 10.1128/spectrum.01358-22] [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] [Indexed: 11/20/2022] Open
Abstract
High-throughput diagnostic assays are required for large-scale population testing for severe acute respiratory coronavirus 2 (SARS-CoV-2). The gold standard technique for SARS-CoV-2 detection in nasopharyngeal swab specimens is nucleic acid extraction followed by real-time reverse transcription-PCR. Two high-throughput commercial extraction and detection systems are used routinely in our laboratory: the Roche cobas SARS-CoV-2 assay (cobas) and the Roche MagNA Pure 96 system combined with the SpeeDx PlexPCR SARS-CoV-2 assay (Plex). As an alternative to more costly instrumentation, or tedious sample pooling to increase throughput, we developed a high-throughput extraction-free sample preparation method for naso-oropharyngeal swabs using the PlexPCR SARS-CoV-2 assay (Direct). A collection of SARS-CoV-2-positive (n = 185) and -negative (n = 354) naso-oropharyngeal swabs in transport medium were tested in parallel to compare Plex to Direct. The overall agreement comparing the qualitative outcomes was 99.3%. The mean cycle of quantification (Cq) increase and corresponding mean reduction in viral load for Direct ORF1ab and RdRp compared to Plex was 3.11 Cq (-0.91 log10 IU/mL) and 4.78 Cq (-1.35 log10 IU/mL), respectively. We also compared Direct to a four-sample pool by combining each positive sample (n = 185) with three SARS-CoV-2-negative samples extracted with MagNA Pure 96 and tested with the PlexPCR SARS-CoV-2 assay (Pool). Although less sensitive than Plex or Pool, the Direct method is a sufficiently sensitive and viable approach to increase our throughput by 12,032 results per day. Combining cobas, Plex, and Direct, an overall throughput of 19,364 results can be achieved in a 24-h period. IMPORTANCE Laboratories have experienced extraordinary demand globally for reagents, consumables, and instrumentation, while facing unprecedented testing demand needed for the diagnosis of SARS-CoV-2 infection. A major bottleneck in testing throughput is the purification of viral RNA. Extraction-based methods provide the greatest yield and purity of RNA for downstream PCR. However, these techniques are expensive, time-consuming, and depend on commercial availability of consumables. Extraction-free methods offer an accessible and cost-effective alternative for sample preparation. However, extraction-free methods often lack sensitivity compared to extraction-based methods. We describe a sensitive extraction-free protocol based on a simple purification step using a chelating resin, combined with proteinase K and thermal treatment. We compare the sensitivity qualitatively and quantitatively to a well-known commercial extraction-based system, using a PCR assay calibrated to the 1st WHO international standard for SARS-CoV-2 RNA. This method entails high throughput and is suitable for all laboratories, particularly in jurisdictions where access to instrumentation and reagents is problematic.
Collapse
|
21
|
Delgado-Diaz DJ, Sakthivel D, Nguyen HHT, Farrokzhad K, Hopper W, Narh CA, Richards JS. Strategies That Facilitate Extraction-Free SARS-CoV-2 Nucleic Acid Amplification Tests. Viruses 2022; 14:v14061311. [PMID: 35746782 PMCID: PMC9230587 DOI: 10.3390/v14061311] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
The COVID-19 pandemic has resulted in an unprecedented global demand for in vitro diagnostic reagents. Supply shortages and hoarding have impacted testing capacity which has led to inefficient COVID-19 case identification and transmission control, predominantly in developing countries. Traditionally, RNA extraction is a prerequisite for conducting SARS-CoV-2 nucleic acid amplification tests (NAAT); however, simplified methods of sample processing have been successful at bypassing typical nucleic acid extraction steps, enabling extraction-free SARS-CoV-2 NAAT workflows. These methods involve chemical and physical approaches that are inexpensive and easily accessible alternatives to overcome extraction kit supply shortages, while offering acceptable test performance. Here we provide an overview of three main sample preparation strategies that have been shown to facilitate extraction-free SARS-CoV-2 NAATs.
Collapse
Affiliation(s)
- David J. Delgado-Diaz
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
- Correspondence:
| | - Dhanasekaran Sakthivel
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - Hanh H. T. Nguyen
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - Khashayar Farrokzhad
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - William Hopper
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - Charles A. Narh
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
- Department of Medicine, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Infectious Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Jack S. Richards
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
- Department of Medicine, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Infectious Diseases, Monash University, Melbourne, VIC 3004, Australia
| |
Collapse
|
22
|
Parikh RY, Nadig SN, Mehrotra S, Howe PH, Gangaraju VK. Direct NP- A cost-effective extraction-free RT-qPCR based test for SARS-CoV-2. Heliyon 2022; 8:e09735. [PMID: 35747323 PMCID: PMC9212976 DOI: 10.1016/j.heliyon.2022.e09735] [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: 09/13/2021] [Revised: 12/01/2021] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Over 2.4 million daily total tests are currently being performed for SARS-CoV-2, in the United States. The most common SARS-CoV-2 tests require RNA extraction and purification. Extraction of RNA is a time-consuming and costly step that requires a constant supply of reagents and accessories. With the current testing demand, the supply chain remains the bottleneck for RNA extraction. Here, we report Direct NP- a cost-effective extraction-free RT-qPCR based dualplex test for SARS-CoV-2 from Nasopharyngeal (NP) swab specimens. Direct NP detects SARS-CoV-2 viral RNA from heat-denatured patient specimens using a dualplex RT-qPCR assay. Direct NP showed 92.5% positive percentage agreement (PPA) (95% Confidence Interval (CI) = 79.61%-98.43%) and 97% negative percent agreement (NPA) (95% CI = 89.11-100%) with the CDC assay. Direct NP reduces the cost per test to $2, making it suitable for broad-scale testing while lowering the cost burden on the healthcare system.
Collapse
Affiliation(s)
- Rasesh Y Parikh
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Satish N Nadig
- Department of Surgery, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shikhar Mehrotra
- Department of Surgery, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.,Department of Microbiology & Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Vamsi K Gangaraju
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| |
Collapse
|
23
|
Development and Testing of a Low-Cost Inactivation Buffer That Allows for Direct SARS-CoV-2 Detection in Saliva. Vaccines (Basel) 2022; 10:vaccines10050730. [PMID: 35632485 PMCID: PMC9143422 DOI: 10.3390/vaccines10050730] [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: 02/15/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022] Open
Abstract
Massive testing is a cornerstone in efforts to effectively track infections and stop COVID-19 transmission, including places with good vaccination coverage. However, SARS-CoV-2 testing by RT-qPCR requires specialized personnel, protection equipment, commercial kits, and dedicated facilities, which represent significant challenges for massive testing in resource-limited settings. It is therefore important to develop testing protocols that are inexpensive, fast, and sufficiently sensitive. Here, we optimized the composition of a buffer (PKTP), containing a protease, a detergent, and an RNase inhibitor, which is compatible with the RT-qPCR chemistry, allowing for direct SARS-CoV-2 detection from saliva without extracting RNA. PKTP is compatible with heat inactivation, reducing the biohazard risk of handling samples. We assessed the PKTP buffer performance in comparison to the RNA-extraction-based protocol of the US Centers for Disease Control and Prevention in saliva samples from 70 COVID-19 patients finding a good sensitivity (85.7% for the N1 and 87.1% for the N2 target) and correlations (R = 0.77, p < 0.001 for N1, and R = 0.78, p < 0.001 for N2). We also propose an auto-collection protocol for saliva samples and a multiplex reaction to minimize the PCR reaction number per patient and further reduce costs and processing time of several samples, while maintaining diagnostic standards in favor of massive testing.
Collapse
|
24
|
Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
Collapse
Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
| |
Collapse
|
25
|
Craig N, Fletcher SL, Daniels A, Newman C, O’Shea M, Tan WS, Warr A, Tait-Burkard C. Direct Lysis RT-qPCR of SARS-CoV-2 in Cell Culture Supernatant Allows for Fast and Accurate Quantification. Viruses 2022; 14:v14030508. [PMID: 35336915 PMCID: PMC8949636 DOI: 10.3390/v14030508] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify the host factors involved and treatments to combat infection. Quantification of released virions often requires lengthy procedures, whereas quantification of viral RNA in supernatant is faster and applicable to clinical isolates. Viral RNA purification is expensive in terms of time and resources, and is often unsuitable for high-throughput screening. Direct lysis protocols were explored for patient swab samples, but the lack of virus inactivation, cost, sensitivity, and accuracy is hampering their application and usefulness for in vitro studies. Here, we show a highly sensitive, accurate, fast, and cheap direct lysis RT-qPCR method for quantification of SARS-CoV-2 in culture supernatant. This method inactivates the virus and permits detection limits of 0.043 TCID50 virus and <1.89 copy RNA template per reaction. Comparing direct lysis with RNA extraction, a mean difference of +0.69 ± 0.56 cycles was observed. Application of the method to established qPCR methods for RSV (-ve RNA), IAV (segmented -ve RNA), and BHV (dsDNA) showed wider applicability to other enveloped viruses, whereby IAV showed poorer sensitivity. This shows that accurate quantification of SARS-CoV-2 and other enveloped viruses can be achieved using direct lysis protocols, facilitating a wide range of high- and low-throughput applications.
Collapse
Affiliation(s)
- Nicky Craig
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
| | - Sarah L. Fletcher
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
| | - Alison Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
- Division of Infection Medicine, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Caitlin Newman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
| | - Marie O’Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
| | - Wenfang Spring Tan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
| | - Amanda Warr
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (N.C.); (S.L.F.); (A.D.); (C.N.); (M.O.); (W.S.T.); (A.W.)
- Correspondence:
| |
Collapse
|
26
|
Ahmadzadeh M, Vahidi H, Mahboubi A, Hajifathaliha F, Nematollahi L, Mohit E. Different Respiratory Samples for COVID-19 Detection by Standard and Direct Quantitative RT-PCR: A Literature Review. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:285-299. [PMID: 34903989 PMCID: PMC8653661 DOI: 10.22037/ijpr.2021.115458.15383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The most common diagnostic method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR). Upper respiratory tract samples, including nasopharyngeal swab (NPS), oropharyngeal swab (OPS), saliva and lower respiratory tract samples such as sputum, are the most widely used specimens for diagnosis of SARS-CoV-2 using RT-qPCR. This study aimed to compare the diagnostic performance of different samples for Coronavirus disease 2019 (COVID-19) detection. It was found that NPS, the reference respiratory specimen for COVID-19 detection, is more sensitive than OPS. However, the application of NPS has many drawbacks, including challenging sampling process and increased risk of transmission to healthcare workers (HCWs). Saliva samples can be collected less invasively and quickly by HCWs with less contact or by own patients, and they can be considered as an alternative to NPS for COVID-19 detection by RT-qPCR. Additionally, sputum, which demonstrates higher viral load can be applied in patients with productive coughs and negative results from NPS. Commonly, after viral RNA purification from patient samples, which is time-consuming and costly, RT-qPCR is performed to diagnose SARS-CoV-2. Herein, different approaches including physical (heat inactivation) and chemical (proteinase K treatment) methods, used in RNA extraction free- direct RT-qPCR, were reviewed. The results of direct RT-qPCR assays were comparable to the results of standard RT-qPCR, while cost and time were saved. However, optimal protocol to decrease cost and processing time, proper transport medium and detection kit should be determined.
Collapse
Affiliation(s)
- Maryam Ahmadzadeh
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Vahidi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Mahboubi
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariba Hajifathaliha
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Nematollahi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Mohit
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
27
|
Shukla A, Gangwar M, Sharma G, Prakash P, Nath G. Vitality of Proteinase K in rRTPCR Detection of SARS-CoV2 Bypassing RNA Extraction. Front Cell Infect Microbiol 2021; 11:717068. [PMID: 34804989 PMCID: PMC8595283 DOI: 10.3389/fcimb.2021.717068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
This study aimed to detect the SARS-COV2 viral component directly from inoculated VTM without RNA extraction. Inoculated VTMs of already tested 50 positive and 50 negative samples were divided into three groups. Group I was treated with Proteinase K (PK) followed by 3-step-heat treatment at different temperatures (25°C, 60°C, and 98°C) and stored at 4°C. Group II was directly subjected to 3-step-heat treatment without PK exposure and stored at 4°C. And group III was set-up as standard group; it was processed using Qiagen's column based QIAamp Nucleic Acid kit and the obtained nucleic acids were stored at 4°C. These stored samples were used as a template to execute real-time polymerase chain reaction, and results were noted. Group I demonstrated 96% and 88% sensitivity for N and ORF1ab genes respectively, whereas group II demonstrated 78% and 60% when compared to the results of standard group III. Overall group I showed better results than group II when compared to group III. Thus, in situations where gold-standard reagents are not available, PK exposure and heat treatment can be employed to carry out molecular detection of SARS-CoV2 viral component.
Collapse
Affiliation(s)
- Alka Shukla
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Mayank Gangwar
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gaurav Sharma
- Department of Public Health Dentistry, SriRama Chandra Bhanj Dental College & Hospital, Cuttack, India
| | - Pradyot Prakash
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal Nath
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| |
Collapse
|
28
|
Gobeille Paré S, Bestman-Smith J, Fafard J, Doualla-Bell F, Jacob-Wagner M, Lavallée C, Charest H, Beauchemin S, Coutlée F, Dumaresq J, Busque L, St-Hilaire M, Lépine G, Boucher V, Desforges M, Goupil-Sormany I, Labbé AC. Natural spring water gargle samples as an alternative to nasopharyngeal swabs for SARS-CoV-2 detection using a laboratory-developed test. J Med Virol 2021; 94:985-993. [PMID: 34672374 PMCID: PMC8661969 DOI: 10.1002/jmv.27407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/28/2021] [Accepted: 10/18/2021] [Indexed: 01/23/2023]
Abstract
The objective of this study was to validate the use of spring water gargle (SWG) as an alternative to oral and nasopharyngeal swab (ONPS) for SARS‐CoV‐2 detection with a laboratory‐developed test. Healthcare workers and adults from the general population, presenting to one of two COVID‐19 screening clinics in Montréal and Québec City, were prospectively recruited to provide a gargle sample in addition to the standard ONPS. The paired specimens were analyzed using thermal lysis followed by a laboratory‐developed nucleic acid amplification test (LD‐NAAT) to detect SARS‐CoV‐2, and comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. A total of 1297 adult participants were recruited. Invalid results (n = 18) were excluded from the analysis. SARS‐CoV‐2 was detected in 144/1279 (11.3%) participants: 126 from both samples, 15 only from ONPS, and 3 only from SWG. Overall, the sensitivity was 97.9% (95% CI: 93.7–99.3) for ONPS and 89.6% (95% CI: 83.4–93.6; p = 0.005) for SWG. The mean ONPS cycle threshold (Ct) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs. 32.1; p < 0.001). In conclusion, using an LD‐NAAT with thermal lysis, SWG is a less sensitive sampling method than the ONPS. However, the higher acceptability of SWG might enable a higher rate of detection from a population‐based perspective. Nonetheless, in patients with a high clinical suspicion of COVID‐19, a repeated analysis with ONPS should be considered. The sensitivity of SWG using NAAT preceded by chemical extraction should be evaluated. Using a laboratory‐developed NAAT preceded by thermal lysis, the overall percent agreement between spring water gargle (SWG) and oral combined with nasopharyngeal swab (ONPS), sampled at the same time among 1297 participants, is excellent (98.6%). Although the SARS‐CoV‐2 NAAT from SWG is globally less sensitive than from ONPS (89.6% vs. 97.9%), the difference is markedly less in individuals symptomatic for <3 days (2.7%; p=NS) than in those whose symptoms started ≥7 days before testing (35.7%; p= 0.005).
Collapse
Affiliation(s)
- Sarah Gobeille Paré
- Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Julie Bestman-Smith
- Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada.,Département de microbiologie et d'infectiologie du Centre hospitalier universitaire (CHU) de Québec, Québec, Québec, Canada
| | - Judith Fafard
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Québec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Québec, Canada
| | - Mariève Jacob-Wagner
- Département de microbiologie et d'infectiologie du Centre hospitalier universitaire (CHU) de Québec, Québec, Québec, Canada
| | - Christian Lavallée
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Service de maladies infectieuses, CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
| | - Hugues Charest
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Québec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Stéphanie Beauchemin
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - François Coutlée
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Jeannot Dumaresq
- Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada.,Département de microbiologie et d'Infectiologie, CISSS de Chaudière-Appalaches, Lévis, Québec, Canada
| | - Lambert Busque
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Manon St-Hilaire
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Guylaine Lépine
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Valérie Boucher
- Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Marc Desforges
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département clinique de médecine de laboratoire, CHU Ste-Justine, Montréal, Québec, Canada
| | - Isabelle Goupil-Sormany
- Direction de la vigie sanitaire, Ministère de la Santé et des Services sociaux du Québec, Québec, Québec, Canada
| | - Annie-Claude Labbé
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Service de maladies infectieuses, CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
| | | |
Collapse
|
29
|
Lista MJ, Matos PM, Maguire TJA, Poulton K, Ortiz-Zapater E, Page R, Sertkaya H, Ortega-Prieto AM, Scourfield E, O’Byrne AM, Bouton C, Dickenson RE, Ficarelli M, Jimenez-Guardeño JM, Howard M, Betancor G, Galao RP, Pickering S, Signell AW, Wilson H, Cliff P, Kia Ik MT, Patel A, MacMahon E, Cunningham E, Doores K, Agromayor M, Martin-Serrano J, Perucha E, Mischo HE, Shankar-Hari M, Batra R, Edgeworth J, Zuckerman M, Malim MH, Neil S, Martinez-Nunez RT. Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation. PLoS One 2021; 16:e0256813. [PMID: 34525109 PMCID: PMC8443028 DOI: 10.1371/journal.pone.0256813] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), RNAdvance Blood/Viral (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared One-step RT-qPCR reagents: TaqMan Fast Virus 1-Step Master Mix (FastVirus, ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna® Universal Probe One-Step RT-qPCR Kit (Luna, NEB). We used primer-probes that detect viral N (EUA CDC) and RdRP. RNA extraction methods provided similar results, with Beckman performing better with our primer-probe combinations. Luna proved most sensitive although overall the three reagents did not show significant differences. N detection was more reliable than that of RdRP, particularly in samples with low viral titres. Importantly, we demonstrated that heat treatment of nasopharyngeal swabs at 70°C for 10 or 30 min, or 90°C for 10 or 30 min (both original variant and B 1.1.7) inactivated SARS-CoV-2 employing plaque assays, and had minimal impact on the sensitivity of the qPCR in clinical samples. These findings make SARS-CoV-2 testing portable in settings that do not have CL-3 facilities. In summary, we provide several testing pipelines that can be easily implemented in other laboratories and have made all our protocols and SOPs freely available at https://osf.io/uebvj/.
Collapse
Affiliation(s)
- Maria Jose Lista
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Pedro M. Matos
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Thomas J. A. Maguire
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Inflammation Biology, School of Immunology and Microbial Sciences, Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College London, London, United Kingdom
| | - Kate Poulton
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
- Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
| | - Robert Page
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- King’s Health Partners Integrated Cancer Centre, School of Cancer and Pharmaceutical Sciences, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Helin Sertkaya
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ana M. Ortega-Prieto
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Edward Scourfield
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Aoife M. O’Byrne
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Centre for Inflammation Biology and Cancer Immunology (CIBCI), Centre for Rheumatic Diseases (CRD–EULAR Centre of Excellence), King’s College London, London, United Kingdom
| | - Clement Bouton
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ruth E. Dickenson
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Mattia Ficarelli
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jose M. Jimenez-Guardeño
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Mark Howard
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
| | - Gilberto Betancor
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rui Pedro Galao
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Suzanne Pickering
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Adrian W. Signell
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Harry Wilson
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Penelope Cliff
- Viapath pathology laboratories at St Thomas’ Hospital, London, United Kingdom
| | - Mark Tan Kia Ik
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Amita Patel
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Eithne MacMahon
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Emma Cunningham
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Katie Doores
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Monica Agromayor
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Juan Martin-Serrano
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Esperanza Perucha
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Centre for Inflammation Biology and Cancer Immunology (CIBCI), Centre for Rheumatic Diseases (CRD–EULAR Centre of Excellence), King’s College London, London, United Kingdom
| | - Hannah E. Mischo
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Manu Shankar-Hari
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rahul Batra
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Jonathan Edgeworth
- Centre for Infectious Diseases Research, St Thomas’ Hospital, London, United Kingdom
| | - Mark Zuckerman
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- South London Specialist Virology Centre, King’s College Hospital, London, United Kingdom
| | - Michael H. Malim
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Stuart Neil
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rocio Teresa Martinez-Nunez
- King’s College London Diagnostics Team at Guy’s Campus, London, United Kingdom
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| |
Collapse
|
30
|
Polvere I, Silvestri E, Sabatino L, Giacco A, Iervolino S, Peluso T, Guida R, Zerillo L, Varricchio R, D’Andrea S, Voccola S, Madera JR, Zullo A, Stilo R, Vito P, Zotti T. Sample-Pooling Strategy for SARS-CoV-2 Detection among Students and Staff of the University of Sannio. Diagnostics (Basel) 2021; 11:diagnostics11071166. [PMID: 34206932 PMCID: PMC8303429 DOI: 10.3390/diagnostics11071166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/28/2022] Open
Abstract
Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, it has been clear that testing large groups of the population was the key to stem infection and prevent the effects of the coronavirus disease of 2019, mostly among sensitive patients. On the other hand, time and cost-sustainability of virus detection by molecular analysis such as reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) may be a major issue if testing is extended to large communities, mainly asymptomatic large communities. In this context, sample-pooling and test grouping could offer an effective solution. Here we report the screening on 1195 oral-nasopharyngeal swabs collected from students and staff of the Università degli Studi del Sannio (University of Sannio, Benevento, Campania, Italy) and analyzed by an in-house developed multiplex RT-qPCR for SARS-CoV-2 detection through a simple monodimensional sample pooling strategy. Overall, 400 distinct pools were generated and, within 24 h after swab collection, five positive samples were identified. Out of them, four were confirmed by using a commercially available kit suitable for in vitro diagnostic use (IVD). High accuracy, sensitivity and specificity were also determined by comparing our results with a reference IVD assay for all deconvoluted samples. Overall, we conducted 463 analyses instead of 1195, reducing testing resources by more than 60% without lengthening diagnosis time and without significant losses in sensitivity, suggesting that our strategy was successful in recognizing positive cases in a community of asymptomatic individuals with minor requirements of reagents and time when compared to normal testing procedures.
Collapse
Affiliation(s)
- Immacolata Polvere
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Elena Silvestri
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Lina Sabatino
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Antonia Giacco
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Stefania Iervolino
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Teresa Peluso
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Rosa Guida
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Lucrezia Zerillo
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Romualdo Varricchio
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Silvia D’Andrea
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Serena Voccola
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
- Consorzio Sannio Tech, SS Appia, 82030 Apollosa, Italy
| | - Jessica Raffaella Madera
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Alberto Zullo
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Romania Stilo
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Pasquale Vito
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
- Correspondence: (P.V.); (T.Z.); Tel.: +39-0824305105 (P.V. & T.Z.)
| | - Tiziana Zotti
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
- Correspondence: (P.V.); (T.Z.); Tel.: +39-0824305105 (P.V. & T.Z.)
| |
Collapse
|
31
|
Torres I, Qualai J, Albert E, Bueno F, Huntley D, Poujois S, Gil MT, Navarro D. Real-life evaluation of a rapid extraction-free SARS-CoV-2 RT-PCR assay (COVID-19 PCR Fast-L) for the diagnosis of COVID-19. J Med Virol 2021; 93:5233-5235. [PMID: 33913561 PMCID: PMC8242721 DOI: 10.1002/jmv.27039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Ignacio Torres
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Jamal Qualai
- Sistemas Genómicos, Grupo Biomédico Ascires, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Felipe Bueno
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Dixie Huntley
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Sandrine Poujois
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | | | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| |
Collapse
|
32
|
Lista MJ, Matos PM, Maguire TJA, Poulton K, Ortiz-Zapater E, Page R, Sertkaya H, Ortega-Prieto AM, O’Byrne AM, Bouton C, Dickenson RE, Ficarelli M, Jimenez-Guardeño JM, Howard M, Betancor G, Galao RP, Pickering S, Signell AW, Wilson H, Cliff P, Ik MTK, Patel A, MacMahon E, Cunningham E, Doores K, Agromayor M, Martin-Serrano J, Perucha E, Mischo HE, Shankar-Hari M, Batra R, Edgeworth J, Zuckerman M, Malim MH, Neil S, Martinez-Nunez RT. Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.04.22.20074351. [PMID: 33851184 PMCID: PMC8043481 DOI: 10.1101/2020.04.22.20074351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), RNAdvance Blood/Viral (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared One-step RT-qPCR reagents: TaqMan Fast Virus 1-Step Master Mix (FastVirus, ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna ® Universal Probe One-Step RT-qPCR Kit (Luna, NEB). We used primer-probes that detect viral N (EUA CDC) and RdRP (PHE guidelines). All RNA extraction methods provided similar results. FastVirus and Luna proved most sensitive. N detection was more reliable than that of RdRP, particularly in samples with low viral titres. Importantly, we demonstrate that treatment of nasopharyngeal swabs with 70 degrees for 10 or 30 min, or 90 degrees for 10 or 30 min (both original variant and B 1.1.7) inactivates SARS-CoV-2 employing plaque assays, and that it has minimal impact on the sensitivity of the qPCR in clinical samples. These findings make SARS-CoV-2 testing portable to settings that do not have CL-3 facilities. In summary, we provide several testing pipelines that can be easily implemented in other laboratories and have made all our protocols and SOPs freely available at https://osf.io/uebvj/ .
Collapse
Affiliation(s)
- Maria Jose Lista
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Pedro M. Matos
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Thomas J. A. Maguire
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Inflammation Biology, School of Immunology and Microbial Sciences. Asthma UK Centre in Allergic Mechanisms of Asthma. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Kate Poulton
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
- All these authors contributed equally to the completion of this work
| | - Elena Ortiz-Zapater
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Randall Centre for Cell & Molecular Biophysics. Guy’s Campus, King’s College London, SE1 1UL, UK
- Peter Gorer Department of Immunobiology. Guy’s Campus, King’s College London, SE1 9RT, UK
| | - Robert Page
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Inflammation Biology, School of Immunology and Microbial Sciences. Asthma UK Centre in Allergic Mechanisms of Asthma. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Helin Sertkaya
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Ana M. Ortega-Prieto
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Aoife M. O’Byrne
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Centre for Inflammation Biology and Cancer Immunology (CIBCI). Centre for Rheumatic Diseases (CRD – EULAR Centre of Excellence). Guy’s Campus, King’s College London SE1 1UL, UK
| | - Clement Bouton
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Ruth E Dickenson
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Mattia Ficarelli
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Jose M. Jimenez-Guardeño
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Mark Howard
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Peter Gorer Department of Immunobiology. Guy’s Campus, King’s College London, SE1 9RT, UK
| | - Gilberto Betancor
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Rui Pedro Galao
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Suzanne Pickering
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Adrian W Signell
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Harry Wilson
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | | | - Mark Tan Kia Ik
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Amita Patel
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Eithne MacMahon
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Emma Cunningham
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Katie Doores
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Monica Agromayor
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Juan Martin-Serrano
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Esperanza Perucha
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Centre for Inflammation Biology and Cancer Immunology (CIBCI). Centre for Rheumatic Diseases (CRD – EULAR Centre of Excellence). Guy’s Campus, King’s College London SE1 1UL, UK
| | - Hannah E. Mischo
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Manu Shankar-Hari
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Rahul Batra
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Jonathan Edgeworth
- Centre for Infectious Diseases Research, St Thomas’ Hospital (London, UK)
| | - Mark Zuckerman
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Virology. King’s College Hospital (London, UK)
| | - Michael H. Malim
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Stuart Neil
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| | - Rocio Teresa Martinez-Nunez
- King’s College London Diagnostics Team at Guy’s Campus (London, UK)
- Dept. Infectious Diseases, School of Immunology and Microbial Sciences. Guy’s Campus, King’s College London SE1 9RT, UK
| |
Collapse
|