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Ding X, Wang Y, Gui Y, Yang C. Two-Stage Mixed-Dye-Based Isothermal Amplification with Ribonuclease-Cleavable Enhanced Probes for Dual-Visualization Detection of SARS-CoV-2 Variants of Interest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401988. [PMID: 38829265 PMCID: PMC11304323 DOI: 10.1002/advs.202401988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Rapid and visual detection of SARS-CoV-2 variants is vital for timely assessment of variant transmission in resource-limited settings. Here, a closed-tube, two-stage, mixed-dye-based isothermal amplification method with ribonuclease-cleavable enhanced probes (REP), termed REP-TMAP, for dual-visualization detection of SARS-CoV-2 variants including JN.1, BA.2, BA.4/5, and Delta is introduced. The first stage of REP-TMAP is reverse transcription recombinase polymerase amplification and the second stage is dual-visualization detection synergistically mediated by the REP and the mixed dyes of cresol red and hydroxy naphthol blue. In REP-TMAP reaction, the color change under ambient light indicates SARS-CoV-2 infection, while the fluorescence change under blue light excitation specifies variant type. On detecting transcribed RNA of SARS-CoV-2 spike gene, this assay is rapid (within 40 min), highly sensitive (10-200 copies per reaction), and highly specific (identification of single-base mutations). Furthermore, the assay has been clinically validated to accurately detect JN.1, BA.2, and BA.4/5 variants from 102 human oropharyngeal swabs. The proposed assay therefore holds great potentials to provide a rapid, dual-visualization, sensitive, specific, point-of-care detection of SARS-CoV-2 variants and beyond.
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Affiliation(s)
- Xiong Ding
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Yaru Wang
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Yuxin Gui
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Chuankun Yang
- Center of Clinical Laboratory MedicineZhongda Hospital, Southeast UniversityNanjing210009P. R. China
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Kumblathan T, Liu Y, Crisol M, Pang X, Hrudey SE, Le XC, Li XF. Advances in wastewater analysis revealing the co-circulating viral trends of noroviruses and Omicron subvariants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170887. [PMID: 38350564 DOI: 10.1016/j.scitotenv.2024.170887] [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: 11/28/2023] [Revised: 01/19/2024] [Accepted: 02/08/2024] [Indexed: 02/15/2024]
Abstract
Co-presence of enveloped and non-enveloped viruses is common both in community circulation and in wastewater. Community surveillance of infections requires robust methods enabling simultaneous quantification of multiple viruses in wastewater. Using enveloped SARS-CoV-2 Omicron subvariants and non-enveloped norovirus (NoV) as examples, this study reports a robust method that integrates electronegative membrane (EM) concentration, viral inactivation, and RNA preservation (VIP) with efficient capture and enrichment of the viral RNA on magnetic (Mag) beads, and direct detection of RNA on the beads. This method provided improved viral recoveries of 80 ± 4 % for SARS-CoV-2 and 72 ± 5 % for Murine NoV. Duplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays with newly designed degenerate primer-probe sets offered high PCR efficiencies (90-91 %) for NoV (GI and GII) targets and were able to detect as few as 15 copies of the viral RNA per PCR reaction. This technique, combined with duplex detection of NoV and multiplex detection of Omicron, successfully quantified NoV (GI and GII) and Omicron variants in the same sets of 94 influent wastewater samples collected from two large wastewater systems between July 2022 and June 2023. The wastewater viral RNA results showed temporal changes of both NoV and Omicron variants in the same wastewater systems and revealed an inverse relationship of their emergence. This study demonstrated the importance of a robust analytical platform for simultaneous surveillance of enveloped and non-enveloped viruses in wastewater. The ability to sensitively determine multiple viral pathogens in wastewater will advance applications of wastewater surveillance as a complementary public health tool.
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Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Mary Crisol
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xiaoli Pang
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2B7, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta T6G 2J2, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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Kumblathan T, Liu Y, Pang X, Hrudey SE, Le XC, Li XF. Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance. ENVIRONMENT & HEALTH (WASHINGTON, D.C.) 2023; 1:203-213. [PMID: 37736345 PMCID: PMC10510104 DOI: 10.1021/envhealth.3c00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 09/23/2023]
Abstract
Wastewater surveillance plays an important role in the monitoring of infections of SARS-CoV-2 at the community level. We report here the determination of SARS-CoV-2 and differentiation of its variants of concern in 294 wastewater samples collected from two major Canadian cities from May 2021 to March 2023. The overall method of analysis involved extraction of the virus and viral components using electronegative membranes, in situ stabilization and concentration of the viral RNA onto magnetic beads, and direct analysis of the viral RNA on the magnetic beads. Multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays, targeting specific and naturally selected mutations in SARS-CoV-2, enabled detection and differentiation of the Alpha, Beta, Gamma, Delta, and Omicron variants. An Omicron triplex RT-qPCR assay targeting three mutations, HV 69-70 deletion, K417N, and L452R, was able to detect and differentiate the Omicron BA.1/BA.3, BA.2/XBB, and BA.4/5. This assay had efficiencies of 90-104% for all three mutation targets and a limit of detection of 28 RNA copies per reaction. Analyses of 294 wastewater samples collected over a two-year span showed the concentrations and trends of Alpha, Beta, Gamma, Delta, and Omicron variants as they emerge in two major Canadian cities participating in the wastewater surveillance program. The trends of specific variants were consistent with clinical reports for the same period. At the beginning of each wave, the corresponding variants were detectable in wastewater. For example, RNA concentrations of the BA.2 variant were as high as 104 copies per 100 mL of wastewater collected in January 2022, when approximately only 50-60 clinical cases of BA.2 infection were reported in Canada. These results show that the strategy and highly sensitive assays for the variants of concern in wastewater are potentially useful for the detection of newly emerging SARS-CoV-2 variants and other viruses for future community biomonitoring.
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Affiliation(s)
- Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xiaoli Pang
- Division
of Diagnostic and Applied Microbiology, Department of Laboratory Medicine
and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2B7
- Public
Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada T6G 2J2
| | - Steve E. Hrudey
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
- Division
of Diagnostic and Applied Microbiology, Department of Laboratory Medicine
and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2B7
- Public
Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada T6G 2J2
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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Liu Y, Kumblathan T, Joyce MA, Tyrrell DL, Tipples G, Pang X, Li XF, Le XC. Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples. ACS MEASUREMENT SCIENCE AU 2023; 3:258-268. [PMID: 37600458 PMCID: PMC10152402 DOI: 10.1021/acsmeasuresciau.3c00005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 08/22/2023]
Abstract
The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4-16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May-June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.
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Affiliation(s)
- Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Michael A. Joyce
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Graham Tipples
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
| | - Xiaoli Pang
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
- Department
of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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5
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Kumblathan T, Liu Y, Qiu Y, Pang L, Hrudey SE, Le XC, Li XF. An efficient method to enhance recovery and detection of SARS-CoV-2 RNA in wastewater. J Environ Sci (China) 2023; 130:139-148. [PMID: 37032030 PMCID: PMC9554329 DOI: 10.1016/j.jes.2022.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 05/25/2023]
Abstract
Wastewater surveillance (WS) of SARS-CoV-2 currently requires multiple steps and suffers low recoveries and poor sensitivity. Here, we report an improved analytical method with high sensitivity and recovery to quantify SARS-CoV-2 RNA in wastewater. To improve the recovery, we concentrated SARS-CoV-2 viral particles and RNA from both the solid and aqueous phases of wastewater using an electronegative membrane (EM). The captured viral particles and RNA on the EM were incubated in our newly developed viral inactivation and RNA preservation (VIP) buffer. Subsequently, the RNA was concentrated on magnetic beads and inhibitors removed by washing. Without eluting, the RNA on the magnetic beads was directly detected using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Analysis of SARS-CoV-2 pseudovirus (SARS-CoV-2 RNA in a noninfectious viral coat) spiked to wastewater samples showed an improved recovery of 80%. Analysis of 120 wastewater samples collected twice weekly between May 2021 and February 2022 from two wastewater treatment plants showed 100% positive detection, which agreed with the results independently obtained by a provincial public health laboratory. The concentrations of SARS-CoV-2 RNA in these wastewater samples ranged from 2.4×102 to 2.9×106 copies per 100 mL of wastewater. Our method's capability of detecting trace and diverse concentrations of SARS-CoV-2 in complex wastewater samples is attributed to the enhanced recovery of SARS-CoV-2 RNA and efficient removal of PCR inhibitors. The improved method for the recovery and detection of viral RNA in wastewater is important for wastewater surveillance, complementing clinical diagnostic tests for public health protection.
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Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yuanyuan Qiu
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2G3, Canada
| | - Lilly Pang
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2G3, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, T6G 2G3, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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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.
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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
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