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Khazaneha M, Tajedini O, Esmaeili O, Abdi M, Khasseh AA, Sadatmoosavi A. Thematic evolution of coronavirus disease: a longitudinal co-word analysis. LIBRARY HI TECH 2022. [DOI: 10.1108/lht-10-2021-0370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PurposeUsing science mapping analysis approach and co-word analysis, the present study explores and visualizes research fields and thematic evolution of the coronavirus. Based on this method, one can get a picture of the real content of the themes in the mentioned thematic area and identify the main minor and emerging themes.Design/methodology/approachThis study was conducted based on co-word science mapping analysis under a longitudinal study (from 1988 to 2020). The collection of documents in this study was further divided into three subperiods: 1988–1998, 1999–2009 and 2010–2020. In order to perform science mapping analysis based on co-word bibliographic networks, SciMAT was utilized as a bibliometric tool. Moreover, WoS, PubMed and Scopus bibliographic databases were used to download all records.FindingsIn this study, strategic diagrams were demonstrated for the coronavirus research for a chronological period to assess the most relevant themes. Each diagram depended on the sum of documents linked to each research topic. In the first period (1988–1998), the most centralizations were on virology and evaluation of coronavirus structure and its structural and nonstructural proteins. In the second period (1999–2009), with due attention to high population density in eastern Asia and the increasing number of people affected with the new generation of coronavirus (named severe acute respiratory syndrome virus or SARS virus), publications have been concentrated on “antiviral activity.” In the third period (2010–2020), there was a tendency to investigate clinical syndromes, and most of the publications and citations were about hot topics like “severe acute respiratory syndrome,” “coronavirus” and “respiratory tract disease.” Scientometric analysis of the field of coronavirus can be regarded as a roadmap for future research and policymaking in this important area.Originality/valueThe originality of this research can be considered in two ways. First, the strategic diagrams of coronavirus are drawn in four thematic areas including motor cluster, basic and transversal cluster, highly developed cluster and emerging and declining cluster. Second, COVID-19 is mentioned as a hot topic of research.
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Chatterjee S, Mishra S, Chowdhury KD, Ghosh CK, Saha KD. Various theranostics and immunization strategies based on nanotechnology against Covid-19 pandemic: An interdisciplinary view. Life Sci 2021; 278:119580. [PMID: 33991549 PMCID: PMC8114615 DOI: 10.1016/j.lfs.2021.119580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/12/2021] [Accepted: 04/25/2021] [Indexed: 02/07/2023]
Abstract
COVID-19 pandemic is still a major risk to human civilization. Besides the global immunization policy, more than five lac new cases are documented everyday. Some countries newly implement partial/complete nationwid lockdown to mitigate recurrent community spreading. To avoid the new modified stain of SARS-CoV-2 spreading, some countries imposed any restriction on the movement of the citizens within or outside the country. Effective economical point of care diagnostic and therapeutic strategy is vigorously required to mitigate viral spread. Besides struggling with repurposed medicines, new engineered materials with multiple unique efficacies and specific antiviral potency against SARS-CoV-2 infection may be fruitful to save more lives. Nanotechnology-based engineering strategy sophisticated medicine with specific, effective and nonhazardous delivery mechanism for available repurposed antivirals as well as remedial for associated diseases due to malfeasance in immuno-system e.g. hypercytokinaemia, acute respiratory distress syndrome. This review will talk about gloomy but critical areas for nanoscientists to intervene and will showcase about the different laboratory diagnostic, prognostic strategies and their mode of actions. In addition, we speak about SARS-CoV-2 pathophysiology, pathogenicity and host specific interation with special emphasis on altered immuno-system and also perceptualized, copious ways to design prophylactic nanomedicines and next-generation vaccines based on recent findings.
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Affiliation(s)
- Sujan Chatterjee
- Molecular Biology and Tissue Culture Laboratory, Post Graduate Department of Zoology, Vidyasagar College, Kolkata-700006, India
| | - Snehasis Mishra
- Cancer and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata-700032, India
| | - Kaustav Dutta Chowdhury
- Cyto-genetics Laboratory, Department of Zoology, Rammohan College, 102/1, Raja Rammohan Sarani, Kolkata-700009, India
| | - Chandan Kumar Ghosh
- School of Material Science and Nanotechnology, Jadavpur University, Kolkata-700032, India.
| | - Krishna Das Saha
- Cancer and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata-700032, India.
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Das A, Ahmed R, Akhtar S, Begum K, Banu S. An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies. GENE REPORTS 2021; 23:101122. [PMID: 33821222 PMCID: PMC8012276 DOI: 10.1016/j.genrep.2021.101122] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/08/2021] [Accepted: 03/24/2021] [Indexed: 01/18/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) manifests as extreme acute respiratory conditions caused by a novel beta coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which is reported to be the seventh coronavirus to infect humans. Like other SARS-CoVs it has a large positive-stranded RNA genome. But, specific furin site in the spike protein, mutation prone and phylogenetically mess open reading frame1ab (Orf1ab) separates SARS-CoV-2 from other RNA viruses. Since the outbreak (February-March 2020), researchers, scientists, and medical professionals are inspecting all possible facts and aspects including its replication, detection, and prevention strategies. This led to the prompt identification of its basic biology, genome characterization, structural and expression based functional information of proteins, and utilization of this information in optimizing strategies to prevent its spread. This review summarizes the recent updates on the basic molecular biology of SARS-CoV-2 and prevention strategies undertaken worldwide to tackle COVID-19. This recent information can be implemented for the development and designing of therapeutics against SARS-CoV-2.
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Key Words
- AEC2, angiotensin-converting enzyme 2
- CD4 and CD8, cluster of differentiation
- CDC, Centers for Disease Control and Prevention
- COVID-19, Coronavirus Diseases 2019
- GM-CSF, macrophage colony-stimulating factor
- Genome organization and expression
- HCV, hepatitis C virus
- HIV, human immune deficiency virus
- LAMP, loop mediated isothermal amplification
- MARS-CoV, Middle East Respiratory Syndrome Coronavirus
- Prevention strategies
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- WHO, World Health Organization
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Affiliation(s)
- Ankur Das
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Raja Ahmed
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Suraiya Akhtar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Khaleda Begum
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Sofia Banu
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
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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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Jang M, Park R, Park YI, Cha YE, Yamamoto A, Lee JI, Park J. EGCG, a green tea polyphenol, inhibits human coronavirus replication in vitro. Biochem Biophys Res Commun 2021; 547:23-28. [PMID: 33588235 PMCID: PMC7874949 DOI: 10.1016/j.bbrc.2021.02.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/04/2021] [Indexed: 01/27/2023]
Abstract
COVID-19 pandemic results in record high deaths in many countries. Although a vaccine for SARS-CoV-2 is now available, effective antiviral drugs to treat coronavirus diseases are not available yet. Recently, EGCG, a green tea polyphenol, was reported to inhibit SARS-CoV-2 3CL-protease, however the effect of EGCG on coronavirus replication is unknown. In this report, human coronavirus HCoV-OC43 (beta coronavirus) and HCoV-229E (alpha coronavirus) were used to examine the effect of EGCG on coronavirus. EGCG treatment decreases 3CL-protease activity of HCoV-OC43 and HCoV-229E. Moreover, EGCG treatment decreased HCoV-OC43-induced cytotoxicity. Finally, we found that EGCG treatment decreased the levels of coronavirus RNA and protein in infected cell media. These results indicate that EGCG inhibits coronavirus replication.
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Affiliation(s)
- Minsu Jang
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Rackhyun Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Yeo-Eun Cha
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Ayane Yamamoto
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Jin I Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea.
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Moneva-Sakelarieva MG, Kobakova YA, Atanasov PY, Obreshkova DP, Ivanova SA, Stankova EK. COVID-19 – the challenge to treat a disease and not a positive RT-PCR test. PHARMACIA 2021. [DOI: 10.3897/pharmacia.68.e61906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The new pandemic disease COVID is quick spread worldwide.The primary method used for diagnosing of COVID-19 is detecting viral nucleic acids. The main problem with RT-PCR test is the false negative results. The negative RT-PCR does not exclude a SARS-CoV-2 infection and this method should not be used as the only diagnostic criteria. The RT-PCR result does not change the complex treatment of the disease. The aim of the current study is to compare the four groups clinical cases of the different parameters: RT-PCR test, rapid test, clinical picture, laboratory tests as hematology, inflammatory markers, coagulation status and chemistry and imaging examinations: Chest X-ray at and Chest CT scan. Complex therapeutic approach has been implemented: antibiotic, inflammatory, anticoagulants, oxygen therapy, hepatoprotectors, antimycotics, fibrinolytics, probiotics, essential oils, vitamins. During the follow-up period, a tendency for significant reduction and resorption of the pulmonary changes on the CT scans has been seen.
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Anantharaj A, Das SJ, Sharanabasava P, Lodha R, Kabra SK, Sharma TK, Medigeshi GR. Visual Detection of SARS-CoV-2 RNA by Conventional PCR-Induced Generation of DNAzyme Sensor. Front Mol Biosci 2020; 7:586254. [PMID: 33425988 PMCID: PMC7793695 DOI: 10.3389/fmolb.2020.586254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
The gold standard for the diagnosis of SARS-CoV-2, the causative agent of COVID-19, is real-time polymerase chain reaction (PCR), which is labor-intensive, expensive, and not widely available in resource-poor settings. Therefore, it is imperative to develop novel, accurate, affordable, and easily accessible assays/sensors to diagnose and isolate COVID-19 cases. To address this unmet need, we utilized the catalytic potential of peroxidase-like DNAzyme and developed a simple visual detection assay for SARS-CoV-2 RNA using a conventional thermal cycler by the PCR-induced generation of DNAzyme sensor. The performance of RT-PCR DNAzyme-based sensor was comparable to that of real-time PCR. The pilot scale validation of RT-PCR DNAzyme-based sensor has shown ~100% sensitivity and specificity in clinical specimens (nasopharyngeal swab, n = 34), with a good correlation (Spearman r = 0.799) with the Ct-value of fluorescence probe-based real-time PCR. These findings clearly indicate the potential of this inexpensive, sensitive, and specific molecular diagnostic test to extend our testing capabilities for the detection of SARS-CoV-2 to curtail COVID-19 transmission.
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Affiliation(s)
- Anbalagan Anantharaj
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Soon Jyoti Das
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Patil Sharanabasava
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sushil K. Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Tarun Kumar Sharma
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Guruprasad R. Medigeshi
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
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Sinha A, Lutter R, Dekker T, Dierdorp B, J. Sterk P, Frey U, Delgado-Eckert E. Can Measurements of Inflammatory Biomarkers be Used to Spot Respiratory Viral Infections? Viruses 2020; 12:v12101175. [PMID: 33080844 PMCID: PMC7594027 DOI: 10.3390/v12101175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022] Open
Abstract
Accurate detection of human respiratory viral infections is highly topical. We investigated how strongly inflammatory biomarkers (FeNO, eosinophils, neutrophils, and cytokines in nasal lavage fluid) and lung function parameters change upon rhinovirus 16 infection, in order to explore their potential use for infection detection. To this end, within a longitudinal cohort study, healthy and mildly asthmatic volunteers were experimentally inoculated with rhinovirus 16, and time series of these parameters/biomarkers were systematically recorded and compared between the pre- and post-infection phases of the study, which lasted two months and one month, respectively. We found that the parameters’/biomarkers’ ability to discriminate between the infected and the uninfected state varied over the observation time period. Consistently over time, the concentration of cytokines, in nasal lavage fluid, showed moderate to very good discrimination performance, thereby qualifying for disease progression monitoring, whereas lung function and FeNO, while quickly and non-invasively measurable using cheap portable devices (e.g., at airports), performed poorly.
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Affiliation(s)
- Anirban Sinha
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (R.L.); (P.J.S.)
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (T.D.); (B.D.)
- Correspondence: ; Tel.: +31-20-566-4356
| | - René Lutter
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (R.L.); (P.J.S.)
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (T.D.); (B.D.)
| | - Tamara Dekker
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (T.D.); (B.D.)
| | - Barbara Dierdorp
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (T.D.); (B.D.)
| | - Peter J. Sterk
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (R.L.); (P.J.S.)
| | - Urs Frey
- Computational Physiology and Biostatistics, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Edgar Delgado-Eckert
- University Children’s Hospital (UKBB), University of Basel, Spitalstrasse 33, Postfach, 4031 Basel, Switzerland; (U.F.); (E.D.-E.)
- Computational Physiology and Biostatistics, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
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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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Llanes A, Restrepo CM, Caballero Z, Rajeev S, Kennedy MA, Lleonart R. Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic. Int J Mol Sci 2020; 21:E4546. [PMID: 32604724 PMCID: PMC7352669 DOI: 10.3390/ijms21124546] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022] Open
Abstract
In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
| | - Carlos M. Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
| | - Zuleima Caballero
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
| | - Sreekumari Rajeev
- College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Melissa A. Kennedy
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA;
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
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Ujjan ID, Devrajani BR, Ghanghro AA, Shah SZA. The clinical and demographical profile of Coronavirus illness: The tale of Tablighi Jamaat and Zaireen in Quarantine / Isolation center at Sukkur and Hyderabad. Pak J Med Sci 2020; 36:S12-S16. [PMID: 32582307 PMCID: PMC7306966 DOI: 10.12669/pjms.36.covid19-s4.2829] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Objectives: To determine the clinical and demographical profile of corona-virus illness among Tablighi Jamaat and Zaireen kept in quarantine / isolation center at Sukkur and Hyderabad Sindh. Methods: The cross-sectional descriptive study (late March-2020 to mid of April-2020) was conducted at Diagnostic & Research Laboratory LUMHS Jamshoro / Hyderabad. All the suspected cases for COVID-19 were recruited and screened for corona virus infection. The study explored the data of the suspected and diagnosed (confirmed) case of COVID-2019 (Tablighi Jamaat and Zaireen) reported by Diagnostic Research Laboratory Liaquat University of Medical and Health Sciences (LUMHS) Jamshoro who belonged to various parts of the country in general and province Sindh in particular. All the individuals regardless of age and gender presented either as asymptomatic, critical ill or having non-specific symptoms as fever, flu, cough; sore throat and shortness of breath were screened for COVID-19 by real time PCR after taking informed consent whereas the frequency / percentages (%) and means ±SD computed for study variables. Results: During study period total 920 patients were explored and screened for Corona virus infection. The mean ± SD for age (yrs) of overall population of city Sukkur and Hyderabad was 57.83±8.84 and 59.62±9.72 respectively. The 700 people from Sukkur city was screened and out of them 276 (39.4%) were positive and 424 (60.5) were negative while the cure rate was 245 (88.7%) along with mean ± SD for recovery time was 9.41±2.97. The 220 people from Hyderabad city was screened and out of them 106 (48.1%) were positive and 114 (51.8%) were negative while the cure rate was 106 (100%) along with mean ± SD for recovery time was 11.54±3.42. The majority of cases at both centers were asymptomatic (90%), symptomatic (7%) and critically ill (3%). The mortality accounted for 2.8% cases at Hyderabad isolation center and all were having smoking history and co-morbidities as ischemic heart diseases, diabetes mellitus, obstructive lung disease and cerebrovascular accident whereas no mortality was observed at Sukkur isolation center. Conclusion: RT-PCR measure allowed fast, delicate, and explicit discovery of SARS-CoV in biochemical diagnosis. The majority of cases at both centers were asymptomatic while the mortality was identified in 2.8% cases (having co-morbidities) at Hyderabad isolation center whereas no mortality was observed at Sukkur isolation center.
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Affiliation(s)
- Ikram Din Ujjan
- Prof. Ikram Din Ujjan, Department of Pathology, LUMHS, Jamshoro, Pakistan
| | | | - Akbar Ali Ghanghro
- Akbar Ali Ghanghro Field Epidemiologist / National Stop Transmission of Polio Program in Pakistan, (CDC-USA, WHO and MOH funded program) LUMHS, Jamshoro, Pakistan
| | - Syed Zulfiquar Ali Shah
- Syed Zulfiquar Ali Shah Assistant Professor, Department of Medicine LUMHS, Jamshoro, Pakistan
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Ching L, Chang SP, Nerurkar VR. COVID-19 Special Column: Principles Behind the Technology for Detecting SARS-CoV-2, the Cause of COVID-19. HAWAI'I JOURNAL OF HEALTH & SOCIAL WELFARE 2020; 79:136-142. [PMID: 32432217 PMCID: PMC7226308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nationwide shortages of tests that detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and diagnose coronavirus disease 2019 (COVID-19) have led the US Food and Drug Administration (FDA) to significantly relax regulations regarding COVID-19 diagnostic testing. To date the FDA has given emergency use authorization (EUA) to 48 COVID-19 in vitro diagnostic tests and 21 high complexity molecular-based laboratory developed tests, as well as implemented policies that give broad authority to clinical laboratories and commercial manufacturers in the development, distribution, and use of COVID-19 diagnostic tests. Currently, there are 2 types of diagnostic tests available for the detection of SARS-CoV-2: (1) molecular and (2) serological tests. Molecular detection of nucleic acid (RNA or DNA) sequences relating to the suspected pathogen is indicative of an active infection with the suspected pathogen. Serological tests detect antibodies against the suspected pathogen, which are produced by an individual's immune system. A positive serological test result indicates recent exposure to the suspected pathogen but cannot be used to determine if the individual is actively infected with the pathogen or immune to reinfection. In this article, the SARS-CoV-2 diagnostic tests currently approved by the FDA under EUA are reviewed, and other diagnostic tests that researchers are developing to detect SARS-CoV-2 infection are discussed.
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Affiliation(s)
| | | | - Vivek R. Nerurkar
- Correspondence to: Vivek R. Nerurkar PhD; Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, 651 Ilalo Street, BSB 320G, Honolulu, HI 96813; Ph: (808) 692-1668;
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Rodrigues ILF, Cruz ACM, Souza AE, Knackfuss FB, Costa CHC, Silveira RL, Castro TX. Retrospective study of porcine circovirus 3 (PCV3) in swine tissue from Brazil (1967-2018). Braz J Microbiol 2020; 51:1391-1397. [PMID: 32347531 DOI: 10.1007/s42770-020-00281-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
In this study, we report the molecular diagnosis and retrospective study of porcine circovirus 3 (PCV3) in frozen and formalin-fixed paraffin-embedded swine tissues (FFPE) collected from 1967 to 2018 in southeastern Brazil (Espírito Santo and Rio de Janeiro states). Frozen tissues from 35 pigs and FFPE tissues from 143 pigs were tested by nested PCR, targeting the PCV3 partial capsid gene. Bidirectional sequencing of 16 positive samples was performed, followed by sequence analysis and haplotype networks. A total of 26/178 samples (14.6%) tested positive for PCV3: 14/35 (40%) frozen tissue and 12/143 (8.4%) FFPE tissue. PCV3 was detected in the 1960s, 1970s, 2000s, and 2010s with the characterization of types PCV3a and PCV3b. A star-like distribution was observed in the grid of haplotypes, with a low haplotype diversity and more recent dispersal of the virus. A total of 40% of asymptomatic animals considered fit for slaughter tested positive for PCV3. In conclusion, PCV3 DNA was detected over 51 years of study, prior to initial reports and, so far, the sample detected in 1967 is the oldest partial capsid sequence described. The circulation of two different genotypes was reported, suggesting more than one introduction event of this virus into Brazil. Moreover, taken together, our studies indicated an ancient origin of PCV3 and its circulation in asymptomatic animals in Brazilian herds.
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Affiliation(s)
- I L F Rodrigues
- Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Rua Prof. Hernani Melo, Niterói, Rio de Janeiro, 24210-130, Brazil.
| | - A C M Cruz
- Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Rua Prof. Hernani Melo, Niterói, Rio de Janeiro, 24210-130, Brazil
| | - A E Souza
- Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Rua Prof. Hernani Melo, Niterói, Rio de Janeiro, 24210-130, Brazil
| | - F B Knackfuss
- Escola de Ciências da Saúde, Medicina Veterinária, Unigranrio, Duque de Caxias, RJ, Brazil
| | - C H C Costa
- Pathological Anatomy Laboratory, State Center for Research in Animal Health, Agricultiural Research Company of the State of Rio de Janeiro-Pesagro-Rio, Alameda São Boaventura, Niterói, Rio de Janeiro, Brazil
| | - R L Silveira
- Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Rua Prof. Hernani Melo, Niterói, Rio de Janeiro, 24210-130, Brazil.,Department of Morphology, Fluminense Federal University, Rua Prof. Hernani Melo, Niterói, Rio de Janeiro, 24210-130, Brazil
| | - T X Castro
- Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Rua Prof. Hernani Melo, Niterói, Rio de Janeiro, 24210-130, Brazil
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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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Pang J, Wang MX, Ang IYH, Tan SHX, Lewis RF, Chen JIP, Gutierrez RA, Gwee SXW, Chua PEY, Yang Q, Ng XY, Yap RK, Tan HY, Teo YY, Tan CC, Cook AR, Yap JCH, Hsu LY. Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review. J Clin Med 2020; 9:E623. [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] [Grants] [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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Affiliation(s)
- Junxiong Pang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
- Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore
| | - Min Xian Wang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
- Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore
| | - Ian Yi Han Ang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Sharon Hui Xuan Tan
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Ruth Frances Lewis
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Jacinta I-Pei Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | | | - Sylvia Xiao Wei Gwee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
- Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore
| | - Pearleen Ee Yong Chua
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
- Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore
| | - Qian Yang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Xian Yi Ng
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Rowena K.S. Yap
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Hao Yi Tan
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | | | - Alex R. Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Jason Chin-Huat Yap
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
| | - Li Yang Hsu
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; (M.X.W.); (I.Y.H.A.); (S.H.X.T.); (R.F.L.); (J.I.-P.C.); (S.X.W.G.); (P.E.Y.C.); (Q.Y.); (X.Y.N.); (R.K.S.Y.); (H.Y.T.); (Y.Y.T.); (A.R.C.); (J.C.-H.Y.); (L.Y.H.)
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Brombilla T, Ogata RA, Nassar AFDC, Cardoso MV, Ruiz VLDA, Fava CD. EFFECT OF BACTERIAL AGENTS OF PORCINE RESPIRATORY DISEASE COMPLEX ON PRODUCTIVE INDICES AND SLAUGHTER WEIGHT. CIÊNCIA ANIMAL BRASILEIRA 2019. [DOI: 10.1590/1809-6891v20e-51615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Abstract Porcine respiratory disease complex comprises the interaction of two or more infectious agents. The major bacterial agents involved were investigated in 115 finishing pigs at a farm in São Paulo State, Brazil: Actinobacillus pleuropneumoniae (serology, bacterial culture, and multiplex PCR), Mycoplasma hyopneumoniae (Mhyo) (nested PCR), Pasteurella multocida (multiplex PCR), Haemophilus parasuis (PCR multiplex), and Streptococcus sp. (bacterial culture). Macroscopic and microscopic lung lesions were evaluated, and zootechnical indices were recorded. Mhyo occurred in 113 animals (98.3%), seventeen of which were co-infected with Streptococcus sp. The finding of emphysematous lung was associated with significantly lower final and carcass weight at slaughter. Although vaccinated against Mhyo with an inactivated immunogen, almost 100% of the animals were infected. Mhyo infection with and without Streptococcus sp. co-infection was related to lung lesions of varying degrees and lower slaughter and carcass weight.
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Alvarenga TCD, Brito WMEDD, Ruiz VLDA, Castro AMMGD, Bersano JG, Ogata RA, Soares P. Micoplasma hyopneumoniae associado ao circovírus suíno tipo 2 em plantéis não vacinados para micoplasmose. ARQUIVOS DO INSTITUTO BIOLÓGICO 2018. [DOI: 10.1590/1808-1657000442016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO: A síndrome circovirose suína e doenças associadas (PCVAD) tem sido descrita em diversas regiões do mundo. Seu agente primário, o circovírus suíno tipo 2 (PCV2), está associado a elevados índices de refugagem nas granjas e a vultuosos prejuízos econômicos. Diversos fatores de risco estão relacionados à manifestação dos quadros clínicos da síndrome, nomeadamente deficiências de manejo, presença de coinfecções e imunização diante do agente. Entre os agentes frequentemente relatados associados ao PCV2 está o Mycoplasma hyopneumoniae. Este estudo objetivou verificar a ocorrência de M. hyopneumoniae em animais diagnosticados estarem acometidos pela PCVAD, em sistemas intensivos de produção de suínos do estado de Goiás. Amostras de secreção nasal de 40 animais foram analisadas para a pesquisa do DNA de M. hyopneumoniae. Do total das amostras de secreção nasal, 6 (15%) foram positivas na reação em cadeia da polimerase (PCR) para o M. hyopneumoniae, apenas em granjas que não praticavam a vacinação contra esse agente. Os resultados relacionados à presença de micoplasma estão de acordo com os achados clínicos dos animais analisados que apresentavam sintomatologia de doenças respiratórias e lesões relacionadas ao trato respiratório. Este é o primeiro relato da associação de PCV2 com M. hyopneumoniae em suínos identificados com PCVAD no estado de Goiás.
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de Castro AMMG, Cruz TF, Yamada KB, Gerber PF, Gabardo MP, Araújo JP, Guedes RMC, Mori CK, Oliveira CP, Santos SS, Richtzenhain LJ. Preliminary evidence of age-dependent clinical signs associated with porcine circovirus 2b in experimentally infected CH3/Rockefeller mice. Res Vet Sci 2015; 103:70-2. [PMID: 26679798 DOI: 10.1016/j.rvsc.2015.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/12/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
Abstract
Mice and rats are susceptible to porcine circovirus 2b (PCV2) infection under field and experimental conditions. However, whether PCV2 induces disease in rodents remains a matter of debate. The objectives of the present study were to determine whether PCV2-induced disease in mice is age-dependent and whether intranasally inoculated animals are able to infect animals they come into contact with. Twenty-five CH3/Rockefeller mice were divided into six groups and intranasally inoculated with 25μL of either PCV2b or PBS on days 0, 3 and 6. One group remained untreated. Two age groups were tested: 3-week-old mice and 6-week-old mice. The administration of three PCV2 intranasal inoculations at intervals of three days was able to induce infection and support virus transmission in susceptible mice, regardless of the age at inoculation. The clinical signs associated with PCV2 infection were more severe in younger mice, and PCV2-DNA load was higher in their faeces. In conclusion, PCV2 induced disease in mice.
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Affiliation(s)
- Alessandra M M G de Castro
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, 05508 270, São Paulo, SP Brazil; Complexo Educacional Faculdades Metropolitana Unidas, Veterinária, Rua Ministro Nelson Hungria, 541, Real Parque, Morumbi, São Paulo, SP, Brazil.
| | - Taís F Cruz
- Departamento de Imunologia e Microbiologia, Instituto de Biociência, Universidade Estadual Paulista "Julio de Mesquita Filho", Campus de Botucatu, Botucatu, SP, 18618-970, Brazil; Biotechnology Institute - IBTEC - Sao Paulo State University - UNESP - Campus de Botucatu, SP
| | - Katarina B Yamada
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, 05508 270, São Paulo, SP Brazil
| | - Priscilla F Gerber
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, MG, Brazil
| | - Michelle P Gabardo
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, MG, Brazil
| | - João P Araújo
- Departamento de Imunologia e Microbiologia, Instituto de Biociência, Universidade Estadual Paulista "Julio de Mesquita Filho", Campus de Botucatu, Botucatu, SP, 18618-970, Brazil; Biotechnology Institute - IBTEC - Sao Paulo State University - UNESP - Campus de Botucatu, SP
| | - Roberto M C Guedes
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, MG, Brazil
| | - Cinthia K Mori
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, 05508 270, São Paulo, SP Brazil
| | - Camila P Oliveira
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, 05508 270, São Paulo, SP Brazil
| | - Sueli S Santos
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, 05508 270, São Paulo, SP Brazil
| | - Leonardo J Richtzenhain
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, 05508 270, São Paulo, SP Brazil
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Abstract
Recently, studies have suggested an association between the Torque teno sus virus (TTSuV) and the Porcine circovirus-2 (PCV2) in PCV2-associated disease cases. The aim of this study was to verify TTSuVs loads in pig faeces from PCV2-positive animals with and without diarrhea from PCVAD-affected and PCV2-unvaccinated herds. A total of 80 faecal samples were collected individually from nursery and grow-finish pigs with (n = 40) or without (n = 40) diarrhea. The samples were tested for PCV2 and TTSuVs by using DNA binding dye SYBR Green quantitative polymerase chain reaction (qPCR). Torque teno sus virus k2 (TTSuVk2) load in the faeces was significantly higher in the nursery pigs with diarrhea, and these pigs also exhibited significantly higher PCV2 (P < 0.01) faecal matter loads compared to the non-diarrheic animals from the same age group. Torque teno sus virus 1 (TTSuV1) viral loads were the same regardless of age group and disease condition. There were no correlations between PCV2 and TTSuV1 or TTSuVk2 and TTSuV1 viral loads; however, a weak correlation (r = 0.23, P = 0.03) was found between TTSuVk2 and PCV2 viral loads. In conclusion, TTSuVk2 viral loads were significantly higher in the diarrheic faeces from the nursery pigs. Additionally, the higher loads of PCV2 and TTSuVk2 in the nursery-diarrheic animals revealed that diarrhea might have an important role in the spread of both viruses in herds.
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Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses. J Clin Microbiol 2015; 53:2722-6. [PMID: 26019210 DOI: 10.1128/jcm.01224-15] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/19/2015] [Indexed: 01/13/2023] Open
Abstract
Based on findings in small RNA-sequencing (Seq) data analysis, we developed highly sensitive and specific real-time reverse transcription (RT)-PCR assays with locked nucleic acid probes targeting the abundantly expressed leader sequences of Middle East respiratory syndrome coronavirus (MERS-CoV) and other human coronaviruses. Analytical and clinical evaluations showed their noninferiority to a commercial multiplex PCR test for the detection of these coronaviruses.
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Franzo G, Cortey M, de Castro AMMG, Piovezan U, Szabo MPJ, Drigo M, Segalés J, Richtzenhain LJ. Genetic characterisation of Porcine circovirus type 2 (PCV2) strains from feral pigs in the Brazilian Pantanal: An opportunity to reconstruct the history of PCV2 evolution. Vet Microbiol 2015; 178:158-62. [PMID: 25975522 DOI: 10.1016/j.vetmic.2015.05.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
Abstract
Since its discovery, Porcine circovirus type 2 has emerged as one of the most relevant swine infectious diseases, causing relevant economic losses for the pig industry. While four genotypes were identified, only three (PCV2a, PCV2b and PCV2d) are currently circulating and display a worldwide distribution. Another genotype, PCV2c, has been described only once in Danish archive samples collected between 1980 and 1990. In addition to commercial pigs, PCV2 has been demonstrated to infect wild boars and other wild species, which can potentially serve as a reservoir for domestic populations. In this study, eight sequences obtained from feral pigs in the Pantanal region (Mato Grosso do Sul State, Brazil) were compared with reference sequences and other Brazilian sequences, and the results revealed remarkable genetic diversity, with all four genotypes currently recognised being detected (PCV2a, PCV2b, PCV2c and PCV2d). This finding represents a remarkable discovery, as it is the first detection of PCV2c since 1990 and the first-ever detection of PCV2c in live animals. The peculiar population history and ecological scenario of feral pigs in the Pantanal coupled with the complex, and still only partially known relationship of feral pigs with other PCV2 susceptible species (i.e., domestic pigs, wild boars and peccaries), open exciting questions concerning PCV2 origin and evolution. Overall, the results of the present study led us to form the following hypothesis: the PCV2 strains found in feral pigs may be the last descent of the strains that circulated among European pigs in the past, or they may have infected these feral pigs more recently through a bridge species.
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Affiliation(s)
| | | | | | - Ubiratan Piovezan
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Pantanal, Corumbá, MS, Brazil
| | - Matias Pablo Juan Szabo
- Laboratório de Ixodologia, Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, MG, Brazil
| | | | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Leonardo José Richtzenhain
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
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SWINE INFECTIOUS AGENTS IN TAYASSU PECARI AND PECARI TAJACU TISSUE SAMPLES FROM BRAZIL. J Wildl Dis 2014; 50:205-9. [DOI: 10.7589/2013-01-021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Castro AMMGD, Castro Junior FGD, Mori CK, Cruz TFD, Baldin CM, Budino FEL, Araujo Junior JP, Richtzenhain LJ. Obtencao de animais negativos para Circovirus suino 2 oriundos de granjas positivas: estrategia de manejo. ARQUIVOS DO INSTITUTO BIOLÓGICO 2013. [DOI: 10.1590/s1808-16572013000400004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
O objetivo do trabalho é descrever uma estratégia para a obtenção de animais negativos para o PCV2 oriundos de uma granja positiva para este vírus. Dezesseis leitões foram obtidos de fêmeas que tiveram os títulos de IgG anti-PCV2 e o DNA viral testados durante a gestação. Esses leitões, aos sete e dez dias de idade, foram transferidos para a unidade de pesquisa. Durante o período de 7 e 10 aos 49 e 52 dias de idade, amostras de soro, suabes nasal e fecal foram coletadas, a cada sete dias. Após esse período, três animais permaneceram na unidade de pesquisa e foram acompanhados dos 49 aos 114 dias de idade, com coletas realizadas a cada 28 dias. Não houve diferença significativa (p = 0,317) de viremia entre marrãs (n = 6) e porcas (n = 10). Com relação aos níveis de IgG, observou-se diferença significativa (p = 0,0213) entre porcas e marrãs. Os leitões (n = 16), obtidos de duas fêmeas, foram transferidos para a unidade de pesquisa. Os animais entre 7 e 10 dias e aos 49 e 52 dias de idade apresentaram queda de IgG e ausência de IgM anti-PCV2; e as amostras de soro, suabe nasal e fecal foram negativos para o DNA de PCV2. Após os 49 dias, nos três animais mantidos isolados, a detecção de IgG, IgM e DNA para PCV2 permaneceu negativa. Concluindo, a estratégia de manejo utilizada permitiu obter suínos negativos para PCV2 oriundo de granjas positivas para o agente.
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Chan JFW, Li KSM, To KKW, Cheng VCC, Chen H, Yuen KY. Is the discovery of the novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) the beginning of another SARS-like pandemic? J Infect 2012; 65:477-89. [PMID: 23072791 PMCID: PMC7112628 DOI: 10.1016/j.jinf.2012.10.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 10/05/2012] [Indexed: 12/23/2022]
Abstract
Fouchier et al. reported the isolation and genome sequencing of a novel coronavirus tentatively named "human betacoronavirus 2c EMC/2012 (HCoV-EMC)" from a Saudi patient presenting with pneumonia and renal failure in June 2012. Genome sequencing showed that this virus belongs to the group C species of the genus betacoronavirus and phylogenetically related to the bat coronaviruses HKU4 and HKU5 previously found in lesser bamboo bat and Japanese Pipistrelle bat of Hong Kong respectively. Another patient from Qatar with similar clinical presentation and positive RT-PCR test was reported in September 2012. We compare and contrast the clinical presentation, laboratory diagnosis and management of infection due to this novel coronavirus and that of SARS coronavirus despite the paucity of published information on the former. Since 70% of all emerging infectious pathogens came from animals, the emergence of this novel virus may represent another instance of interspecies jumping of betacoronavirus from animals to human similar to the group A coronavirus OC43 possibly from a bovine source in the 1890s and the group B SARS coronavirus in 2003 from bat to civet and human. Despite the apparently low transmissibility of the virus at this stage, research preparedness against another SARS-like pandemic is an important precautionary strategy.
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Affiliation(s)
- Jasper F W Chan
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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de Castro AMMG, Cruz TF, Salgado VR, Kanashiro TM, Ferrari KL, Araujo JP, Brandão PE, Richtzenhain LJ. Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil. Acta Vet Scand 2012; 54:29. [PMID: 22554105 PMCID: PMC3434114 DOI: 10.1186/1751-0147-54-29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
Background Porcine circovirus type 2 (PCV2) has been associated with several disease complexes, including reproductive failure. The aim of this study was to identify the subtypes of PCV2 that are associated with reproductive failure in pigs from the State of São Paulo, Brazil and to investigate co-infections with other infectious organisms. Findings Samples of 168 aborted foetuses or mummified foetuses from five farrow-to-finish swine farms known to be infected with PCV2 and located in the State of São Paulo were tested for PCV2 by polymerase chain reaction (PCR). Positive samples were additionally tested for porcine parvovirus (PPV), Leptospira spp. and Brucella spp. by PCR. PCV2 was detected in 18 of the samples (10.7%). PPV, Brucella spp. and Leptospira spp were found in 2, 10 and 0 cases, respectively. Eleven PCV2 strains were sequenced and determined to be either genotype 2a (n = 1) or 2b (n = 10). Conclusions The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. No repeatable, characteristic amino acid motifs for regions of the PCV2 capsid protein seemed to be associated with abortion in sows.
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Affiliation(s)
- J. Daniel Stanley
- University of Tennessee College of Medicine, Chattanooga Department of Surgery, Chattanooga, Tennessee
| | - R. Phillip Burns
- University of Tennessee College of Medicine, Chattanooga Department of Surgery, Chattanooga, Tennessee
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Specific real-time reverse transcription-polymerase chain reaction for detection and quantitation of turkey coronavirus RNA in tissues and feces from turkeys infected with turkey coronavirus. J Virol Methods 2009; 163:452-8. [PMID: 19917315 PMCID: PMC7112835 DOI: 10.1016/j.jviromet.2009.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 10/28/2009] [Accepted: 11/05/2009] [Indexed: 11/21/2022]
Abstract
Turkey coronavirus (TCoV) infection causes acute atrophic enteritis in the turkey poults, leading to significant economic loss in the U.S. turkey industry. Rapid detection, differentiation, and quantitation of TCoV are critical to the diagnosis and control of the disease. A specific one-step real-time reverse transcription-polymerase chain reaction (RRT-PCR) assay for detection and quantitation of TCoV in the turkey tissues was developed using a dual-labeled fluorescent probe. The fluorogenic probe labeled with a reporter dye (FAM, 6-carboxytetramethylrhodamin) and a quencher dye (AbsoluteQuencher) was designed to bind to a 186 base-pair fragment flanked by the two PCR primers targeting the 3' end of spike gene of TCoV. The assay was performed on different avian viruses and bacteria to determine the specificity as well as serial dilutions of TCoV for the sensitivity. Three animal trials were conducted to further validate the assay. Ten-day-old turkey poults were inoculated orally with 100 EID(50) of TCoV. Intestinal tissues (duodenum, jejunum, ileum, cecum), feces from the cloacal swabs, or feces from the floor were collected at 12 h, 1, 2, 3, 5, 7, and/or 14 days post-inoculation (DPI). RNA was extracted from each sample and subjected to the RRT-PCR. The designed primers and probe were specific for TCoV. Other non-TCoV avian viruses and bacteria were not amplified by RRT-PCR. The assay was highly sensitive and could quantitate between 10(2) and 10(10) copies/microl of viral genome. The viral RNA in the intestine segments reached the highest level, 6x10(15) copies/microl, in the jejunum at 5 DPI. Eighty-four intestine segments assayed by the developed RRT-PCR and immunofluorescence antibody assay (IFA) revealed that there were 6 segments negative for TCoV by both assays, 45 positive for TCoV by IFA, and 77 positive for TCoV by RRT-PCR. Turkey coronavirus was detected in the feces from the cloacal swabs or floor 1-14 DPI; however, the viral RNA load varied among different turkey poults at different intervals from different trials. The highest amount of viral RNA, 2.8x10(10) copies/microl, in the feces was the one from the cloacal swab collected at 1 DPI. The average amount of TCoV RNA in the cloacal fecal samples was 10 times higher than that in the fecal droppings on the floor. Taken together, the results indicated that the developed RRT-PCR assay is rapid, sensitive, and specific for detection, differentiation, and quantitation of TCoV in the turkey tissues and should be helpful in monitoring the progression of TCoV induced acute enteritis in the turkey flocks.
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Evaluation of sensitivities and specificities of SARS-CoV detection by real-time quantitative reverse transcription-PCR assays. Virol Sin 2009. [PMCID: PMC7090980 DOI: 10.1007/s12250-009-3021-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The etiological agent of severe acute respiratory syndrome (SARS) was identified as a new coronavirus, termed SARS-CoV. Establishment of an efficient and sensitive diagnostic system of SARS-CoV genetic materials is crucial for SARS control. In this study, we quantified SARS-CoV mRNAs in both infected cell culture lysate and in supernatant by using Real-time quantitative revere transcription-PCR based on EvaGreen™ dye and Taqman-MGB probes. For extensive evaluation of sensitivities and specificities, 13 pairs of primers and 4 probes were designed based on different genes of SARS-CoV. Glyceraldehydes-3-phosphate dehydrogenase (GAPDH) was selected as the internal control gene. Results showed that S-gene-specific PCR was the most sensitive for detection, but because of its sequence variability in the different viral strains, primers and a probe based on the N gene were suitable substitutions. Meanwhile, we found the mRNA concentrations in cell culture lysates were much higher than in cell supernatant and facilited more sensitive detection of the SARS-CoV.
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Abstract
The notion that developing countries must wait for the developed world to make advances in science and technology that they later import at great cost is being challenged. We have previously argued that developing countries can harness human genetic variation to benefit their populations and economies. Based on our empirical studies of large-scale population genotyping projects in Mexico, India and Thailand, we describe how these resources are being adopted to improve public health and create knowledge-based economies. A significant additional benefit is building the capacity for scientific research and internalizing advances in technology, whatever their source.
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Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev 2007; 20:660-94. [PMID: 17934078 DOI: 10.1128/cmr.00023-07] [Citation(s) in RCA: 657] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Before the emergence of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in 2003, only 12 other animal or human coronaviruses were known. The discovery of this virus was soon followed by the discovery of the civet and bat SARS-CoV and the human coronaviruses NL63 and HKU1. Surveillance of coronaviruses in many animal species has increased the number on the list of coronaviruses to at least 36. The explosive nature of the first SARS epidemic, the high mortality, its transient reemergence a year later, and economic disruptions led to a rush on research of the epidemiological, clinical, pathological, immunological, virological, and other basic scientific aspects of the virus and the disease. This research resulted in over 4,000 publications, only some of the most representative works of which could be reviewed in this article. The marked increase in the understanding of the virus and the disease within such a short time has allowed the development of diagnostic tests, animal models, antivirals, vaccines, and epidemiological and infection control measures, which could prove to be useful in randomized control trials if SARS should return. The findings that horseshoe bats are the natural reservoir for SARS-CoV-like virus and that civets are the amplification host highlight the importance of wildlife and biosecurity in farms and wet markets, which can serve as the source and amplification centers for emerging infections.
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Escutenaire S, Mohamed N, Isaksson M, Thorén P, Klingeborn B, Belák S, Berg M, Blomberg J. SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses. Arch Virol 2006; 152:41-58. [PMID: 16941059 PMCID: PMC7087200 DOI: 10.1007/s00705-006-0840-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 07/12/2006] [Indexed: 12/02/2022]
Abstract
Coronaviruses are etiologic agents of respiratory and enteric diseases in humans and in animals. In this study, a one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay based on SYBR Green chemistry and degenerate primers was developed for the generic detection of coronaviruses. The primers, designed in the open reading frame 1b, enabled the detection of 32 animal coronaviruses including strains of canine coronavirus, feline coronavirus, transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). A specific amplification was also observed with the human coronaviruses (HCoV) HCoV-NL63, HCoV-OC43, HCoV-229E and severe acute respiratory syndrome coronavirus (SARS-CoV). The real-time RT-PCR detected down to 10 cRNA copies from TGEV, BCoV, SARS-CoV and IBV. In addition, the assay exhibited a high sensitivity and specificity on clinical samples from different animal species. The developed assay represents a potential tool for laboratory diagnostics and for detecting still uncharacterized coronaviruses.
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Affiliation(s)
- S Escutenaire
- Department of Virology, National Veterinary Institute, Uppsala, Sweden
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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: 317] [Impact Index Per Article: 16.7] [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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Inoue M, Barkham T, Keong LK, Gee LS, Wanjin H. Performance of single-step gel-based reverse transcription-PCR (RT-PCR) assays equivalent to that of real-time RT-PCR assays for detection of the severe acute respiratory syndrome-associated coronavirus. J Clin Microbiol 2005; 43:4262-5. [PMID: 16081995 PMCID: PMC1233944 DOI: 10.1128/jcm.43.8.4262-4265.2005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simple gel-based one-step reverse transcription-PCR (RT-PCR) assays, used to investigate patients during the 2003 severe acute respiratory syndrome (SARS) outbreak in Singapore, were found to be as sensitive as commercial and in-house real-time RT-PCR assays. The detection limit was approximately 1 genome equivalent (GE) per 5 microl PCR mixture. One PFU of SARS coronavirus was estimated to be 258 +/- 46 GE.
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Affiliation(s)
- Masafumi Inoue
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673.
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Hu W, Bai B, Hu Z, Chen Z, An X, Tang L, Yang J, Wang H, Wang H. Development and evaluation of a multitarget real-time Taqman reverse transcription-PCR assay for detection of the severe acute respiratory syndrome-associated coronavirus and surveillance for an apparently related coronavirus found in masked palm civets. J Clin Microbiol 2005; 43:2041-6. [PMID: 15872219 PMCID: PMC1153763 DOI: 10.1128/jcm.43.5.2041-2046.2005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) is the etiological agent of SARS. It is believed that SARS-CoV originates from wild animals. We have developed a multitarget real-time Taqman reverse transcription-PCR (RT-PCR) assay for the quantitative detection of SARS-CoV. The sequences of the Taqman probes with a minor groove binder and the corresponding primers were based on the sequences of the N gene, open reading frame (ORF) 3, and ORF 8. The overall linear range of this assay was from at least 10(1) to 10(6) copies per reaction, and the detection limit could reach less than 10 copies per reaction. The quantification results for SARS-CoV from cell culture correlated well with those of the RT-PCR by using any two of the three sets of primer and probe used in this assay. However, the results of quantification of SARS-CoV obtained by using a few available throat swab specimens from SARS patients and the N gene as the target were almost 10 times higher than those obtained by using ORF 3 and ORF 8. Using this assay, we also detected an apparently SARS-CoV-related coronavirus in the throat swab specimens from masked palm civets in the west part of Hubei Province, People's Republic of China.
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Affiliation(s)
- Wenqian Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430072 Hubei, People's Republic of China
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Performance evaluation of a Bayer Healthcare Diagnostics research-based SARS coronavirus assay. CORONAVIRUSES WITH SPECIAL EMPHASIS ON FIRST INSIGHTS CONCERNING SARS 2005. [PMCID: PMC7123157 DOI: 10.1007/3-7643-7339-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Measurements of the number of copies of DNA or mRNA with the quantitative polymerase chain reaction (qPCR) have transformed the drug development process. This transformation is driven by the information these measurements have contributed for a better understanding of the molecular definition of disease and of the mechanisms of efficacy and toxicity for new drugs. As this information is translated into accurate genomic biomarkers of efficacy and toxicity, drug development processes supported by these measurements are becoming more efficient. This transformation is exemplified in the conversion of P450 enzyme activity measurements to gene expression in drug metabolism studies, the measurement of cytokine and chemokine genomic expression levels as clinical markers, and the identification and evaluation of genomic biomarkers of nephrotoxicity. A good understanding of factors affecting qPCR measurements can simplify their implementation, as will high‐throughput platforms for these assays. Drug Dev. Res. 62:151–158, 2004. © 2004 Wiley‐Liss, Inc.
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