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Jung J, Bong JH, Sung JS, Park JH, Kim TH, Kwon S, Kang MJ, Jose J, Pyun JC. Immunoaffinity biosensors for the detection of SARS-CoV-1 using screened Fv-antibodies from an autodisplayed Fv-antibody library. Biosens Bioelectron 2023; 237:115439. [PMID: 37301177 PMCID: PMC10223632 DOI: 10.1016/j.bios.2023.115439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
The detection of severe acute respiratory syndrome coronavirus (SARS-CoV-1) was demonstrated using screened Fv-antibodies for SPR biosensor and impedance spectrometry. The Fv-antibody library was first prepared on the outer membrane of E. coli using autodisplay technology and the Fv-variants (clones) with a specific affinity toward the SARS-CoV-1 spike protein (SP) were screened using magnetic beads immobilized with the SP. Upon screening the Fv-antibody library, two target Fv-variants (clones) with a specific binding affinity toward the SARS-CoV-1 SP were determined and the Fv-antibodies on two clones were named "Anti-SP1" (with CDR3 amino acid sequence: 1GRTTG5NDRPD11Y) and "Anti-SP2" (with CDR3 amino acid sequence: 1CLRQA5GTADD11V). The binding affinities of the two screened Fv-variants (clones) were analyzed using flow cytometry and the binding constants (KD) were estimated to be 80.5 ± 3.6 nM for Anti-SP1 and 45.6 ± 8.9 nM for Anti-SP2 (n = 3). In addition, the Fv-antibody including three CDR regions (CDR1, CDR2, and CDR3) and frame regions (FRs) between the CDR regions was expressed as a fusion protein (Mw. 40.6 kDa) with a green fluorescent protein (GFP) and the KD values of the expressed Fv-antibodies toward the SP estimated to be 15.3 ± 1.5 nM for Anti-SP1 (n = 3) and 16.3 ± 1.7 nM for Anti-SP2 (n = 3). Finally, the expressed Fv-antibodies screened against SARS-CoV-1 SP (Anti-SP1 and Anti-SP2) were applied for the detection of SARS-CoV-1. Consequently, the detection of SARS-CoV-1 was demonstrated to be feasible using the SPR biosensor and impedance spectrometry utilizing the immobilized Fv-antibodies against the SARS-CoV-1 SP.
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Affiliation(s)
- Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jeong Soo Sung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jun-Hee Park
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Tae-Hun Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Soonil Kwon
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST), Seoul, South Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, Westphalian Wilhelms-University Münster, Münster, 48149, Germany
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.
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2
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Hartman WR. An Executed Plan to Combat COVID-19 in the United States. Adv Anesth 2022; 40:45-62. [PMID: 36333051 PMCID: PMC9276922 DOI: 10.1016/j.aan.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019. To date, this coronavirus is responsible for greater than 90 million cases in the United States and more than 1 million confirmed deaths. When this virus came to the United States, testing was unorganized, no effective treatments were known, and no vaccines had been discovered. A plan to correct these deficiencies through cooperative science and efficient clinical trials was implemented to combat this novel virus. This plan developed efficient and inexpensive tests, highly effective medicines to treat and prevent disease progression, and vaccines to immunize the population.
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Affiliation(s)
- William R Hartman
- Department of Anesthesiology, Office of Clinical Research, University of Wisconsin-Madison, Madison, WI, USA.
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3
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da Silva Torres MK, Bichara CDA, de Almeida MDNDS, Vallinoto MC, Queiroz MAF, Vallinoto IMVC, dos Santos EJM, de Carvalho CAM, Vallinoto ACR. The Complexity of SARS-CoV-2 Infection and the COVID-19 Pandemic. Front Microbiol 2022; 13:789882. [PMID: 35222327 PMCID: PMC8870622 DOI: 10.3389/fmicb.2022.789882] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the death of millions of people worldwide and thousands more infected individuals developed sequelae due to the disease of the new coronavirus of 2019 (COVID-19). The development of several studies has contributed to the knowledge about the evolution of SARS-CoV2 infection and the disease to more severe forms. Despite this information being debated in the scientific literature, many mechanisms still need to be better understood in order to control the spread of the virus and treat clinical cases of COVID-19. In this article, we carried out an extensive literature review in order to bring together, in a single article, the biological, social, genetic, diagnostic, therapeutic, immunization, and even socioeconomic aspects that impact the SAR-CoV-2 pandemic. This information gathered in this article will enable a broad and consistent reading of the main aspects related to the current pandemic.
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Affiliation(s)
- Maria Karoliny da Silva Torres
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | - Carlos David Araújo Bichara
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | - Maria de Nazaré do Socorro de Almeida
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
- Laboratory of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Mariana Cayres Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- University Center of the State of Pará, Belém, Brazil
| | - Maria Alice Freitas Queiroz
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | | | - Eduardo José Melo dos Santos
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
- Laboratory of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Antonio Carlos R. Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
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4
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Zhu Y, Oishi W, Maruo C, Bandara S, Lin M, Saito M, Kitajima M, Sano D. COVID-19 case prediction via wastewater surveillance in a low-prevalence urban community: a modeling approach. JOURNAL OF WATER AND HEALTH 2022; 20:459-470. [PMID: 36366998 DOI: 10.2166/wh.2022.183] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Estimating and predicting the epidemic size from wastewater surveillance results remains challenging for the practical implementation of wastewater-based epidemiology (WBE). In this study, by employing a highly sensitive detection method, we documented the time series of SARS-CoV-2 RNA occurrence in the wastewater influent from an urban community with a 360,000 population in Japan, from August 2020 to February 2021. The detection frequency of the viral RNA increased during the outbreak events of COVID-19 and the highest viral RNA concentration was recorded at the beginning of January 2021, amid the most serious outbreak event during the study period. We found that: (1) direct back-calculation still suffers from great uncertainty dominated by inconsistent detection and the varying gap between the observed wastewater viral load and the estimated patient viral load, and (2) the detection frequency correlated well with reported cases and the prediction of the latter can be carried out via data-driven modeling methods. Our results indicate that wastewater virus occurrence can contribute to epidemic surveillance in ways more than back-calculation, which may spawn future wastewater surveillance implementations.
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Affiliation(s)
- Yifan Zhu
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan E-mail: ; These authors contributed equally to this work
| | - Wakana Oishi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan; These authors contributed equally to this work
| | - Chikako Maruo
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan
| | - Sewwandi Bandara
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan E-mail:
| | - Mu Lin
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan E-mail:
| | - Mayuko Saito
- Department of Virology, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan E-mail: ; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan; Research Institute for Humanity and Nature, 457-4 Kamigamo Motoyama, Kita Ward, Kyoto 603-8047, Japan
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Abdeldayem OM, Dabbish AM, Habashy MM, Mostafa MK, Elhefnawy M, Amin L, Al-Sakkari EG, Ragab A, Rene ER. Viral outbreaks detection and surveillance using wastewater-based epidemiology, viral air sampling, and machine learning techniques: A comprehensive review and outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:149834. [PMID: 34525746 PMCID: PMC8379898 DOI: 10.1016/j.scitotenv.2021.149834] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/05/2021] [Accepted: 08/18/2021] [Indexed: 05/06/2023]
Abstract
A viral outbreak is a global challenge that affects public health and safety. The coronavirus disease 2019 (COVID-19) has been spreading globally, affecting millions of people worldwide, and led to significant loss of lives and deterioration of the global economy. The current adverse effects caused by the COVID-19 pandemic demands finding new detection methods for future viral outbreaks. The environment's transmission pathways include and are not limited to air, surface water, and wastewater environments. The wastewater surveillance, known as wastewater-based epidemiology (WBE), can potentially monitor viral outbreaks and provide a complementary clinical testing method. Another investigated outbreak surveillance technique that has not been yet implemented in a sufficient number of studies is the surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in the air. Artificial intelligence (AI) and its related machine learning (ML) and deep learning (DL) technologies are currently emerging techniques for detecting viral outbreaks using global data. To date, there are no reports that illustrate the potential of using WBE with AI to detect viral outbreaks. This study investigates the transmission pathways of SARS-CoV-2 in the environment and provides current updates on the surveillance of viral outbreaks using WBE, viral air sampling, and AI. It also proposes a novel framework based on an ensemble of ML and DL algorithms to provide a beneficial supportive tool for decision-makers. The framework exploits available data from reliable sources to discover meaningful insights and knowledge that allows researchers and practitioners to build efficient methods and protocols that accurately monitor and detect viral outbreaks. The proposed framework could provide early detection of viruses, forecast risk maps and vulnerable areas, and estimate the number of infected citizens.
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Affiliation(s)
- Omar M Abdeldayem
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands.
| | - Areeg M Dabbish
- Biotechnology Graduate Program, Biology Department, School of Science and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Mahmoud M Habashy
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
| | - Mohamed K Mostafa
- Faculty of Engineering and Technology, Badr University in Cairo (BUC), Cairo 11829, Egypt
| | - Mohamed Elhefnawy
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada; Department of Mathematics and Industrial Engineering, Polytechnique Montréal 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Lobna Amin
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands; Department of Built Environment, Aalto University, PO Box 15200, FI-00076, Aalto, Finland
| | - Eslam G Al-Sakkari
- Chemical Engineering Department, Cairo University, Cairo University Road, 12613 Giza, Egypt
| | - Ahmed Ragab
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada; Department of Mathematics and Industrial Engineering, Polytechnique Montréal 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada; Faculty of Electronic Engineering, Menoufia University, 32952, Menouf, Egypt
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
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6
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Zandi M, Farahani A, Zakeri A, Akhavan Rezayat S, Mohammadi R, Das U, Dimmock JR, Afzali S, Nakhaei MA, Doroudi A, Erfani Y, Soltani S. Clinical Symptoms and Types of Samples Are Critical Factors for the Molecular Diagnosis of Symptomatic COVID-19 Patients: A Systematic Literature Review. Int J Microbiol 2021; 2021:5528786. [PMID: 34545287 PMCID: PMC8449726 DOI: 10.1155/2021/5528786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Currently, a novel coronavirus found in 2019 known as SARS-CoV-2 is the etiological agent of the COVID-19 pandemic. Various parameters including clinical manifestations and molecular evaluation can affect the accuracy of diagnosis. This review aims to discuss the various clinical symptoms and molecular evaluation results in COVID-19 patients, to point out the importance of onset symptoms, type, and timing of the sampling, besides the methods that are used for detection of SARS-CoV-2. METHODS A systematic literature review of current articles in the Web of Science, PubMed, Scopus, and EMBASE was conducted according to the PRISMA guideline. RESULTS Of the 12946 patients evaluated in this investigation, 7643 were confirmed to be COVID-19 positive by molecular techniques, particularly the RT-PCR/qPCR combined technique (qRT-PCR). In most of the studies, all of the enrolled cases had 100% positive results for molecular evaluation. Among the COVID-19 patients who were identified as such by positive PCR results, most of them showed fever or cough as the primary clinical signs. Less common symptoms observed in clinically confirmed cases were hemoptysis, bloody sputum, mental disorders, and nasal congestion. The most common clinical samples for PCR-confirmed COVID-19 patients were obtained from throat, oropharyngeal, and nasopharyngeal swabs, while tears and conjunctival secretions seem to be the least common clinical samples for COVID-19 diagnosis among studies. Also, different conserved SARS-CoV-2 gene sequences could be targeted for qRT-PCR detection. The suggested molecular assay being used by most laboratories for the detection of SARS-CoV-2 is qRT-PCR. CONCLUSION There is a worldwide concern on the COVID-19 pandemic and a lack of well-managed global control. Hence, it is crucial to update the molecular diagnostics protocols for handling the situation. This is possible by understanding the available advances in assays for the detection of the SARS-CoV-2 infection. Good sampling procedure and using samples with enough viral loads, also considering the onset symptoms, may reduce the qRT-PCR false-negative results in symptomatic COVID-19 patients. Selection of the most efficient primer-probe for target genes and samples containing enough viral loads to search for the existence of SARS-CoV-2 helps detecting the virus on time using qRT-PCR.
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Affiliation(s)
- Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Farahani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Armin Zakeri
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sara Akhavan Rezayat
- Department of Health Economics and Management, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Mohammadi
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Umashankar Das
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Jonathan R. Dimmock
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Shervin Afzali
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Mohammadvala Ashtar Nakhaei
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Alireza Doroudi
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Yousef Erfani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University Medical Sciences, Tehran, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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7
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Graham TG, Dugast‐Darzacq C, Dailey GM, Darzacq X, Tjian R. Simple, Inexpensive RNA Isolation and One-Step RT-qPCR Methods for SARS-CoV-2 Detection and General Use. Curr Protoc 2021; 1:e130. [PMID: 33905620 PMCID: PMC8206771 DOI: 10.1002/cpz1.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The most common method for RNA detection involves reverse transcription followed by quantitative polymerase chain reaction (RT-qPCR) analysis. Commercial one-step master mixes-which include both a reverse transcriptase and a thermostable polymerase and thus allow performing both the RT and qPCR steps consecutively in a sealed well-are key reagents for SARS-CoV-2 diagnostic testing; yet, these are typically expensive and have been affected by supply shortages in periods of high demand. As an alternative, we describe here how to express and purify Taq polymerase and M-MLV reverse transcriptase and assemble a homemade one-step RT-qPCR master mix. This mix can be easily assembled from scratch in any laboratory equipped for protein purification. We also describe two simple alternative methods to prepare clinical swab samples for SARS-CoV-2 RNA detection by RT-qPCR: heat-inactivation for direct addition, and concentration of RNA by isopropanol precipitation. Finally, we describe how to perform RT-qPCR using the homemade master mix, how to prepare in vitro-transcribed RNA standards, and how to use a fluorescence imager for endpoint detection of RT-PCR amplification in the absence of a qPCR machine In addition to being useful for diagnostics, these versatile protocols may be adapted for nucleic acid quantification in basic research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of a one-step RT-qPCR master mix using homemade enzymes Basic Protocol 2: Preparation of swab samples for direct RT-PCR Alternate Protocol 1: Concentration of RNA from swab samples by isopropanol precipitation Basic Protocol 3: One-step RT-qPCR of RNA samples using a real-time thermocycler Support Protocol: Preparation of RNA concentration standards by in vitro transcription Alternate Protocol 2: One-step RT-PCR using endpoint fluorescence detection.
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Affiliation(s)
- Thomas G.W. Graham
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Claire Dugast‐Darzacq
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Gina M. Dailey
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Robert Tjian
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
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Anu K. Ramachandran, Das S, Joseph A. Crosstalk Between Covid-19 and Associated Neurological Disorders: A Review. Curr Neuropharmacol 2021; 19:1688-1700. [PMID: 33441073 PMCID: PMC8977634 DOI: 10.2174/1570159x19666210113154342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/19/2020] [Accepted: 12/26/2020] [Indexed: 11/22/2022] Open
Abstract
COVID-19 is a global pandemic, primarily affecting the pulmonary system but its effects on other systems are not certain. Coronavirus, the causative organism, binds with angiotensinconverting enzyme 2 (ACE2) receptors in the lungs and produces pneumonia-like symptoms. Other than lungs, ACE2 receptors are also seen in the endothelium of blood vessels. Therefore, viruses can bind to the ACE2 that is present in the endothelium of brain blood vessels and thus can invade BBB, leading to neuronal damage. It is also believed that olfactory cells rich in ACE2 receptors may act as the main route of viral spread into various parts of the brain. The reported neurological effects of SARS-CoV-2 include cerebrovascular diseases, ageusia and anosmia, Guillain Barre Syndrome, and viral encephalitis. The extent of neurological involvement in SARS-CoV-2 infection warrants the necessity of further research to systematically classify neurological complications associated with SARS-CoV-2 infection, its diagnosis, and treatment. As ACE2 receptors are present in various other organs, it is obligatory to study the effect of coronavirus on other organs also. Since the long-lasting effects of the COVID-19 are unclear, more studies should be conducted to confirm the effect of the virus on the central nervous system. This review highlights the reported neurological manifestations of SARS-CoV-2 and its mechanism.
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Affiliation(s)
- Anu K. Ramachandran
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
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9
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Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2. Processes (Basel) 2020. [DOI: 10.3390/pr8111425] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A major challenge in controlling the COVID-19 pandemic is the high false-negative rate of the commonly used RT-PCR methods for SARS-CoV-2 detection in clinical samples. Accurate detection is particularly challenging in samples with low viral loads that are below the limit of detection (LoD) of standard one- or two-step RT-PCR methods. In this study, we implemented a three-step approach for SARS-CoV-2 detection and quantification that employs reverse transcription, targeted cDNA preamplification, and nano-scale qPCR based on a commercially available microfluidic chip. Using SARS-CoV-2 synthetic RNA and plasmid controls, we demonstrate that the addition of a preamplification step enhances the LoD of this microfluidic RT-qPCR by 1000-fold, enabling detection below 1 copy/µL. We applied this method to analyze 182 clinical NP swab samples previously diagnosed using a standard RT-qPCR protocol (91 positive, 91 negative) and demonstrate reproducible and quantitative detection of SARS-CoV-2 over five orders of magnitude (<1 to 106 viral copies/µL). Crucially, we detect SARS-CoV-2 with relatively low viral load estimates (<1 to 40 viral copies/µL) in 17 samples with negative clinical diagnosis, indicating a potential false-negative rate of 18.7% by clinical diagnostic procedures. In summary, this three-step nano-scale RT-qPCR method can robustly detect SARS-CoV-2 in samples with relatively low viral loads (<1 viral copy/µL) and has the potential to reduce the false-negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV-2 and other viral infections.
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10
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Li C, Zhao C, Bao J, Tang B, Wang Y, Gu B. Laboratory diagnosis of coronavirus disease-2019 (COVID-19). Clin Chim Acta 2020; 510:35-46. [PMID: 32621814 PMCID: PMC7329657 DOI: 10.1016/j.cca.2020.06.045] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of Coronavirus Disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened health worldwide. As of the end of 2020, there were nearly 10 million confirmed cases and nearly 5 million deaths associated with COVID-19. Rapid and early laboratory diagnosis of COVID-19 is the main focus of treatment and control. Molecular tests are the basis for confirmation of COVID-19, but serological tests for SARS-CoV-2 are widely available and play an increasingly important role in understanding the epidemiology of the virus and in identifying populations at higher risk for infection. Point-of-care tests have the advantage of rapid, accurate, portable, low cost and non-specific device requirements, which provide great help for disease diagnosis and detection. This review will discuss the performance of different laboratory diagnostic tests and platforms, as well as suitable clinical samples for testing, and related biosafety protection. This review shall guide for the diagnosis of COVID-19 caused by SARS-CoV-2.
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Affiliation(s)
- Chenxi Li
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China
| | - Chengxue Zhao
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China
| | - Jingfeng Bao
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China
| | - Bo Tang
- Nanjing Vazyme Medical Technology Co. Ltd., Nanjing 210046, China
| | - Yunfeng Wang
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, USA.
| | - Bing Gu
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China; Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221006, China.
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Shirani K, Sheikhbahaei E, Torkpour Z, Ghadiri Nejad M, Kamyab Moghadas B, Ghasemi M, Akbari Aghdam H, Ehsani A, Saber-Samandari S, Khandan A. A Narrative Review of COVID-19: The New Pandemic Disease. IRANIAN JOURNAL OF MEDICAL SCIENCES 2020; 45:233-249. [PMID: 32801413 PMCID: PMC7395956 DOI: 10.30476/ijms.2020.85869.1549] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/06/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023]
Abstract
Nearly every 100 years, humans collectively face a pandemic crisis. After the Spanish flu, now the world is in the grip of coronavirus disease 2019 (COVID-19). First detected in 2019 in the Chinese city of Wuhan, COVID-19 causes severe acute respiratory distress syndrome. Despite the initial evidence indicating a zoonotic origin, the contagion is now known to primarily spread from person to person through respiratory droplets. The precautionary measures recommended by the scientific community to halt the fast transmission of the disease failed to prevent this contagious disease from becoming a pandemic for a whole host of reasons. After an incubation period of about two days to two weeks, a spectrum of clinical manifestations can be seen in individuals afflicted by COVID-19: from an asymptomatic condition that can spread the virus in the environment, to a mild/moderate disease with cold/flu-like symptoms, to deteriorated conditions that need hospitalization and intensive care unit management, and then a fatal respiratory distress syndrome that becomes refractory to oxygenation. Several diagnostic modalities have been advocated and evaluated; however, in some cases, diagnosis is made on the clinical picture in order not to lose time. A consensus on what constitutes special treatment for COVID-19 has yet to emerge. Alongside conservative and supportive care, some potential drugs have been recommended and a considerable number of investigations are ongoing in this regard.
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Affiliation(s)
- Kiana Shirani
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Sheikhbahaei
- Student Research Committee, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Torkpour
- Student Research Committee, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mazyar Ghadiri Nejad
- Industrial Engineering Department, Girne American University, Kyrenia, TRNC, Turkey
| | | | - Matina Ghasemi
- Faculty of Business and Economics, Business Department, Girne American University, Kyrenia, TRNC, Turkey
| | - Hossein Akbari Aghdam
- Department of Orthopedic Surgery, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Athena Ehsani
- Department of Biomedical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Amirsalar Khandan
- Department of Electrical Engineering, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
- 0Technology Incubator Center, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
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Amawi H, Abu Deiab GI, A Aljabali AA, Dua K, Tambuwala MM. COVID-19 pandemic: an overview of epidemiology, pathogenesis, diagnostics and potential vaccines and therapeutics. Ther Deliv 2020; 11:245-268. [PMID: 32397911 PMCID: PMC7222554 DOI: 10.4155/tde-2020-0035] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
At the time of writing this review, severe acute respiratory coronavirus syndrome-2 (SARS-CoV-2) has infected more than 2,355,853 patients and resulted in more than 164,656 deaths worldwide (as of 20 April 2020). This review highlights the preventive measures, available clinical therapies and the potential of vaccine development against SARS-CoV-2 by taking into consideration the strong genetic similarities of the 2003 epidemic SARS-CoV. Recent studies are investigating the repurposing of US FDA-approved drugs as there is no available vaccine yet with many attempts under clinical evaluation. Several antivirals, antimalarials and immunomodulators that have shown activity against SARS-CoV and Middle East coronavirus respiratory syndromes are being evaluated. In particular, hydroxychloroquine, remdesivir, favipiravir, arbidol, tocilizumab and bevacizumab have shown promising results. The main aim of this review is to provide an overview of this pandemic and where we currently stand.
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Affiliation(s)
- Haneen Amawi
- Faculty of Pharmacy, Department of Pharmacy Practice, Yarmouk University, Irbid-Jordan
| | - Ghina'a I Abu Deiab
- Faculty of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy, Yarmouk University, Irbid-Jordan
| | - Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid-Jordan
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Murtaza M Tambuwala
- School of Pharmacy & Pharmaceutical Sciences, Ulster University, Coleraine, County Londonderry, BT52 1SA, Northern Ireland, UK
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Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review. J Clin Med 2020; 9:jcm9030623. [PMID: 32110875 PMCID: PMC7141113 DOI: 10.3390/jcm9030623] [Citation(s) in RCA: 320] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 01/09/2023] Open
Abstract
Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus (2019-nCoV) outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus (MERS-CoV) and severe acute respiratory syndrome (SARS)-CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases (PubMed, Embase and Cochrane Library) to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction (RT-PCR) have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.
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Aleanizy FS, Mohmed N, Alqahtani FY, El Hadi Mohamed RA. Outbreak of Middle East respiratory syndrome coronavirus in Saudi Arabia: a retrospective study. BMC Infect Dis 2017; 17:23. [PMID: 28056850 PMCID: PMC5217314 DOI: 10.1186/s12879-016-2137-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/17/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Middle East respiratory syndrome (MERS) is proposed to be a zoonotic disease. Dromedary camels have been implicated due to reports that some confirmed cases were exposed to camels. Risk factors for MERS coronavirus (MERS-CoV) infections in humans are incompletely understood. This study aimed to describe the demographic characteristics, mortality rate, clinical manifestations and comorbidities with confirmed cases of MERS-CoV. METHODS Retrospective chart review were performed to identify all laboratory-confirmed cases of MERS-CoV in Saudi Arabia who reported to the Ministry of Health (MOH) of Saudi Arabia and WHO between April 23, 2014 and August 31, 2015. Patients' charts were also reviewed for demographic information, mortality, comorbidities, clinical presentations, health care facility and presented with descriptive and comparative statistics using non parametric binomial test and Chi-square test. RESULTS Confirmed cases of male patients (61.1%) exceeded those of female patients (38.9%). Infections among Saudi patients (62.6%) exceeded those among non-Saudi patients (37.4%; P = 0.001). The majority of the patients were aged 21-40 years (37.4%) or 41-60 years (35.8%); 43 (22.6%) were aged >61 years, and (8) 4.2% were aged 0-20 years. There was a difference in mortality between confirmed MERS-CoV cases (63.7% alive versus 36.3% dead cases, respectively). Furthermore, fever with cough and shortness of breath (SOB) (n = 39; 20.5%), fever with cough (n = 29; 15.3%), fever (n = 18; 9.5%), and fever with SOB (n = 13; 6.8%), were the most common clinical manifestations associated with confirmed MERS-CoV cases. CONCLUSION MERS-CoV is considered an epidemic in Saudi Arabia. The results of the present study showed that the frequency of cases is higher among men than women, in Saudi patients than non-Saudi, and those between 21 to 60 years are most affected. Further studies are required to improve the surveillance associated with MERS-CoV to get definite and clear answers and better understanding of the MERS-CoV outbreak as well the source, and route of infection transmission in Saudi Arabia.
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Affiliation(s)
- Fadilah Sfouq Aleanizy
- College of Pharmacy, Department of Pharmaceutics, King Saud University, 22452, Riyadh, 11495 Saudi Arabia
| | - Nahla Mohmed
- College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, 12484 Saudi Arabia
| | - Fulwah Y. Alqahtani
- College of Pharmacy, Department of Pharmaceutics, King Saud University, 22452, Riyadh, 11495 Saudi Arabia
| | - Rania Ali El Hadi Mohamed
- College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 12484 Saudi Arabia
- Scientific research, Federal Ministry of Health, Khartoum, 303 Sudan
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15
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Yu ACH, Vatcher G, Yue X, Dong Y, Li MH, Tam PHK, Tsang PYL, Wong AKY, Hui MHK, Yang B, Tang H, Lau LT. Nucleic acid-based diagnostics for infectious diseases in public health affairs. Front Med 2012; 6:173-86. [PMID: 22660977 PMCID: PMC7088663 DOI: 10.1007/s11684-012-0195-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 03/03/2012] [Indexed: 11/29/2022]
Abstract
Infectious diseases, mostly caused by bacteria and viruses but also a result of fungal and parasitic infection, have been one of the most important public health concerns throughout human history. The first step in combating these pathogens is to get a timely and accurate diagnosis at an affordable cost. Many kinds of diagnostics have been developed, such as pathogen culture, biochemical tests and serological tests, to help detect and fight against the causative agents of diseases. However, these diagnostic tests are generally unsatisfactory because they are not particularly sensitive and specific and are unable to deliver speedy results. Nucleic acid-based diagnostics, detecting pathogens through the identification of their genomic sequences, have shown promise to overcome the above limitations and become more widely adopted in clinical tests. Here we review some of the most popular nucleic acid-based diagnostics and focus on their adaptability and applicability to routine clinical usage. We also compare and contrast the characteristics of different types of nucleic acid-based diagnostics.
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Affiliation(s)
- Albert Cheung-Hoi Yu
- Neuroscience Research Institute, Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Peking University, Beijing, 100191, China.
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16
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Efficient identification of Microtus cabrerae excrements using noninvasive molecular analysis. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9306-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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BEJA‐PEREIRA ALBANO, OLIVEIRA RITA, ALVES PAULOC, SCHWARTZ MICHAELK, LUIKART GORDON. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 2009; 9:1279-301. [DOI: 10.1111/j.1755-0998.2009.02699.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ALBANO BEJA‐PEREIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
| | - RITA OLIVEIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - PAULO C. ALVES
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - MICHAEL K. SCHWARTZ
- USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - GORDON LUIKART
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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18
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Zhao Y, Lu M, Lau LT, Lu J, Gao Z, Liu J, Yu ACH, Cao Q, Ye J, McNutt MA, Gu J. Neutrophils may be a vehicle for viral replication and dissemination in human H5N1 avian influenza. Clin Infect Dis 2008; 47:1575-8. [PMID: 18990065 PMCID: PMC7107848 DOI: 10.1086/593196] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The mechanism of systemic spread of H5N1 virus in patients with avian influenza is unknown. Here, H5N1 nucleoprotein and hemagglutinin were identified by immunohistochemistry in the nucleus and cytoplasm of neutrophils in the placental blood of a pregnant woman. Viral RNA was detected in neutrophils by in situ hybridization and enhanced real-time polymerase chain reaction. Therefore, neutrophils may serve as a vehicle for viral replication and transportation in avian influenza.
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Affiliation(s)
- Yingying Zhao
- Department of Pathology, School of Basic Medical Sciences, Peking University, Beijing, China
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19
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Suresh MR, Bhatnagar PK, Das D. Molecular targets for diagnostics and therapeutics of severe acute respiratory syndrome (SARS-CoV). JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES 2008; 11:1s-13s. [PMID: 19203466 DOI: 10.18433/j3j019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE The large number of deaths in a short period of time due to the spread of severe acute respiratory syndrome (SARS) infection led to the unparalleled collaborative efforts world wide to determine and characterize the new coronavirus (SARS-CoV). The full genome sequence was determined within weeks of the first outbreak by the Canadian group with international collaboration. As per the World Health Organization (WHO), the continual lack of a rapid laboratory test to aid the early diagnosis of suspected cases of SARS makes this area a priority for future research. To prevent deaths in the future, early diagnosis and therapy of this infectious disease is of paramount importance. METHODS This review describes the specific molecular targets for diagnostics and therapeutics of viral infection. RESULTS The three major diagnostic methods available for SARS includes viral RNA detection by reverse transcription polymerase chain reaction (RT-PCR), virus induced antibodies by immunofluorescence assay (IFA) or by enzyme linked immunosorbant assay (ELISA) of nucleocapsid protein (NP). The spike glycoprotein of SARS-CoV is the major inducer of neutralizing antibodies. The receptor binding domain (RBD) in the S1 region of the spike glycoprotein contains multiple conformational epitopes that induces highly potent neutralizing antibodies. The genetically engineered attenuated form of the virus or viral vector vaccine encoding for the SARS-CoV spike glycoprotein has been shown to elicit protective immunity in vaccinated animals. CONCLUSION NP is the preferred target for routine detection of SARS-CoV infection by ELISA which is an economical method compared to other methods. The RBD of the spike glycoprotein is both a functional domain for cell receptor binding and also a major neutralizing determinant of SARS-CoV. The progress in evaluating a therapeutic or vaccine would depend on the avail ability of clinically relevant animal model.
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Affiliation(s)
- Mavanur R Suresh
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada.
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20
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Velanki S, Ji HF. Detection of feline coronavirus using microcantilever sensors. MEASUREMENT SCIENCE & TECHNOLOGY 2006; 17:2964-2968. [PMID: 32288326 PMCID: PMC7115745 DOI: 10.1088/0957-0233/17/11/015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This work demonstrated the feasibility of detecting severe acute respiratory syndrome associated coronavirus (SARS-CoV) using microcantilever technology by showing that the feline coronavirus (FIP) type I virus can be detected by a microcantilever modified by feline coronavirus (FIP) type I anti-viral antiserum. A microcantilever modified by FIP type I anti-viral antiserum was developed for the detection of FIP type I virus. When the FIP type I virus positive sample is injected into the fluid cell where the microcantilever is held, the microcantilever bends upon the recognition of the FIP type I virus by the antiserum on the surface of the microcantilever. A negative control sample that does not contain FIP type I virus did not cause any bending of the microcantilever. The detection limit of the sensor was 0.1 µg ml-1 when the assay time was <1 h.
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Affiliation(s)
- Sreepriya Velanki
- Chemistry Program and Institute for Micromanufacturing, Louisiana Tech University, Ruston, LA 71270, USA
| | - Hai-Feng Ji
- Chemistry Program and Institute for Micromanufacturing, Louisiana Tech University, Ruston, LA 71270, USA
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21
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Qi C, Duan JZ, Wang ZH, Chen YY, Zhang PH, Zhan L, Yan XY, Cao WC, Jin G. Investigation of interaction between two neutralizing monoclonal antibodies and SARS virus using biosensor based on imaging ellipsometry. Biomed Microdevices 2006; 8:247-53. [PMID: 16718402 PMCID: PMC7087585 DOI: 10.1007/s10544-006-8305-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Two neutralizing human scFv, b1 and h12 were identified initially using ELISA,employing highly purified virus as the coating antigen. The biosensor technique based on imaging ellipsometry was employed directly to detect two neutralizing monoclonal antibodies and serial serum samples from 10 SARS patients and 12 volunteers who had not SARS. Further, the kinetic process of interaction between the antibodies and SARS-CoV was studied using the real-time function of the biosensor. The biosensor is consistent with ELISA that the antibody h12 showed a higher affinity in encountering the virus than antibody b1. The affinity of antibody b1 and antibody h12 was 9.5 x 10(6) M(-1) and 1.36 x 10(7) M(- 1), respectively. As a label free method, the biosensor based on imaging ellipsometry proved to be a more competent mechanism for measuring serum samples from SARS patients and the affinity between these antibodies and the SARS coronavirus.
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Affiliation(s)
- Cai Qi
- Institute of Mechanics, Chinese Academy of Sciences, #15, Bei-si-huan West Rd., Beijing, 100080 China
- Graduate School of the Chinese Academy of Sciences, 19, Yu-quan Rd, Shi-jing-shan District, Beijing, 100049 P.R. China
| | - Jin-Zhu Duan
- Institute of Biophysics, Chinese Academy of Sciences, #15, Da-tun Rd., Beijing, 100101 China
| | - Zhan-Hui Wang
- Institute of Mechanics, Chinese Academy of Sciences, #15, Bei-si-huan West Rd., Beijing, 100080 China
| | - Yan-Yan Chen
- Institute of Mechanics, Chinese Academy of Sciences, #15, Bei-si-huan West Rd., Beijing, 100080 China
- Graduate School of the Chinese Academy of Sciences, 19, Yu-quan Rd, Shi-jing-shan District, Beijing, 100049 P.R. China
| | - Pan-He Zhang
- Institute of Microbiology and Epidemiology, The Academy of Military Medical Sciences, #27 Taiping Rd., Beijing, 10085 China
| | - Lin Zhan
- Institute of Microbiology and Epidemiology, The Academy of Military Medical Sciences, #27 Taiping Rd., Beijing, 10085 China
| | - Xi-Yun Yan
- Institute of Biophysics, Chinese Academy of Sciences, #15, Da-tun Rd., Beijing, 100101 China
| | - Wu-Chun Cao
- Institute of Microbiology and Epidemiology, The Academy of Military Medical Sciences, #27 Taiping Rd., Beijing, 10085 China
| | - Gang Jin
- Institute of Mechanics, Chinese Academy of Sciences, #15, Bei-si-huan West Rd., Beijing, 100080 China
- Institute of Biophysics, Chinese Academy of Sciences, #15, Da-tun Rd., Beijing, 100101 China
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22
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Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JDC, Wengenack NL, Rosenblatt JE, Cockerill FR, Smith TF. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 2006; 19:165-256. [PMID: 16418529 PMCID: PMC1360278 DOI: 10.1128/cmr.19.1.165-256.2006] [Citation(s) in RCA: 800] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.
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Affiliation(s)
- M J Espy
- Mayo Clinic, 200 First St. SW, Hilton 470, Rochester, MN 55905, USA.
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23
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Bustin SA, Mueller R. Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin Sci (Lond) 2005; 109:365-79. [PMID: 16171460 DOI: 10.1042/cs20050086] [Citation(s) in RCA: 309] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
qRT-PCR (real-time reverse transcription-PCR) has become the benchmark for the detection and quantification of RNA targets and is being utilized increasingly in novel clinical diagnostic assays. Quantitative results obtained by this technology are not only more informative than qualitative data, but simplify assay standardization and quality management. qRT-PCR assays are most established for the detection of viral load and therapy monitoring, and the development of SARS (severe acute respiratory syndrome)-associated coronavirus qRT-PCR assays provide a textbook example of the value of this technology for clinical diagnostics. The widespread use of qRT-PCR assays for diagnosis and the detection of disease-specific prognostic markers in leukaemia patients provide further examples of their usefulness. Their value for the detection of disease-associated mRNA expressed by circulating tumour cells in patients with solid malignancies is far less apparent, and the clinical significance of results obtained from such tests remains unclear. This is because of conceptual reservations as well as technical limitations that can interfere with the diagnostic specificity of qRT-PCR assays. Therefore, although it is evident that qRT-PCR assay has become a useful and important technology in the clinical diagnostic laboratory, it must be used appropriately and it is essential to be aware of its limitations if it is to fulfil its potential.
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Affiliation(s)
- Stephen A Bustin
- Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and The London, Queen Mary's School of Medicine and Dentistry, University of London, London E1 1BB, U.K.
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Pinna D, Sampson-Johannes A, Clementi M, Poli G, Rossini S, Lin L, Vicenzi E. Amotosalen photochemical inactivation of severe acute respiratory syndrome coronavirus in human platelet concentrates. Transfus Med 2005; 15:269-76. [PMID: 16101804 PMCID: PMC7169868 DOI: 10.1111/j.0958-7578.2005.00588.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
summary. A novel human coronavirus causing severe acute respiratory syndrome (SARS) emerged in epidemic form in early 2003 in China and spread worldwide in a few months. Every newly emerging human pathogen is of concern for the safety of the blood supply during and after an epidemic crisis. For this purpose, we have evaluated the inactivation of SARS‐coronavirus (CoV) in platelet concentrates using an approved pathogen inactivation device, the INTERCEPT Blood System. Apheresis platelet concentrates (APCs) were inoculated with approximately 106 pfu mL−1 of either Urbani or HSR1 isolates of SARS‐CoV. The inoculated units were mixed with 150 µm amotosalen and illuminated with 3 J cm−2 UV‐A light. The viral titres were determined by plaque formation in Vero E6 cells. Mixing SARS‐CoV with APC in the absence of any treatment decreased viral infectivity by approximately 0·5–1 log10. Following photochemical treatment, SARS‐CoV was consistently inactivated to the limit of detection in seven independent APC units. No infectious virus was detected after treatment when up to one‐third of the APC unit was assayed, demonstrating a mean log10‐reduction of >6·2. Potent inactivation of SARS‐CoV therefore extends the capability of the INTERCEPT Blood System in inactivating a broad spectrum of human pathogens including recently emerging respiratory viruses.
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Affiliation(s)
- D Pinna
- AIDS Immunopathogenesis Unit, San Raffaele Scientific Institute, Milano, Italy
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25
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Mahony JB, Richardson S. Molecular diagnosis of severe acute respiratory syndrome: the state of the art. J Mol Diagn 2005; 7:551-9. [PMID: 16258152 PMCID: PMC1867551 DOI: 10.1016/s1525-1578(10)60587-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2005] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) first appeared in Guangdong Province, China, in November 2002. Although virus isolation and serology were useful early in the SARS outbreak for diagnosing new cases, these tests are not generally useful because virus culture requires a BSL-3 laboratory and seroconversion is often delayed until 2 to 3 weeks after infection. The first qualitative reverse transcriptase-polymerase chain reaction tests for SARS-coronavirus (CoV) were sensitive and capable of detecting 1 to 10 genome equivalents. These assays were quickly supplemented with quantitative real-time assays that helped elucidate the natural history of SARS, particularly the initial presence of low viral loads in the upper respiratory tract and high viral loads in the lower respiratory tract. The unique natural history of SARS-CoV infection dictates the testing of both respiratory and nonrespiratory specimens, the testing of multiple specimens from the same patient, and sending out positives to be confirmed by a reference laboratory. Commercially available reverse transcriptase-polymerase chain reaction tests for SARS have recently appeared; however, meaningful evaluations of these assays have not yet been performed and their true performance has not been determined. These and other issues related to diagnosis of SARS-CoV infection are discussed in this review.
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Affiliation(s)
- James B Mahony
- Regional Virology Laboratory, St. Joseph's Hospital, 50 Charlton Ave. East, Hamilton, ON L8N 4A6, Canada.
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Tang T, Wu MP, Chen S, Hou M, Hong M, Pan F, Yu H, Chen J, Yao C, Wang AH. Biochemical and immunological studies of nucleocapsid proteins of severe acute respiratory syndrome and 229E human coronaviruses. Proteomics 2005; 5:925-37. [PMID: 15759315 PMCID: PMC7167620 DOI: 10.1002/pmic.200401204] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Severe acute respiratory syndrome (SARS) is a serious health threat and its early diagnosis is important for infection control and potential treatment of the disease. Diagnostic tools require rapid and accurate methods, of which a capture ELISA method may be useful. Toward this goal, we have prepared and characterized soluble full‐length nucleocapsid proteins (N protein) from SARS and 229E human coronaviruses. N proteins form oligomers, mostly as dimers at low concentration. These two N proteins degrade rapidly upon storage and the major degraded N protein is the C‐terminal fragment of amino acid (aa) 169–422. Taken together with other data, we suggest that N protein is a two‐domain protein, with the N‐terminal aa 50–150 as the RNA‐binding domain and the C‐terminal aa 169–422 as the dimerization domain. Polyclonal antibodies against the SARS N protein have been produced and the strong binding sites of the anti‐nucleocapsid protein (NP) antibodies produced were mapped to aa 1–20, aa 150–170 and aa 390–410. These sites are generally consistent with those mapped by sera obtained from SARS patients. The SARS anti‐NP antibody was able to clearly detect SARS virus grown in Vero E6 cells and did not cross‐react with the NP from the human coronavirus 229E. We have predicted several antigenic sites (15–20 amino acids) of S, M and N proteins and produced antibodies against those peptides, some of which could be recognized by sera obtained from SARS patients. Antibodies against the NP peptides could detect the cognate N protein clearly. Further refinement of these antibodies, particularly large‐scale production of monoclonal antibodies, could lead to the development of useful diagnostic kits for diseases associated with SARS and other human coronaviruses.
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MESH Headings
- Amino Acid Sequence
- Amino Acids/chemistry
- Animals
- Antibodies, Viral/chemistry
- Antigens/chemistry
- Antigens, Viral/chemistry
- Binding Sites
- Chlorocebus aethiops
- Chromatography, Gel
- Circular Dichroism
- Cloning, Molecular
- Coronavirus 229E, Human/metabolism
- Coronavirus Nucleocapsid Proteins
- Cross-Linking Reagents/pharmacology
- DNA/chemistry
- DNA, Complementary/metabolism
- Dimerization
- Electrophoresis, Polyacrylamide Gel
- Enzyme-Linked Immunosorbent Assay
- Epitopes/chemistry
- Humans
- Microscopy, Fluorescence
- Molecular Sequence Data
- Nucleocapsid/chemistry
- Nucleocapsid Proteins/chemistry
- Open Reading Frames
- Peptides/chemistry
- Protein Array Analysis/methods
- Protein Binding
- Protein Structure, Tertiary
- Proteomics/methods
- RNA/chemistry
- Rabbits
- Severe acute respiratory syndrome-related coronavirus/metabolism
- Sequence Homology, Amino Acid
- Severe Acute Respiratory Syndrome/diagnosis
- Vero Cells
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Affiliation(s)
| | | | | | - Ming‐Hon Hou
- Institute of Biological Chemistry, Academia Sinica
| | | | - Fu‐Ming Pan
- Institute of Biological Chemistry, Academia Sinica
| | - Hui‐Ming Yu
- Institute of Biological Chemistry, Academia Sinica
| | - Jenn‐Han Chen
- School of Dentistry, National Defense Medical Center
- Biochip R&D Center, Department of Pathology, Tri‐Service General Hospital, National Defense University, Taipei, Taiwan
| | - Chen‐Wen Yao
- Biochip R&D Center, Department of Pathology, Tri‐Service General Hospital, National Defense University, Taipei, Taiwan
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Zhang Z, Xie YW, Hong J, Zhang X, Kwok SY, Huang X, Wong SW, Wong BL. Purification of severe acute respiratory syndrome hyperimmune globulins for intravenous injection from convalescent plasma. Transfusion 2005; 45:1160-4. [PMID: 15987362 PMCID: PMC7201861 DOI: 10.1111/j.1537-2995.2005.00179.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome (SARS) is a new infectious disease caused by the SARS virus. Current first-line treatments are experimental, and their effectiveness remains open to question. For more effective treatment and prevention of SARS, human SARS hyperimmune globulins for intravenous (IV) injection were purified in this study. STUDY DESIGN AND METHODS A combination of cold ethanol precipitation and ion-exchange chromatography was used to process pooled SARS convalescent plasma samples. Virus inactivation and removal approaches were taken to ensure safety. RESULTS The purified hyperimmune globulins were formulated as a 5 percent solution, with an antibody titer specifically against the SARS virus of 1:83, 1:1600, and 1:200, as determined by enzyme-linked immunosorbent assay, immunofluorescence assay, and neutralizing antibody test, respectively. The purity of the SARS hyperimmune globulins was 99.0 percent, and the monomer and dimer content was 100 percent. Other variables analyzed met the Chinese Requirements of Biologics for IV immune globulin. The SARS hyperimmune globulins prepared were subsequently approved for clinical evaluation by the Chinese National Institute for the Control of Pharmaceutical & Biological Products. CONCLUSION IV-injectable, purified, and concentrated human SARS hyperimmune globulins were prepared from pooled convalescent plasma samples, which are ready to be further evaluated.
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Affiliation(s)
- Zhan Zhang
- Shenzhen Weiwu Guangming Biological Products Co. Ltd., Guangdong, PR China
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Keyaerts E, Vijgen L, Maes P, Duson G, Neyts J, Van Ranst M. Viral load quantitation of SARS-coronavirus RNA using a one-step real-time RT-PCR. Int J Infect Dis 2005; 10:32-7. [PMID: 16023880 PMCID: PMC7110610 DOI: 10.1016/j.ijid.2005.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 01/20/2005] [Accepted: 02/01/2005] [Indexed: 12/20/2022] Open
Abstract
Introduction Severe acute respiratory syndrome (SARS) is an emerging infectious disease that first occurred in humans in the People's Republic of China in November 2002 and has subsequently spread worldwide. A novel virus belonging to the Coronaviridae family has been identified as the cause of this pulmonary disease. The severity of the disease combined with its rapid spread requires the development of fast and sensitive diagnostic assays. Results A real-time quantitative RT-PCR was designed in the nsp11 region of the replicase 1B domain of the SARS-coronavirus (SARS-CoV) genome. To evaluate this quantitative RT-PCR, cRNA standards were constructed by in vitro transcription of SARS-CoV Frankfurt 1 RNA using T7 RNA polymerase, followed by real-time RT-PCR. The assay allowed quantitation over a range of 102 to 108 RNA copies per reaction. Conclusions Extrapolated to clinical samples, this novel assay has a detection range of 104 to 1010 copies of viral genome equivalents per millilitre. In comparison to the current de facto cRNA Artus Biotech standard, the in-house cRNA standard gives a 100-fold higher absolute quantity, suggesting a possible underestimation of the viral load when using the Artus Biotech standard.
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Affiliation(s)
- Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Leen Vijgen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Griet Duson
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
- Laboratory of Clinical Virology, University Hospital Gasthuisberg, University of Leuven, Belgium
- Corresponding author. Tel.: +32 16 347908; fax: +32 16 347900.
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Abstract
Molecular diagnostic techniques, such as PCR, have become useful tools for the rapid etiological diagnosis of lower respiratory tract infections. Nucleic acid amplification tests (NAATs) have been evaluated for detecting most respiratory pathogens, and commercial assays are available for some pathogens. However, standardized protocols are needed before these assays are introduced into routine diagnostic use. For pneumonia, NAATs offer advantages over conventional tests for the detection of Mycoplasma pneumoniae, Legionella spp. and Chlamydia pneumoniae. For pneumococcal pneumonia in adults, PCR adds little to existing diagnostic tests, and is unable to distinguish pneumococcal colonization from infection when testing respiratory samples. Although less sensitive than culture-based methods, several commercial molecular diagnostic assays have been developed for tuberculosis and are useful rapid tests for selected patients. PCR can now be considered the rapid diagnostic test of choice for pertussis and some respiratory virus infections. Further work is required to better characterize the role of molecular diagnostic tests for diagnosing lower respiratory tract infections, and to develop standard assays that can be readily adopted by routine diagnostic laboratories.
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Affiliation(s)
- David R Murdoch
- Department of Pathology, Christchurch School of Medicine and Health Sciences, and Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand.
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Matsubara Y, Kerman K, Kobayashi M, Yamamura S, Morita Y, Tamiya E. Microchamber array based DNA quantification and specific sequence detection from a single copy via PCR in nanoliter volumes. Biosens Bioelectron 2005; 20:1482-90. [PMID: 15626601 DOI: 10.1016/j.bios.2004.07.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 07/07/2004] [Accepted: 07/08/2004] [Indexed: 10/26/2022]
Abstract
A novel method for DNA quantification and specific sequence detection in a highly integrated silicon microchamber array is described. Polymerase chain reaction (PCR) mixture of only 40 nL volume could be introduced precisely into each chamber of the mineral oil layer coated microarray by using a nanoliter dispensing system. The elimination of carry-over and cross-contamination between microchambers, and multiple DNA amplification and detection by TaqMan chemistry were demonstrated, for the first time, by using our system. Five different gene targets, related to Escherichia coli were amplified and detected simultaneously on the same chip by using DNA from three different serotypes as the templates. The conventional method of DNA quantification, which depends on the real-time monitoring of variations in fluorescence intensity, was not applied to our system, instead a simple method was established. Counting the number of the microchambers with a high fluorescence signal as a consequence of TaqMan PCR provided the precise quantification of trace amounts of DNA. The initial DNA concentration for Rhesus D (RhD) gene in each microchamber was ranged from 0.4 to 12 copies, and quantification was achieved by observing the changes in the released fluorescence signals of the microchambers on the chip. DNA target could be detected as small as 0.4 copies. The amplified DNA was detected with a CCD camera built-in to a fluorescence microscope, and also evaluated by a DNA microarray scanner with associated software. This simple method of counting the high fluorescence signal released in microchambers as a consequence of TaqMan PCR was further integrated with a portable miniaturized thermal cycler unit. Such a small device is surely a strong candidate for low-cost DNA amplification, and detected as little as 0.4 copies of target DNA.
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Affiliation(s)
- Yasutaka Matsubara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Nomi-gun, Ishikawa 923-1292, Japan
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Poon LLM, Guan Y, Nicholls JM, Yuen KY, Peiris JSM. The aetiology, origins, and diagnosis of severe acute respiratory syndrome. THE LANCET. INFECTIOUS DISEASES 2004; 4:663-71. [PMID: 15522678 PMCID: PMC7106534 DOI: 10.1016/s1473-3099(04)01172-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a new infectious disease that first emerged in Guangdong province, China, in November, 2002. A novel coronavirus was later identified in patients with SARS. The detection of the virus in these patients, its absence in healthy controls or other patients with atypical pneumonia, and the reproduction of a similar disease in a relevant animal model fulfilled Koch's postulates for implicating this coronavirus as the causal agent of SARS. The full genome sequence was determined within weeks of the virus's identification. The rapid progress in the aetiology, the development of laboratory diagnostic tests, and the defining of routes of viral transmission were facilitated through a unique WHO-coordinated virtual network of laboratories, which shared information on a real-time basis through daily teleconferences. Subsequent studies have indicated that the SARS coronavirus is of animal origin, that its precursor is still present in animal populations within the region, and that live-animal markets in southern China may have provided the animal-human interphase that allowed this precursor virus to adapt to human-human transmission. These findings underscore the potential for the re-emergence of SARS and the need for laboratory tests for early diagnosis. However, the low viral load in the respiratory tract makes early diagnosis of SARS a diagnostic challenge, although improvements in the sensitivity of molecular diagnostic methods continue to be made.
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Affiliation(s)
- LLM Poon
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - Y Guan
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - JM Nicholls
- Department of Pathology, University of Hong Kong, Hong Kong SAR, China
| | - KY Yuen
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - JSM Peiris
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
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32
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Han DP, Kim HG, Kim YB, Poon LL, Cho MW. Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein. Virology 2004; 326:140-9. [PMID: 15262502 PMCID: PMC7127165 DOI: 10.1016/j.virol.2004.05.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 05/14/2004] [Accepted: 05/17/2004] [Indexed: 11/28/2022]
Abstract
The etiological agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus SARS-CoV. Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. Accordingly, S-protein plays an important role in virus infection cycle and is the primary target of neutralizing antibodies. To begin to understand its biochemical and immunological properties, we expressed both full-length and ectodomain of the protein in various primate cells. Our results show that the protein has an electrophoretic mobility of about 160–170 kDa. The protein is glycosylated with high mannose and/or hybrid oligosaccharides, which account for approximately 30 kDa of the apparent protein mass. The detection of S-protein by immunoassays was difficult using human convalescent sera, suggesting that the protein may not elicit strong humoral immune response in virus-infected patients. We were able to pseudotype murine leukemia virus particles with S-protein and produce SARS pseudoviruses. Pseudoviruses infected Vero E6 cells in a pH-independent manner and the infection could be specifically inhibited by convalescent sera. Consistent with low levels of antibodies against S-protein, neutralizing activity was weak with 50% neutralization titers ranging between 1:15 to 1:25. To facilitate quantifying pseudovirus-infected cells, which are stained blue with X-Gal, we devised an automated procedure using an ELISPOT analyzer. The high-throughput capacity of this procedure and the safety of using SARS pseudoviruses should make possible large-scale analyses of neutralizing antibody responses against SARS-CoV.
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Affiliation(s)
- Dong P Han
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Hyung G Kim
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Young B Kim
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Leo L.M Poon
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Michael W Cho
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Corresponding author. Department of Medicine, Division of Infectious Diseases, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106-4984. Fax: +1-216-844-1409.
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Abstract
The serious respiratory disease, SARS (Severe Acute Respiratory Syndrome), outbreaking in winter of 2003 to 2004 remained in a sporadic patient's generating at this winter. However, there is also a possibility that wild animals as the source of infection may not be specified and that it may be much in fashion again. The paper regarding SARS and SARS-CoV is published at one per day now which has passed since fashion of SARS in one or so year. There are many papers which the researchers of other viruses enter into the research field of SARS-CoV using their own technology in addition to the researchers of coronavirus. Topics of the research on the present SARS-research field are development of vaccine, inspecting of medicine and establishment of diagnostic method. Here, the newest information is offered about these researches.
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Affiliation(s)
- Tetsuya Mizutani
- Virology 1, Gakuen 4-7-1, Musashimurayama-city, Tokyo 208-0011, Japan.
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Vinayagamoorthy T, Mulatz K, Hodkinson R. Identification of the severe acute respiratory syndrome coronavirus by simultaneous multigene DNA sequencing. J Clin Microbiol 2004; 42:3291-4. [PMID: 15243096 PMCID: PMC446234 DOI: 10.1128/jcm.42.7.3291-3294.2004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recent severe acute respiratory syndrome (SARS) outbreak resulted in calls for an accurate diagnostic test that can be used not only for routine testing but also for generating nucleotide sequences to monitor the epidemic. Although the identity of the SARS coronavirus (SARS-CoV) genome was confirmed by DNA sequencing, it is impractical to sequence the entire 29-kb SARS-CoV genome on a routine basis. Therefore, alternative assay methods such as the enzyme-linked immunosorbent assay and PCR have been pursued for routine testing, primarily to resolve probable cases. We report here a modification of standard DNA sequencing technology for accurate identification of SARS-CoV in routine testing. Instead of requiring the sequencing of the whole SARS-CoV genome, our modification enables the simultaneous sequencing of three regions of the SARS-CoV genome, the spike protein-encoding gene (35 nucleotides), gene M (43 nucleotides), and gene N (45 nucleotides), in a single electropherogram. Comparing these nucleotide sequences to DNA databank entries (National Institutes of Health) conclusively identified them as SARS-CoV sequences.
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Affiliation(s)
- T Vinayagamoorthy
- Bio-ID Diagnostic Inc., No. 1, 410 Downey Rd., LFK Biotechnology Complex, Saskatoon, Saskatchewan, Canada S7N 4N1.
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Fung YWW, Lau LT, Wong FPF, Choi KW, Chau TN, Lai ST, Wang CG, Dillon N, Yu ACH. Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection. Clin Infect Dis 2004; 39:604-6. [PMID: 15356838 PMCID: PMC7204107 DOI: 10.1086/422887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yin-Wan Wendy Fung
- Neuroscience Research Institute, Key Laboratory of Neuroscience, Peking University and Department of Neurobiology, Peking University Health Science Center, Ministry of Education, Beijing
- Hong Kong DNA Chips, Hong Kong Special Administrative Region, China
| | - Lok Ting Lau
- Neuroscience Research Institute, Key Laboratory of Neuroscience, Peking University and Department of Neurobiology, Peking University Health Science Center, Ministry of Education, Beijing
- Hong Kong DNA Chips, Hong Kong Special Administrative Region, China
| | | | - Kin-Wing Choi
- Princess Margaret Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Tai-Nin Chau
- Princess Margaret Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Sik-To Lai
- Princess Margaret Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Chen G Wang
- National Emergency Action on SARS Research (Beijing Group), Beijing
| | - Natalie Dillon
- Hong Kong DNA Chips, Hong Kong Special Administrative Region, China
| | - Albert Cheung-Hoi Yu
- Neuroscience Research Institute, Key Laboratory of Neuroscience, Peking University and Department of Neurobiology, Peking University Health Science Center, Ministry of Education, Beijing
- National Emergency Action on SARS Research (Beijing Group), Beijing
- Hong Kong DNA Chips, Hong Kong Special Administrative Region, China
- Reprints or correspondence: Dr. Albert Cheung-Hoi Yu, Neuroscience Research Institute, Key Laboratory of Neuroscience, Peking University and Dept. of Neurobiology, Peking University Health Science Ctr., Ministry of Education, 38 Xue Yuan Rd., Beijing 100083, China ()
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