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Shahi F, Rasti M, Moradi M. Overview of the different methods for RNA preparation in COVID-19 diagnosis process during the pandemic. Anal Biochem 2024; 686:115410. [PMID: 38006951 DOI: 10.1016/j.ab.2023.115410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
The COVID-19 pandemic brought to light the impact of a widespread disease on various aspects of human relationships, communities, and economies. One notable consequence was the increased demand for diagnostic kits, laboratory reagents, and personal health equipment. This surge in testing capacity worldwide led to shortages in the supply of essential items, including RNA extraction kits, which are crucial for detecting COVID-19 infections. To address this scarcity, researchers have proposed alternative and cost-effective strategies for RNA extraction, utilizing both chemical and physical solutions and extraction-free methods. These approaches aim to alleviate the challenges associated with the overwhelming number of tests being conducted in laboratories. The purpose of this review is intends to provide a comprehensive summary of the various kit-free RNA extraction methods available for COVID-19 diagnosis during the pandemic.
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Affiliation(s)
- Fatemeh Shahi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mojtaba Rasti
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Melika Moradi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
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Song Y, Song J, Kim S, Jang H, Kim H, Jeong B, Park N, Kim S, Yong D, Lim EK, Lee KG, Kang T, Im SG. Charge-shifting polyplex as a viral RNA extraction carrier for streamlined detection of infectious viruses. MATERIALS HORIZONS 2023; 10:4571-4580. [PMID: 37581348 DOI: 10.1039/d3mh00861d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for rapid, user-friendly nucleic acid testing that involves simple but efficient RNA extraction. Here, we present a charge-shifting polyplex as an RNA extraction carrier for advanced diagnosis of infectious viral diseases. The polyplex comprises poly(2-(dimethylamino) ethyl acrylate) (pDMAEA) electrostatically conjugated with RNA. The pDMAEA film can rapidly dissolve in the viral RNA solution, promoting immediate binding with RNA to form the polyplex, which enables the efficient capture of a substantial quantity of RNA. Subsequently, the captured RNA can be readily released by the quick hydrolysis of pDMAEA at the onset of quantitative reverse transcription-polymerase chain reaction (qRT-PCR), streamlining the entire process from RNA extraction to analysis. The developed method requires only 5 min of centrifugation and enables the detection of RNA in a one-pot setup. Moreover, the proposed method is fully compatible with high-speed qRT-PCR kits and can identify clinical samples within 1 h including the entire extraction to detection procedure. Indeed, the method successfully detected influenza viruses, SARS-CoV-2, and their delta and omicron variants in 260 clinical samples with a sensitivity of 99.4% and specificity of 98.9%. This rapid, user-friendly polyplex-based approach represents a significant breakthrough in molecular diagnostics.
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Affiliation(s)
- Younseong Song
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Seongeun Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hogi Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Booseok Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Nahyun Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do 52727, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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Lee G, Schauner R, Burke J, Borocz J, Vasana S, Sobieraj L, Giraudo M, Jackson Z, Ansari Q, Navas M, Sakr H, Wald D. NK cells from COVID-19 positive patients exhibit enhanced cytotoxic activity upon NKG2A and KIR2DL1 blockade. Front Immunol 2023; 14:1022890. [PMID: 37483595 PMCID: PMC10360118 DOI: 10.3389/fimmu.2023.1022890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
SARS CoV-2 has caused a global pandemic leading to significant morbidity and mortality. There is a need to elucidate and further understand the implications of COVID-19 disease on the immune system to develop improved therapeutic strategies. In particular, Natural Killer (NK) cells play an essential role in mediating the innate immune response against viral infections. To better understand the role of innate immunity in COVID-19, we characterized the phenotype of circulating NK cells from 74 COVID-19 patients and 25 controls. Through evaluating the protein expression of activating and inhibitory NK cell surface molecules using dimension reduction analysis and clustering, we identified 4 specific clusters of NK cells specific to disease state (COVID-19 positive or COVID-19 negative) and characterized COVID-19 positive NK cells as: NGK2A+KIR2DL1+NKG2C-. Utilizing blocking antibodies specific for receptors NKG2A and KIR2DL1, we found that both NKG2A and KIR2DL1 blockade markedly enhances the ability of NK cells from COVID-19 positive patients to lyse SARS-Cov-2 infected cells. Overall, this study reveals new insights into NK cell phenotypes during SARS-CoV-2 infection and suggests a therapeutic approach worthy of further investigation to enhance NK cell-mediated responses against the virus.
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Affiliation(s)
- Grace Lee
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Robert Schauner
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Juanita Burke
- Department of Pathology, Louis Stokes Cleveland Veteran Affairs (VA) Medical Center, Cleveland, OH, United States
| | - Jade Borocz
- Department of Pathology, Louis Stokes Cleveland Veteran Affairs (VA) Medical Center, Cleveland, OH, United States
| | - Smitha Vasana
- Department of Pediatrics, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Lukasz Sobieraj
- Midwestern University Chicago College of Osteopathic Medicine, Downers Grove, IL, United States
| | - Maria Giraudo
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Zachary Jackson
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Qasim Ansari
- Department of Pathology, Louis Stokes Cleveland Veteran Affairs (VA) Medical Center, Cleveland, OH, United States
| | - Maria Navas
- Department of Pathology, Louis Stokes Cleveland Veteran Affairs (VA) Medical Center, Cleveland, OH, United States
| | - Hany Sakr
- Department of Pathology, Louis Stokes Cleveland Veteran Affairs (VA) Medical Center, Cleveland, OH, United States
| | - David Wald
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
- Department of Pathology, Louis Stokes Cleveland Veteran Affairs (VA) Medical Center, Cleveland, OH, United States
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Jain S, Bhowmick A, Pandey AK. A rapid One-Pot RNA isolation method for simplified clinical detection of SARS-COV-2 infection in India. Front Cell Infect Microbiol 2022. [DOI: 10.3389/fcimb.2022.962057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BackgroundWith the rapid increase in COVID-19 cases and the discovery of new viral variants within India over multiple waves, the expensive reagents and time-consuming sample pretreatment required for qPCR analysis have led to slower detection of the disease. The vast Indian population demands an inexpensive and competent sample preparation strategy for rapid detection of the disease facilitating early and efficient containment of the disease.MethodsIn this study, we have surveyed the spread of COVID-19 infection over Faridabad, Haryana, India for 6 months. We also devised a simple single-step method for total RNA extraction using a single tube and compared its efficacy with the commercially available RNA isolation kits.FindingsOur findings suggest that determining Ct values for samples subjected to the One Pot RNA extraction method was as efficient as the commercially available kits but delivers a subtle advantage in a way, by minimizing the cost, labor and sample preparation time.ConclusionThis novel crude RNA extraction method is stable and capable of operating in developing countries like India for low resource settings, without the use of expensive reagents and instruments. Additionally, this method can be further adapted to pooling samples strategies owing to its high sensitivity.
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Naito A, Kiyasu Y, Akashi Y, Sugiyama A, Michibuchi M, Takeuchi Y, Notake S, Nakamura K, Ishikawa H, Suzuki H. The evaluation of the utility of the GENECUBE HQ SARS-CoV-2 for anterior nasal samples and saliva samples with a new rapid examination protocol. PLoS One 2021; 16:e0262159. [PMID: 34972195 PMCID: PMC8719657 DOI: 10.1371/journal.pone.0262159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION GENECUBE® is a rapid molecular identification system, and previous studies demonstrated that GENECUBE® HQ SARS-CoV-2 showed excellent analytical performance for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with nasopharyngeal samples. However, other respiratory samples have not been evaluated. METHODS This prospective comparison between GENECUBE® HQ SARS-CoV-2 and reference real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed for the detection of SARS-CoV-2 using anterior nasal samples and saliva samples. Additionally, we evaluated a new rapid examination protocol using GENECUBE® HQ SARS-CoV-2 for the detection of SARS-CoV-2 with saliva samples. For the rapid protocol, in the preparation of saliva samples, purification and extraction processes were adjusted, and the total process time was shortened to approximately 35 minutes. RESULTS For 359 anterior nasal samples, the total-, positive-, and negative concordance of the two assays was 99.7% (358/359), 98.1% (51/52), and 100% (307/307), respectively. For saliva samples, the total-, positive-, and negative concordance of the two assays was 99.6% (239/240), 100% (56/56), and 99.5% (183/184), respectively. With the new protocol, total-, positive-, and negative concordance of the two assays was 98.8% (237/240), 100% (56/56), and 98.4% (181/184), respectively. In all discordance cases, SARS-CoV-2 was detected by additional molecular examinations. CONCLUSION GENECUBE® HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.
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Affiliation(s)
- Asami Naito
- Tsukuba i-Laboratory LLP, Tsukuba, Ibaraki, Japan
| | - Yoshihiko Kiyasu
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
| | - Yusaku Akashi
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Akashi Internal Medicine Clinic, Kashiwara, Osaka, Japan
| | - Akio Sugiyama
- Diagnostic System Department, TOYOBO Co., Ltd., Kita-ku, Osaka, Japan
| | | | - Yuto Takeuchi
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
| | - Shigeyuki Notake
- Department of Clinical Laboratory, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Koji Nakamura
- Department of Clinical Laboratory, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Hiroichi Ishikawa
- Department of Respiratory Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Hiromichi Suzuki
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Clinical evaluation of antiseptic mouth rinses to reduce salivary load of SARS-CoV-2. Sci Rep 2021; 11:24392. [PMID: 34937855 PMCID: PMC8695582 DOI: 10.1038/s41598-021-03461-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023] Open
Abstract
Most public health measures to contain the COVID-19 pandemic are based on preventing the pathogen spread, and the use of oral antiseptics has been proposed as a strategy to reduce transmission risk. The aim of this manuscript is to test the efficacy of mouthwashes to reduce salivary viral load in vivo. This is a multi-centre, blinded, parallel-group, placebo-controlled randomised clinical trial that tests the effect of four mouthwashes (cetylpyridinium chloride, chlorhexidine, povidone-iodine and hydrogen peroxide) in SARS-CoV-2 salivary load measured by qPCR at baseline and 30, 60 and 120 min after the mouthrinse. A fifth group of patients used distilled water mouthrinse as a control. Eighty-four participants were recruited and divided into 12–15 per group. There were no statistically significant changes in salivary viral load after the use of the different mouthwashes. Although oral antiseptics have shown virucidal effects in vitro, our data show that salivary viral load in COVID-19 patients was not affected by the tested treatments. This could reflect that those mouthwashes are not effective in vivo, or that viral particles are not infective but viral RNA is still detected by PCR. Viral infectivity studies after the use of mouthwashes are therefore required. (https://clinicaltrials.gov/ct2/show/NCT04707742; Identifier: NCT04707742)
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Yang J, Kidd M, Nordquist AR, Smith SD, Hurth C, Modlin IM, Zenhausern F. A Sensitive, Portable Microfluidic Device for SARS-CoV-2 Detection from Self-Collected Saliva. Infect Dis Rep 2021; 13:1061-1077. [PMID: 34940407 PMCID: PMC8701218 DOI: 10.3390/idr13040097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Since the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in December 2019, the spread of SARS-CoV2 infection has been escalating rapidly around the world. In order to provide more timely access to medical intervention, including diagnostic tests and medical treatment, the FDA authorized multiple test protocols for diagnostic tests from nasopharyngeal swab, saliva, urine, bronchoalveolar lavage and fecal samples. The traditional diagnostic tests for this novel coronavirus 2019 require standard processes of viral RNA isolation, reverse transcription of RNA to cDNA, then real-time quantitative PCR with the RNA templates extracted from the patient samples. Recently, many reports have demonstrated a direct detection of SARS-Co-V2 genomic material from saliva samples without any RNA isolation step. To make the rapid detection of SARS-Co-V2 infection more accessible, a point-of-care type device was developed for SARS-CoV-2 detection. Herein, we report a portable microfluidic-based integrated detection-analysis system for SARS-CoV-2 nucleic acids detection directly from saliva samples. The saliva cartridge is self-contained and capable of microfluidic evaluation of saliva, from heating, mixing with the primers to multiplex real-time quantitative polymerase chain reaction, detecting SARS-CoV-2 with different primer sets and internal control. The approach has a detection sensitivity of 1000 copies/mL of SARS-CoV-2 RNA or virus, with consistency and automation, from saliva sample-in to result-out.
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Affiliation(s)
- Jianing Yang
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Mark Kidd
- WREN Laboratories, Branford, CT 06405, USA; (M.K.); (I.M.M.)
| | - Alan R. Nordquist
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Stanley D. Smith
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Cedric Hurth
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Irvin M. Modlin
- WREN Laboratories, Branford, CT 06405, USA; (M.K.); (I.M.M.)
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
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False-Negative Results in Taqman One-Step RT-PCR Test: Evaluation of Endogenous Internal Control Function Used in SARS-CoV-2 Detection Tests. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.116533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Taqman one-step real-time PCR (RT-PCR) has special importance due to its high sensitivity and specificity in the diagnosis of infectious diseases such as viral infections. In the recent pandemic of SARS-CoV-2, diagnostic kits based on this method are commonly used for molecular detection. One of the main systematic errors that misinterpret the results is using inaccurate internal control in RT-PCR diagnostic kits. Designing primers and probes that span exon-exon junction will avoid genomic DNA amplification and lead to obtaining high specific results. Objectives: This study aimed to evaluate the endogenous internal control of primers and probe for RNase P RNA to reduce false-negative results in respiratory samples. Methods: In this study, 30 samples of patients who were negative for SARS-CoV-2, influenza A, and influenza B were re-evaluated for SARS-CoV-2 using newly designed primers and probes for RNase P RNA (ultra-specific primers and probe). We also performed bioinformatics analysis on CDC-approved primers and probes of RNase P endogenous internal control. Results: In this analysis, we specified the location of these newly designed primers and probe on target mRNA and genomic DNA. Then, the Taqman one-step RT-PCR method was performed using both CDC-approved primers and probes along with our ultra-specific primers and probe for RNase P RNA. Based on bioinformatics analysis, the attachment sites of the CDC-approved primers and probe for endogenous internal control of RNase P are located on the first exon of this gene. In addition to identifying the target gene sequence, these primers and probe also non-specifically detect similar sequences on the genomic DNA. Conclusions: The present study showed that the use of specific primers and probes introduced by CDC for SARS-CoV-2 and influenza virus may cause false results due to non-specific binding to the genomic DNA. Therefore, choosing the right internal control for RNase P RNA can be useful in achieving very accurate results.
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Kabir MA, Ahmed R, Chowdhury R, Iqbal SMA, Paulmurugan R, Demirci U, Asghar W. Management of COVID-19: current status and future prospects. Microbes Infect 2021; 23:104832. [PMID: 33872807 PMCID: PMC8052512 DOI: 10.1016/j.micinf.2021.104832] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 12/12/2022]
Abstract
COVID-19, a highly transmissible pandemic disease, is affecting millions of lives around the world. Severely infected patients show acute respiratory distress symptoms. Sustainable management strategies are required to save lives of the infected people and further preventing spread of the virus. Diagnosis, treatment, and vaccination development initiatives are already exhibited from the scientific community to fight against this virus. In this review, we primarily discuss the management strategies including prevention of spread, prophylaxis, vaccinations, and treatment for COVID-19. Further, analysis of vaccine development status and performance are also briefly discussed. Global socioeconomic impact of COVID-19 is also analyzed as part of this review.
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Affiliation(s)
- Md Alamgir Kabir
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA; Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Rajib Ahmed
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA 94304, USA
| | - Rasheduzzaman Chowdhury
- Cardiovascular Research Institute, Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94143, USA
| | - Sheikh Muhammad Asher Iqbal
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA; Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Ramasamy Paulmurugan
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA 94304, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA 94304, USA
| | - Waseem Asghar
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA; Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA.
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Cao R, Bao L, Pan M, Zhang C, Liao H, Liu L, Li Y, Li M. Detection of SARS-CoV-2 in fecal samples with different pretreatment methods and PCR kits. BMC Microbiol 2021; 21:56. [PMID: 33607939 PMCID: PMC7893130 DOI: 10.1186/s12866-021-02118-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023] Open
Abstract
Background Gastrointestinal symptoms are common in COVID-19 patients and SARS-CoV-2 RNA has been detected in the patients’ feces, which could lead to fecal–oral transmission. Therefore, fecal sample testing with real-time RT-PCR is highly recommended as a routine test for SARS-CoV-2 infection. However, varying rates of detection in fecal sample have been reported. The aim of this study was to provide insights into the detection rates of SARS-CoV-2 in COVID-19 patients’ fecal sample by using four real-time RT-PCR kits and two pretreatment methods (inactive and non-inactive). Results The detection rate of Trizol pretreatment group was slightly higher than that of Phosphate Buffered Saline (PBS) groups, showing that pretreatment and inactivation by Trizol had no influence to SARS-CoV-2 nucleic acid test (NAT) results. 39.29% detection rate in fecal sample by DAAN was obtained, while Bio-germ was 40.48%, Sansure 34.52%, and GeneoDx 33.33%. The former three kits had no significant difference. The DAAN kit detection rates of ORF1ab and N gene were nearly equal and Ct value distribution was more scattered, while the Bio-germ kit distribution was more clustered. The positive rate of SARS-COV-2 in fecal samples correlated with the severity of the disease, specifically, severe cases were less likely to be identified than asymptomatic infection in the DAAN group (adjusted OR 0.05, 95%CI = 0.00 ~ 0.91). Conclusions Trizol should be of choice as a valid and safe method for pretreatment of fecal samples of SARS-CoV-2. All real-time RT-PCR kits assessed in this study can be used for routine detection of SARS-CoV-2 in fecal samples. While DAAN, with high NAT positive rate, could be the best out of the 4 kits used in this study. SARS-CoV-2 positive rate in fecal sample was related to the severity of illness. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02118-0.
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Affiliation(s)
- Ranran Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.,Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China
| | - Lirong Bao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Ming Pan
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China
| | - Cheng Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Hongyu Liao
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China
| | - Li Liu
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Mingyuan Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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