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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.
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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
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2
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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.
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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
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3
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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.
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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
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4
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Faruque MRJ, Bikker FJ, Laine ML. Comparing SARS-CoV-2 Viral Load in Human Saliva to Oropharyngeal Swabs, Nasopharyngeal Swabs, and Sputum: A Systematic Review and Meta-Analysis. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:5807370. [PMID: 37600753 PMCID: PMC10435302 DOI: 10.1155/2023/5807370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/04/2022] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
A systematic review and meta-analysis were conducted to investigate the SARS-CoV-2 viral load in human saliva and compared it with the loads in oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, the salivary viral loads of symptomatic and asymptomatic COVID-19 patients were compared. Searches were conducted using four electronic databases: PubMed, Embase, Scopus, and Web of Science, for studies published on SARS-CoV-2 loads expressed by CT values or copies/mL RNA. Three reviewers evaluated the included studies to confirm eligibility and assessed the risk of bias. A total of 37 studies were included. Mean CT values in saliva ranged from 21.5 to 39.6 and mean copies/mL RNA ranged from 1.91 × 101 to 6.98 × 1011. Meta-analysis revealed no significant differences in SARS-CoV-2 load in saliva compared to oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, no significant differences were observed in the salivary viral load of symptomatic and asymptomatic COVID-19 patients. We conclude that saliva specimen can be used as an alternative for SARS-CoV-2 detection in oropharyngeal swabs, nasopharyngeal swabs, and sputum.
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Affiliation(s)
- Mouri R. J. Faruque
- Department of Periodontology, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
| | - Marja L. Laine
- Department of Periodontology, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
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5
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Bayati M, Hsieh HY, Hsu SY, Li C, Rogers E, Belenchia A, Zemmer SA, Blanc T, LePage C, Klutts J, Reynolds M, Semkiw E, Johnson HY, Foley T, Wieberg CG, Wenzel J, Lyddon T, LePique M, Rushford C, Salcedo B, Young K, Graham M, Suarez R, Ford A, Lei Z, Sumner L, Mooney BP, Wei X, Greenlief CM, Johnson MC, Lin CH. Identification and quantification of bioactive compounds suppressing SARS-CoV-2 signals in wastewater-based epidemiology surveillance. WATER RESEARCH 2022; 221:118824. [PMID: 35830746 PMCID: PMC9253601 DOI: 10.1016/j.watres.2022.118824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 05/21/2023]
Abstract
Recent SARS-CoV-2 wastewater-based epidemiology (WBE) surveillance have documented a positive correlation between the number of COVID-19 patients in a sewershed and the level of viral genetic material in the wastewater. Efforts have been made to use the wastewater SARS-CoV-2 viral load to predict the infected population within each sewershed using a multivariable regression approach. However, reported clear and sustained variability in SARS-CoV-2 viral load among treatment facilities receiving industrial wastewater have made clinical prediction challenging. Several classes of molecules released by regional industries and manufacturing facilities, particularly the food processing industry, can significantly suppress the SARS-CoV-2 signals in wastewater by breaking down the lipid-bilayer of the membranes. Therefore, a systematic ranking process in conjugation with metabolomic analysis was developed to identify the wastewater treatment facilities exhibiting SARS-CoV-2 suppression and identify and quantify the chemicals suppressing the SARS-COV-2 signals. By ranking the viral load per diagnosed case among the sewersheds, we successfully identified the wastewater treatment facilities in Missouri, USA that exhibit SARS-CoV-2 suppression (significantly lower than 5 × 1011 gene copies/reported case) and determined their suppression rates. Through both untargeted global chemical profiling and targeted analysis of wastewater samples, 40 compounds were identified as candidates of SARS-CoV-2 signal suppressors. Among these compounds, 14 had higher concentrations in wastewater treatment facilities that exhibited SARS-CoV-2 signal suppression compared to the unsuppressed control facilities. Stepwise regression analyses indicated that 4-nonylphenol, palmitelaidic acid, sodium oleate, and polyethylene glycol dioleate are positively correlated with SARS-CoV-2 signal suppression rates. Suppression activities were further confirmed by incubation studies, and the suppression kinetics for each bioactive compound were determined. According to the results of these experiments, bioactive molecules in wastewater can significantly reduce the stability of SARS-CoV-2 genetic marker signals. Based on the concentrations of these chemical suppressors, a correction factor could be developed to achieve more reliable and unbiased surveillance results for wastewater treatment facilities that receive wastewater from similar industries.
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Affiliation(s)
- Mohamed Bayati
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Hsin-Yeh Hsieh
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Shu-Yu Hsu
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65211, USA
| | - Chenhui Li
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Elizabeth Rogers
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65211, USA
| | - Anthony Belenchia
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Sally A Zemmer
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Todd Blanc
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Cindy LePage
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Jessica Klutts
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Melissa Reynolds
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Elizabeth Semkiw
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Hwei-Yiing Johnson
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Trevor Foley
- Missouri Department of Corrections, Jefferson City, MO 65109, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Terri Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Mary LePique
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Clayton Rushford
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Braxton Salcedo
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Kara Young
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Madalyn Graham
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Reinier Suarez
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Anarose Ford
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Zhentian Lei
- Metabolomics Center, Department of Biochemistry, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Lloyd Sumner
- Metabolomics Center, Department of Biochemistry, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Brian P Mooney
- Charles W. Gehrke Proteomics Center, Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Xing Wei
- Charles W. Gehrke Proteomics Center, Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - C Michael Greenlief
- Charles W. Gehrke Proteomics Center, Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Chung-Ho Lin
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65211, USA.
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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.
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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
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7
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Evaluation of sample treatments in a safe and straightforward procedure for the detection of SARS-CoV-2 in saliva. Int J Infect Dis 2021; 108:413-418. [PMID: 34044144 PMCID: PMC8142814 DOI: 10.1016/j.ijid.2021.05.053] [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: 03/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 01/23/2023] Open
Abstract
Objectives To evaluate four sample treatments in a safe and straightforward procedure to detect SARS-CoV-2 in saliva. Methods Four sample treatments were evaluated in a 3-step procedure to detect SARS-CoV-2 in saliva: 1) heating at 95 °C for 5 min for sample inactivation; 2) sample treatment; 3) analysis by reverse-transcription loop-mediated isothermal amplification (LAMP). Saliva samples used were from infected individuals or were spiked with known quantities of viral particles. Results Three treatments had a limit of detection (LOD) of 500.000 viral particles per ml of saliva and could be used to detect individuals with potential to transmit the disease. The treatment of phosphate buffer, dithiothreitol, ethylenediaminetetraacetic acid and proteinase K, with an additional 95 °C heating step, yielded a lower LOD of 95; its sensitivity ranged from 100% in patients with nasopharyngeal swab reverse-transcriptase polymerase chain reaction cycle threshold values <20 to 47.8% for values >30. Conclusions This report highlights the importance of an adequate sample treatment for saliva to detect SARS-CoV-2 and describes a flexible procedure that can be adapted to point-of-care. Although its sensitivity when LAMP is used is lower than reverse-transcriptase polymerase chain reaction, this procedure can contribute to COVID-19 control by detecting individuals able to transmit the disease.
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8
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Panchal D, Prakash O, Bobde P, Pal S. SARS-CoV-2: sewage surveillance as an early warning system and challenges in developing countries. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:22221-22240. [PMID: 33733417 PMCID: PMC7968922 DOI: 10.1007/s11356-021-13170-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/22/2021] [Indexed: 04/15/2023]
Abstract
Transmission of novel coronavirus (SARS-CoV-2) in humans happens either through airway exposure to respiratory droplets from an infected patient or by touching the virus contaminated surface or objects (fomites). Presence of SARS-CoV-2 in human feces and its passage to sewage system is an emerging concern for public health. Pieces of evidence of the occurrence of viral RNA in feces and municipal wastewater (sewage) systems have not only warned reinforcing the treatment facilities but also suggest that these systems can be monitored to get epidemiological data for checking trend of COVID-19 infection in the community. This review summarizes the occurrence and persistence of novel coronavirus in sewage with an emphasis on the possible water environment contamination. Monitoring of novel coronavirus (SARS-CoV-2) via sewage-based epidemiology could deliver promising information regarding rate of infection providing a valid and complementary tool for tracking and diagnosing COVID-19 across communities. Tracking the sewage systems could act as an early warning tool for alerting the public health authorities for necessary actions. Given the impracticality of testing every citizen with limited diagnostic resources, it is imperative that sewage-based epidemiology can be tested as an early warning system. The need for the development of robust sampling strategies and subsequent detection methodologies and challenges for developing countries are also discussed.
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Affiliation(s)
- Deepak Panchal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Om Prakash
- Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Prakash Bobde
- Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
- Department of Research & Development, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
| | - Sukdeb Pal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Wastewater Technology Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.
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9
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Genoud V, Stortz M, Waisman A, Berardino BG, Verneri P, Dansey V, Salvatori M, Remes Lenicov F, Levi V. Extraction-free protocol combining proteinase K and heat inactivation for detection of SARS-CoV-2 by RT-qPCR. PLoS One 2021; 16:e0247792. [PMID: 33635936 PMCID: PMC7909620 DOI: 10.1371/journal.pone.0247792] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Real-time reverse transcription PCR (RT-qPCR) is the gold-standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in nasopharyngeal swabs specimens. The analysis by RT-qPCR usually requires a previous extraction step to obtain the purified viral RNA. Unfortunately, RNA extraction constitutes a bottleneck for early detection in many countries since it is expensive, time-consuming and depends on the availability of commercial kits. Here, we describe an extraction-free protocol for SARS-CoV-2 detection by RT-qPCR from nasopharyngeal swab clinical samples in saline solution. The method includes a treatment with proteinase K followed by heat inactivation (PK+HID method). We demonstrate that PK+HID improves the RT-qPCR performance in comparison to the heat-inactivation procedure. Moreover, we show that this extraction-free protocol can be combined with a variety of multiplexing RT-qPCR kits. The method combined with a multiplexing detection kit targeting N and ORF1ab viral genes showed a sensitivity of 0.99 and a specificity of 0.99 from the analysis of 106 positive and 106 negative clinical samples. In conclusion, PK+HID is a robust, fast and inexpensive procedure for extraction-free RT-qPCR determinations of SARS-CoV-2. The National Administration of Drugs, Foods and Medical Devices of Argentina has recently authorized the use of this method.
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Affiliation(s)
- Valeria Genoud
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martin Stortz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Bruno G. Berardino
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Verneri
- Facultad de Ciencias Exactas y Naturales, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Virginia Dansey
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Melina Salvatori
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Valeria Levi
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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10
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Matic N, Lawson T, Ritchie G, Stefanovic A, Leung V, Champagne S, Romney MG, Lowe CF. Automated molecular testing of saliva for SARS-CoV-2 detection. Diagn Microbiol Infect Dis 2021; 100:115324. [PMID: 33529938 PMCID: PMC7826079 DOI: 10.1016/j.diagmicrobio.2021.115324] [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: 09/21/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 01/12/2023]
Abstract
With surging global demand for SARS-CoV-2 testing capacity, laboratories seek automated, high-throughput molecular solutions, particularly for specimens not requiring specialized collection devices or viral transport media. Saliva specimens submitted from patients under investigation for COVID-19 from March to July 2020 were processed in the laboratory with sterile phosphate-buffered saline in a 1:2 dilution and tested using manual extraction and a commercial assay for detection of the SARS-CoV-2 E gene (LightMix®) in comparison to the Roche cobas® SARS-CoV-2 Test on the cobas® 6800 instrument. 34.4% (22/64) of saliva samples were positive for SARS-CoV-2. Positive and negative concordance between the LightMix® and cobas® assays were 100%. The overall invalid rate for saliva on the cobas® 6800 (1/128, 0.78%) was similar to the baseline invalid rate observed for nasopharyngeal swabs/viral transport media. Saliva is a feasible specimen type for SARS-CoV-2 testing on the cobas® 6800 platform, with potential to improve turnaround time and enhance testing capacity.
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Affiliation(s)
- Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sylvie Champagne
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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11
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Liu Z, Tong Y, Wu J, Du L, Wei C, Cui W, Cao Y, Chen M, Cai Z, Chen W, Ding H, Guan M, Guo W, Gao C, Hao X, Hu C, Huang S, Jiang Y, Li J, Li P, Li Z, Ming L, Pan S, Shen Z, Su J, Sun Z, Wang H, Wang J, Xu B, Yu N, Zheng L, Zhang Y, Zhang X, Zhang Y, Duan Y, Wang C. Chinese Expert Consensus on the Nucleic Acid Detection of SARS-CoV-2. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1631. [PMID: 33490143 PMCID: PMC7812184 DOI: 10.21037/atm-20-4060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The coronavirus disease 2019 (COVID-19) has already become a pandemic wherein the infection's timely diagnosis has proven beneficial to patient treatment and disease control. Nucleic acid detection has been the primary laboratory diagnostic method for the detection of SARS-CoV-2. To ensure laboratory staff safety and quality nucleic acid testing, the Chinese Society of Laboratory Medicine formulated this consensus, based on the Chinese National Recommendations and previous literature for nucleic acid detection. A working group comprises 34 hospital professionals experience with real-time polymerase chain reactions (PCR) testing for SARS-CoV-2 drafted guidance statements during online discussions. A modified Delphi methodology was used in forming a consensus among a wider group of hospital professionals with SARS-CoV-2 detection experience. Guidance statements were developed for four categories: (I) specimen type, priority, collecting, transportation and receiving; (II) nucleic acid isolation and amplification; (III) quality control; (IV) biosafety management and decontamination. The modified Delphi voting process included a total of 29 guidance statements and final agreement. Consensus was reached after two rounds of voting. Recommendations were established for the detection of SARS-CoV-2 using real time PCR testing based on evidence and group consensus. The manuscript was evaluated against The Appraisal of Guidelines for Research & Evaluation Instrument (AGREE II) and was developed to aid medical laboratory staff in the detection of the ribonucleic acid (RNA) of SARS-CoV-2.
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Affiliation(s)
- Zijie Liu
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Department of Laboratory Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yongqing Tong
- Laboratory Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jun Wu
- Department of Clinical Laboratory, Shanghai General Hospital Jiading Branch, Shanghai, China
| | - Lutao Du
- Laboratory Medicine Center of The Second Hospital of Shandong University, Jinan, China
| | - Chaojun Wei
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, Lanzhou, China
| | - Wei Cui
- Department of Laboratory Medicine, Cancer Hospital Chinese Academy of Medical Sciences, Beijing, China
| | - Yongtong Cao
- Laboratory Department of China-Japan Friendship Hospital, Beijing, China
| | - Ming Chen
- Laboratory Department of Southwest Hospital, Chongqing, China
| | - Zhen Cai
- Department of Laboratory Medicine, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Wei Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haitao Ding
- Department of Laboratory Medicine, People's Hospital of Inner Mongolia Autonomous Region, Hohhot, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Xiaoke Hao
- Department of Laboratory Medicine, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Chengjin Hu
- Department of Laboratory Diagnosis, 960th Hospital of Chinese PLA, Jinan, China
| | - Shan Huang
- Guizhou Province Center for Clinical Laboratory, Guiyang, China
| | - Yanfang Jiang
- Gene Diagnostic Center of the First Hospital of Jilin University, Changchun, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing, China
| | - Ping Li
- Medical Laboratory and Pathology Center, the First Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Zhuo Li
- Department of Laboratory Medicine, the First Affiliated Hospital of Xi'an Medical College, Xian, China
| | - Liang Ming
- Department of Laboratory Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shiyang Pan
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zuojun Shen
- Scientific Research Department of the First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Jianrong Su
- Department of Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Laboratory Medicine, Peking University People's Hospital, Beijing, China
| | - Junjun Wang
- Department of Laboratory Medicine, Eastern Theater General Hospital; Nanjing, China
| | - Bin Xu
- Provincial Clinical Inspection Center of Jiangsu Cancer Hospital, Nanjing, China
| | - Nong Yu
- Laboratory of Suzhou Branch of Xinhua Hospital Affiliated to Shanghai Jiaotong University, Suzhou, China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Department of Laboratory Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Zhang
- Department of Laboratory Medicine of Xinjiang Production and Construction Corps Hospital, Urumqi, China
| | - Ying Zhang
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yong Duan
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Department of Laboratory Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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12
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Premraj A, Aleyas AG, Nautiyal B, Rasool TJ. Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls. Diagnostics (Basel) 2020; 10:E866. [PMID: 33114057 PMCID: PMC7690661 DOI: 10.3390/diagnostics10110866] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is a pandemic that has affected 214 countries affecting more than 37.4 million people causing 1.07 million deaths as of the second week of October 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a checklist of factors to be considered to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories.
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Affiliation(s)
| | | | | | - Thaha J Rasool
- Camel Biotechnology Center, Presidential Camels and Camel Racing Affairs Centre, Department of the President’s Affairs, P.O. Box 17292, Al Ain 17292, UAE; (A.P.); (A.G.A.); (B.N.)
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13
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Sung H, Han MG, Yoo CK, Lee SW, Chung YS, Park JS, Kim MN, Lee H, Hong KH, Seong MW, Lee K, Chun S, Lee WG, Kwon GC, Min WK. Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea. Emerg Infect Dis 2020; 26:2353-2360. [PMID: 32723432 PMCID: PMC7510727 DOI: 10.3201/eid2610.202551] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. A total of 110 (93.2%) laboratories reported correct results for all qualitative tests; 29 (24.6%) laboratories had >1 outliers according to cycle threshold values. Our EQA panel identified the potential weaknesses of currently available commercial reagent kits. The methodology we used can provide practical experience for those planning to conduct evaluations for testing of SARS-CoV-2 and other emerging pathogens in the future.
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Affiliation(s)
| | - Myung-Guk Han
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Cheon-Kwon Yoo
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Sang-Won Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Yoon-Seok Chung
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Jae-Sun Park
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Mi-Na Kim
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Hyukmin Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Ki Ho Hong
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Moon-Woo Seong
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Kyunghoon Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Sail Chun
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Wee Gyo Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Gye-Cheol Kwon
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
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14
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Amoah ID, Kumari S, Bux F. Coronaviruses in wastewater processes: Source, fate and potential risks. ENVIRONMENT INTERNATIONAL 2020; 143:105962. [PMID: 32711332 PMCID: PMC7346830 DOI: 10.1016/j.envint.2020.105962] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/04/2020] [Accepted: 07/05/2020] [Indexed: 05/18/2023]
Abstract
The last 17 years have seen three major outbreaks caused by coronaviruses, with the latest outbreak, COVID-19, declared a pandemic by the World Health Organization. The frequency of these outbreaks, their mortality and associated disruption to normal life calls for concerted efforts to understand their occurrence and fate in different environments. There is an increased interest in the occurrence of coronaviruses in wastewater from the perspective of wastewater-based epidemiology. However, there is no comprehensive review of the knowledge on coronavirus occurrence, fate and potential transmission in wastewater. This paper, provides a review of the literature on the occurrence of coronaviruses in wastewater treatment processes. We discuss the presence of viral RNA in feces as a result of diarrhoea caused by gastrointestinal infections. We also reviewed the literature on the presence, survival and potential removal of coronaviruses in common wastewater treatment processes. The detection of infectious viral particles in feces of patients raises questions on the potential risks of infection for people exposed to untreated sewage/wastewater. We, therefore, highlighted the potential risk of infection with coronaviruses for workers in wastewater treatment plants and the public that may be exposed through faulty plumbing or burst sewer networks. The mortalities and morbidities associated with the current COVID-19 pandemic warrants a much more focused research on the role of environments, such as wastewater and surface water, in disease transmission. The current wealth of knowledge on coronaviruses in wastewater based on the reviewed literature is scant and therefore calls for further studies.
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Affiliation(s)
- Isaac Dennis Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
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15
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Peng J, Lu Y, Song J, Vallance BA, Jacobson K, Yu HB, Sun Z. Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2. Front Med (Lausanne) 2020; 7:549860. [PMID: 33043036 PMCID: PMC7530184 DOI: 10.3389/fmed.2020.549860] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/27/2020] [Indexed: 01/08/2023] Open
Abstract
One of the primary tools for diagnosing COVID-19 is the nucleic acid-based real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test performed on respiratory specimens. The detection rate of SARS-CoV-2 in lower respiratory specimens (such as sputum) is higher than that for upper respiratory specimens (such as nasal and pharyngeal swabs). However, sputum specimens are usually quite viscous, requiring a homogenization process prior to nucleic acid (NA) extraction for RT-PCR. Sputum specimens from COVID-19 and non-COVID-19 patients were treated with four commonly used reagents—saline, N-acetyl-L-cysteine (NALC), proteinase K (PK), and dithiothreitol (DTT), prior to NA extraction. These reagents were then compared for their performance in diagnosing COVID-19 in real clinical practice. The detection rate of SARS-CoV-2 in PK- or DTT-treated sputum was comparable, and higher than that in sputum treated with NALC or saline. While there was a 4.8% (1/21) false negative rate for the PK- and DTT-treated sputum, neither treatment showed any false positive cases among patients with non-COVID diseases. Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. Taken together, we provide direct evidence recommending the use of PK or DTT to pretreat sputum samples to facilitate SARS-CoV-2 detection by clinical laboratories. Moreover, our methods should help to standardize the procedure of processing sputum specimens and improve the ability to detect SARS-CoV-2 in these samples.
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Affiliation(s)
- Jing Peng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Song
- Department of Gastroenterology & Endocrinology, Wuhan No. 9 Hospital, Wuhan, China
| | - Bruce A Vallance
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kevan Jacobson
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Hong Bing Yu
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Yang Z, Wu J, Ye F, Zhu B, Guan W, Huang J, Songyang Z, Liu Y, Chen Y, Du Q, Chen J, Zhang Y, Ke C, Lin Y, Sun B, Zeng J, Chen L, Ren J, Jiang X, Yu M, Di B, Zhong N, Zheng L. Expert consensus-based laboratory testing of SARS-CoV-2. J Thorac Dis 2020; 12:4378-4390. [PMID: 32944351 PMCID: PMC7475603 DOI: 10.21037/jtd-20-1928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jie Wu
- Guangdong Provincial Center of Disease Prevention and Control, Guangzhou, China
| | - Feng Ye
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bing Zhu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenda Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jicheng Huang
- Technology Center, Guangzhou Customs, Guangzhou, China
| | - Zhou Songyang
- School of Life Sciences, Sun Yat-sen University; Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Yong Liu
- Kingmed Virology Diagnostic & Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Yi Chen
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiuling Du
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jingxian Chen
- Kingmed Virology Diagnostic & Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Yu Zhang
- Guangdong Laboratory Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Changwen Ke
- Guangdong Provincial Center of Disease Prevention and Control, Guangzhou, China
| | - Yongping Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Zeng
- Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiankang Ren
- Kingmed Virology Diagnostic & Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Xiwen Jiang
- Da An Gene Co., Ltd of Sun Yat-sen University, Guangzhou, China
| | - Minfei Yu
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, China
| | - Biao Di
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lei Zheng
- Nanfang Hospital, Southern Medical University, Guangzhou, China
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17
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Chu AWH, Chan WM, Ip JD, Yip CCY, Chan JFW, Yuen KY, To KKW. Evaluation of simple nucleic acid extraction methods for the detection of SARS-CoV-2 in nasopharyngeal and saliva specimens during global shortage of extraction kits. J Clin Virol 2020; 129:104519. [PMID: 32629187 PMCID: PMC7309780 DOI: 10.1016/j.jcv.2020.104519] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/16/2020] [Accepted: 06/21/2020] [Indexed: 01/13/2023]
Abstract
Proteinase K-heat method improves nucleic acid extraction from respiratory specimens. Proteinase K-heat method is most useful during shortage of nucleic acid extraction kits. Proteinase-K-heat method is inexpensive.
Background The severe shortage of nucleic acid extraction kits during the current COVID-19 pandemic represents a key limiting factor in testing capacity. Objectives This study compared the results of SARS-CoV-2 RT-PCR using different simple nucleic acid extraction methods on nasopharyngeal and saliva specimens. Study design Fifty nasopharyngeal swab and saliva specimens previously tested positive for SARS-CoV-2 were retrieved. Three different methods of nucleic acid extraction were compared. The first method involves incubating the specimen with proteinase K, and then heat treatment at 98 °C for 5 min (PKH); the second method involves heat treatment at 98 °C for 5 min without proteinase K pre-incubation (heat only); the third method involves no pre-processing steps (direct). The products from all 3 methods were tested by SARS-CoV-2 RT-PCR. Results PKH had significantly higher positive rate in SARS-CoV-2 RT-PCR (80 %) than those of heat only (58 %; P = 0.001) or direct (56 %; P = 0.002). The median Ct value was significantly earlier for PKH (median Ct: 37.0, IQR 31.7–40) than that of heat only (median Ct: 40, IQR 36.2–41; P < 0.0001) and direct (median Ct, 37.5; IQR 33.9–41.0; P = 0.0049). Subgroup analysis showed that PKH had higher detection rate, lower limit of detection and earlier Ct values than the other two groups for both NPS and saliva specimens. Conclusions PKH pre-processing resulted in the highest detection rate of SARS-CoV-2 by RT-PCR, and represents an alternative method for nucleic acid extraction when commercial extraction kits are not available.
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Affiliation(s)
- Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China.
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18
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Sung H, Roh KH, Hong KH, Seong MW, Ryoo N, Kim HS, Lee J, Kim SY, Ryu SW, Kim MN, Han MG, Lee SW, Lee H, Yoo CK. COVID-19 Molecular Testing in Korea: Practical Essentials and Answers From Experts Based on Experiences of Emergency Use Authorization Assays. Ann Lab Med 2020; 40:439-447. [PMID: 32539299 PMCID: PMC7295959 DOI: 10.3343/alm.2020.40.6.439] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/28/2020] [Accepted: 05/29/2020] [Indexed: 01/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Early detection of COVID-19 and immediate isolation of infected patients from the naive population are important to prevent further pandemic spread of the infection. Real-time reverse transcription (RT)-PCR to detect SARS-CoV-2 RNA is currently the most reliable diagnostic method for confirming COVID-19 worldwide. Guidelines for clinical laboratories on the COVID-19 diagnosis have been recently published by Korean Society for Laboratory Medicine and the Korea Centers for Disease Control and Prevention. However, these formal guidelines do not address common practical laboratory issues related to COVID-19 real-time RT-PCR testing and their solutions. Therefore, this guideline is intended as a practical and technical supplement to the “Guidelines for Laboratory Diagnosis of COVID-19 in Korea”.
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Affiliation(s)
- Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service, Ilsan Hospital, Goyang, Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Sook Won Ryu
- Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Myung Guk Han
- Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Sang Won Lee
- Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Cheon Kwon Yoo
- Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
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19
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Lee YJ, Lim Y, Hur KW, Sung H, Kim MN. Quality of Ribonucleic Acid Extraction for Real-Time Reverse Transcription-PCR (rRT-PCR) of SARS-CoV-2: Importance of Internal Control Monitoring. Ann Lab Med 2020; 40:490-492. [PMID: 32539306 PMCID: PMC7295956 DOI: 10.3343/alm.2020.40.6.490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/06/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yeon Joo Lee
- Konkuk University School of Medicine, Seoul, Korea
| | - Youngeun Lim
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul, Korea
| | - Kyu Wha Hur
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul, Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul, Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul, Korea
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20
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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21
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Thakore N, Norville R, Franke M, Calderon R, Lecca L, Villanueva M, Murray MB, Cooney CG, Chandler DP, Holmberg RC. Automated TruTip nucleic acid extraction and purification from raw sputum. PLoS One 2018; 13:e0199869. [PMID: 29975759 PMCID: PMC6033430 DOI: 10.1371/journal.pone.0199869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
Automated nucleic acid extraction from primary (raw) sputum continues to be a significant technical challenge for molecular diagnostics. In this work, we developed a prototype open-architecture, automated nucleic acid workstation that includes a mechanical homogenization and lysis function integrated with heating and TruTip purification; optimized an extraction protocol for raw sputum; and evaluated system performance on primary clinical specimens. Eight samples could be processed within 70 min. The system efficiently homogenized primary sputa and doubled nucleic acid recovery relative to an automated protocol that did not incorporate sample homogenization. Nucleic acid recovery was at least five times higher from raw sputum as compared to that of matched sediments regardless of smear or culture grade, and the automated workstation reproducibly recovered PCR-detectable DNA to at least 80 CFU mL-1 raw sputum. M. tuberculosis DNA was recovered and detected from 122/123 (99.2%) and 124/124 (100%) primary sputum and sediment extracts, respectively. There was no detectable cross-contamination across 53 automated system runs and amplification or fluorescent inhibitors (if present) were not detectable. The open fluidic architecture of the prototype automated workstation yields purified sputum DNA that can be used for any molecular diagnostic test. The ability to transfer TruTip protocols between personalized, on-demand pipetting tools and the fully automated workstation also affords public health agencies an opportunity to standardize sputum nucleic acid sample preparation procedures, reagents, and quality control across multiple levels of the health care system.
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Affiliation(s)
- Nitu Thakore
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Ryan Norville
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Molly Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Perú, Carabayllo, Lima, Peru
| | | | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
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22
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Underlying trend, seasonality, prediction, forecasting and the contribution of risk factors: an analysis of globally reported cases of Middle East Respiratory Syndrome Coronavirus. Epidemiol Infect 2018; 146:1343-1349. [PMID: 29886854 DOI: 10.1017/s0950268818001541] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
This study set out to identify and analyse trends and seasonal variations of monthly global reported cases of the Middle East respiratory syndrome coronavirus (MERS-CoV). It also made a prediction based on the reported and extrapolated into the future by forecasting the trend. Finally, the study assessed contributions of various risk factors in the reported cases. The motivation for this study is that MERS-CoV remains among the list of blueprint priority and potential pandemic diseases globally. Yet, there is a paucity of empirical literature examining trends and seasonality as the available evidence is generally descriptive and anecdotal. The study is a time series analysis using monthly global reported cases of MERS-CoV by the World Health Organisation between January 2015 and January 2018. We decomposed the series into seasonal, irregular and trend components and identified patterns, smoothened series, generated predictions and employed forecasting techniques based on linear regression. We assessed contributions of various risk factors in MERS-CoV cases over time. Successive months of the MERS-CoV cases suggest a significant decreasing trend (P = 0.026 for monthly series and P = 0.047 for Quarterly series). The MERS-CoV cases are forecast to wane by end 2018. Seasonality component of the cases oscillated below or above the baseline (the centred moving average), but no association with the series over time was noted. The results revealed contributions of risk factors such as camel contact, male, old age and being from Saudi Arabia and Middle East regions to the overall reported cases of MERS-CoV. The trend component and several risk factors for global MERS-CoV cases, including camel contact, male, age and geography/region significantly affected the series. Our statistical models appear to suggest significant predictive capacity and the findings may well inform healthcare practitioners and policymakers about the underlying dynamics that produced the globally reported MERS-CoV cases.
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23
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Ahmed AE, Al-Jahdali H, Alshukairi AN, Alaqeel M, Siddiq SS, Alsaab H, Sakr EA, Alyahya HA, Alandonisi MM, Subedar AT, Aloudah NM, Baharoon S, Alsalamah MA, Al Johani S, Alghamdi MG. Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia. Int J Infect Dis 2018; 70:51-56. [PMID: 29550445 PMCID: PMC7110544 DOI: 10.1016/j.ijid.2018.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 01/13/2023] Open
Abstract
Background The rapid and accurate identification of individuals who are at high risk of Middle East respiratory syndrome coronavirus (MERS-CoV) infection remains a major challenge for the medical and scientific communities. The aim of this study was to develop and validate a risk prediction model for the screening of suspected cases of MERS-CoV infection in patients who have developed pneumonia. Methods A two-center, retrospective case–control study was performed. A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. According to the rRT-PCR results, 135 patients were positive for MERS-CoV and 225 were negative. Demographic characteristics, clinical presentations, and radiological and laboratory findings were collected for each subject. Results A risk prediction model to identify pneumonia patients at increased risk of MERS-CoV was developed. The model included male sex, contact with a sick patient or camel, diabetes, severe illness, low white blood cell (WBC) count, low alanine aminotransferase (ALT), and high aspartate aminotransferase (AST). The model performed well in predicting MERS-CoV infection (area under the receiver operating characteristics curves (AUC) 0.8162), on internal validation (AUC 0.8037), and on a goodness-of-fit test (p = 0.592). The risk prediction model, which produced an optimal probability cut-off of 0.33, had a sensitivity of 0.716 and specificity of 0.783. Conclusions This study provides a simple, practical, and valid algorithm to identify pneumonia patients at increased risk of MERS-CoV infection. This risk prediction model could be useful for the early identification of patients at the highest risk of MERS-CoV infection. Further validation of the prediction model on a large prospective cohort of representative patients with pneumonia is necessary.
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Affiliation(s)
- Anwar E Ahmed
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), Ministry of National Guard - Health Affairs, Riyadh 11426, Saudi Arabia.
| | - Hamdan Al-Jahdali
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), Ministry of National Guard - Health Affairs, Riyadh 11426, Saudi Arabia.
| | - Abeer N Alshukairi
- King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia.
| | - Mody Alaqeel
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), Ministry of National Guard - Health Affairs, Riyadh 11426, Saudi Arabia.
| | | | - Hanan Alsaab
- King Fahad General Hospital, Jeddah, Saudi Arabia.
| | | | | | | | | | | | - Salim Baharoon
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), Ministry of National Guard - Health Affairs, Riyadh 11426, Saudi Arabia.
| | - Majid A Alsalamah
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), Ministry of National Guard - Health Affairs, Riyadh 11426, Saudi Arabia.
| | - Sameera Al Johani
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), Ministry of National Guard - Health Affairs, Riyadh 11426, Saudi Arabia.
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24
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Yu F, Qiu T, Zeng Y, Wang Y, Zheng S, Chen X, Chen Y. Comparative Evaluation of Three Preprocessing Methods for Extraction and Detection of Influenza A Virus Nucleic Acids from Sputum. Front Med (Lausanne) 2018; 5:56. [PMID: 29552562 PMCID: PMC5840144 DOI: 10.3389/fmed.2018.00056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/16/2018] [Indexed: 11/13/2022] Open
Abstract
Viscous sputum specimens usually cannot undergo automated extraction, and thus, a pre-homogenization process is desirable before isolating nucleic acids for real-time reverse transcription PCR. In this study, we compared three preprocessing methods [preprocessing with normal saline (NS), dithiothreitol (DTT), and proteinase K (PK)] of sputum specimens on the extraction and detection of influenza A virus (IAV) nucleic acids. Based on the experimental results of 217 specimens, we found that DTT and PK could be used to improve the homogenization effects of sputum and increase the positive rates by 5.53-6.91% higher than that of the NS group. Comparison of 49 positive specimens in all of the three groups demonstrated that the threshold cycle values of the DTT group and PK group were significantly lower and their nucleic acid concentration and A260/A280 ratio within 1.8-2.0 were higher than those of the NS group. Thus, sputum homogenization before nucleic acid extraction is essential for the accurate diagnosis of IAV infection.
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Affiliation(s)
- Fei Yu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ting Qiu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ying Zeng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yiyin Wang
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shufa Zheng
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Chen
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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25
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Chan JFW, Sridhar S, Yip CCY, Lau SKP, Woo PCY. The role of laboratory diagnostics in emerging viral infections: the example of the Middle East respiratory syndrome epidemic. J Microbiol 2017; 55:172-182. [PMID: 28243939 PMCID: PMC7090747 DOI: 10.1007/s12275-017-7026-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023]
Abstract
Rapidly emerging infectious disease outbreaks place a great strain on laboratories to develop and implement sensitive and specific diagnostic tests for patient management and infection control in a timely manner. Furthermore, laboratories also play a role in real-time zoonotic, environmental, and epidemiological investigations to identify the ultimate source of the epidemic, facilitating measures to eventually control the outbreak. Each assay modality has unique pros and cons; therefore, incorporation of a battery of tests using traditional culture-based, molecular and serological diagnostics into diagnostic algorithms is often required. As such, laboratories face challenges in assay development, test evaluation, and subsequent quality assurance. In this review, we describe the different testing modalities available for the ongoing Middle East respiratory syndrome (MERS) epidemic including cell culture, nucleic acid amplification, antigen detection, and antibody detection assays. Applications of such tests in both acute clinical and epidemiological investigation settings are highlighted. Using the MERS epidemic as an example, we illustrate the various challenges faced by laboratories in test development and implementation in the setting of a rapidly emerging infectious disease. Future directions in the diagnosis of MERS and other emerging infectious disease investigations are also highlighted.
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Affiliation(s)
- Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
| | - Cyril C Y Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China.
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China.
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, P. R. China.
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