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Article ; Online: SARS-CoV-2 detection by direct rRT-PCR without RNA extraction.

Merindol, Natacha / Pépin, Geneviève / Marchand, Caroline / Rheault, Marylène / Peterson, Christine / Poirier, André / Houle, Claudia / Germain, Hugo / Danylo, Alexis

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 128, Page(s) 104423

Abstract: ... the pandemic we are facing. In this study, we compared direct rRT-PCR method (without RNA extraction) using ... SeeGene AllplexTM 2019-nCoV rRT-PCR with the RealStar® SARS-CoV-2 rRT-PCR kit (Altona Diagnostics ... Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit ...

Abstract	Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study, we compared direct rRT-PCR method (without RNA extraction) using SeeGene AllplexTM 2019-nCoV rRT-PCR with the RealStar® SARS-CoV-2 rRT-PCR kit (Altona Diagnostics). Furthermore, we assessed the impact of swab storage media composition on PCR efficiency. We show that SeeGene and Altona's assays provide similar efficiency. Importantly, we provide evidence that RNA extraction can be successfully bypassed when samples are stored in UTM medium or in molecular water but not when samples are stored in saline solution and in Hanks medium.
MeSH term(s)	Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; COVID-19 ; Coronavirus Infections/diagnosis ; Coronavirus Infections/virology ; Humans ; Nasopharynx/virology ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/virology ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction/methods ; SARS-CoV-2 ; Specimen Handling
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-05-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104423
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Article ; Online: SARS-CoV-2 detection by direct rRT-PCR without RNA extraction

Merindol, Natacha / Pépin, Geneviève / Marchand, Caroline / Rheault, Marylène / Peterson, Christine / Poirier, André / Houle, Claudia / Germain, Hugo / Danylo, Alexis

Journal of Clinical Virology

2020 Volume 128, Page(s) 104423

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104423
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: SARS-CoV-2 detection by direct rRT-PCR without RNA extraction

Merindol, Natacha / Pépin, Geneviève / Marchand, Caroline / Rheault, Marylène / Peterson, Christine / Poirier, André / Houle, Claudia / Germain, Hugo / Danylo, Alexis

J Clin Virol

Abstract	Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study, we compared direct rRT-PCR method (without RNA extraction) using SeeGene AllplexTM 2019-nCoV rRT-PCR with the RealStar® SARS-CoV-2 rRT-PCR kit (Altona Diagnostics). Furthermore, we assessed the impact of swab storage media composition on PCR efficiency. We show that SeeGene and Altona's assays provide similar efficiency. Importantly, we provide evidence that RNA extraction can be successfully bypassed when samples are stored in UTM medium or in molecular water but not when samples are stored in saline solution and in Hanks medium.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #197471
Database	COVID19

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Article ; Online: SARS-CoV-2 detection by direct rRT-PCR without RNA extraction

Mérindol, Natacha / Pépin, Geneviève / Marchand, Caroline / Rheault, Marylène / Peterson, Christine / Poirier, André / Houle, Claudia / Germain, Hugo / Danylo, Alexis

2020

Abstract	Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study, we compared direct rRT-PCR method (without RNA extraction) using SeeGene AllplexTM 2019-nCoV rRT-PCR with the RealStar® SARS-CoV-2 rRT-PCR kit (Altona Diagnostics). Furthermore, we assessed the impact of swab storage media composition on PCR efficiency. We show that SeeGene and Altona's assays provide similar efficiency. Importantly, we provide evidence that RNA extraction can be successfully bypassed when samples are stored in UTM medium or in molecular water but not when samples are stored in saline solution and in Hanks medium. © 2020 The Author(s)
Keywords	covid19
Language	French
Publishing country	ca
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Diagnostic Salivary Tests for SARS-CoV-2.

Azzi, L / Maurino, V / Baj, A / Dani, M / d'Aiuto, A / Fasano, M / Lualdi, M / Sessa, F / Alberio, T

Journal of dental research

2020 Volume 100, Issue 2, Page(s) 115–123

Abstract: ... on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed ... the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT ... The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies ...

Abstract	The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed with respiratory specimens, especially nasopharyngeal swabs. However, this procedure requires specialized medical personnel, centralized laboratory facilities, and time to provide results (from several hours up to 1 d). In addition, there is a non-negligible risk of viral transmission for the operator who performs the procedure. For these reasons, several studies have suggested the use of other body fluids, including saliva, for the detection of SARS-CoV-2. The use of saliva as a diagnostic specimen has numerous advantages: it is easily self-collected by the patient with almost no discomfort, it does not require specialized health care personnel for its management, and it reduces the risks for the operator. In the past few months, several scientific papers, media, and companies have announced the development of new salivary tests to detect SARS-CoV-2 infection. Posterior oropharyngeal saliva should be distinguished from oral saliva, since the former is a part of respiratory secretions, while the latter is produced by the salivary glands, which are outside the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT-PCR without extraction), although, in a hospital setting, these procedures may be performed only in addition to nasopharyngeal swabs to minimize the incidence of false-negative results. Conversely, the promising role of saliva in the diagnosis of SARS-CoV-2 infection is highlighted by the emergence of point-of-care technologies and, most important, point-of-need devices. Indeed, these devices can be directly used in workplaces, airports, schools, cinemas, and shopping centers. An example is the recently described Rapid Salivary Test, an antigen test based on the lateral flow assay, which detects the presence of the virus by identifying the spike protein in the saliva within a few minutes.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing/methods ; Humans ; RNA, Viral ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/isolation & purification ; Saliva/virology
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	80207-4
ISSN	1544-0591 ; 0022-0345
ISSN (online)	1544-0591
ISSN	0022-0345
DOI	10.1177/0022034520969670
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Article: Diagnostic Salivary Tests for SARS-CoV-2

Azzi, L / Maurino, V / Baj, A / Dani, M / d039, / Aiuto, A / Fasano, M / Lualdi, M / Sessa, F / Alberio, T

J Dent Res

Abstract	The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed with respiratory specimens, especially nasopharyngeal swabs. However, this procedure requires specialized medical personnel, centralized laboratory facilities, and time to provide results (from several hours up to 1 d). In addition, there is a non-negligible risk of viral transmission for the operator who performs the procedure. For these reasons, several studies have suggested the use of other body fluids, including saliva, for the detection of SARS-CoV-2. The use of saliva as a diagnostic specimen has numerous advantages: it is easily self-collected by the patient with almost no discomfort, it does not require specialized health care personnel for its management, and it reduces the risks for the operator. In the past few months, several scientific papers, media, and companies have announced the development of new salivary tests to detect SARS-CoV-2 infection. Posterior oropharyngeal saliva should be distinguished from oral saliva, since the former is a part of respiratory secretions, while the latter is produced by the salivary glands, which are outside the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT-PCR without extraction), although, in a hospital setting, these procedures may be performed only in addition to nasopharyngeal swabs to minimize the incidence of false-negative results. Conversely, the promising role of saliva in the diagnosis of SARS-CoV-2 infection is highlighted by the emergence of point-of-care technologies and, most important, point-of-need devices. Indeed, these devices can be directly used in workplaces, airports, schools, cinemas, and shopping centers. An example is the recently described Rapid Salivary Test, an antigen test based on the lateral flow assay, which detects the presence of the virus by identifying the spike protein in the saliva within a few minutes.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #901605
Database	COVID19

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Article ; Online: Diagnostic Salivary Tests for SARS-CoV-2

Azzi, L. / Maurino, V. / Baj, A. / Dani, M. / d’Aiuto, A. / Fasano, M. / Lualdi, M. / Sessa, F. / Alberio, T.

Journal of Dental Research

2020 , Page(s) 2203452096967

Abstract	The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed with respiratory specimens, especially nasopharyngeal swabs. However, this procedure requires specialized medical personnel, centralized laboratory facilities, and time to provide results (from several hours up to 1 d). In addition, there is a non-negligible risk of viral transmission for the operator who performs the procedure. For these reasons, several studies have suggested the use of other body fluids, including saliva, for the detection of SARS-CoV-2. The use of saliva as a diagnostic specimen has numerous advantages: it is easily self-collected by the patient with almost no discomfort, it does not require specialized health care personnel for its management, and it reduces the risks for the operator. In the past few months, several scientific papers, media, and companies have announced the development of new salivary tests to detect SARS-CoV-2 infection. Posterior oropharyngeal saliva should be distinguished from oral saliva, since the former is a part of respiratory secretions, while the latter is produced by the salivary glands, which are outside the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT-PCR without extraction), although, in a hospital setting, these procedures may be performed only in addition to nasopharyngeal swabs to minimize the incidence of false-negative results. Conversely, the promising role of saliva in the diagnosis of SARS-CoV-2 infection is highlighted by the emergence of point-of-care technologies and, most important, point-of-need devices. Indeed, these devices can be directly used in workplaces, airports, schools, cinemas, and shopping centers. An example is the recently described Rapid Salivary Test, an antigen test based on the lateral flow assay, which detects the presence of the virus by identifying the spike protein in the saliva within a few minutes.
Keywords	General Dentistry ; covid19
Language	English
Publisher	SAGE Publications
Publishing country	us
Document type	Article ; Online
ZDB-ID	80207-4
ISSN	1544-0591 ; 0022-0345
ISSN (online)	1544-0591
ISSN	0022-0345
DOI	10.1177/0022034520969670
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Alternative RNA extraction-free techniques for the real-time RT-PCR detection of SARS-CoV-2 in nasopharyngeal swab and sputum samples.

Villota, Stephany D / Nipaz, Victoria E / Carrazco-Montalvo, Andrés / Hernandez, Sarah / Waggoner, Jesse J / Ponce, Patricio / Coloma, Josefina / Orlando, Alberto / Cevallos, Varsovia

Journal of virological methods

2021 Volume 298, Page(s) 114302

Abstract: Standard diagnoses of SARS-CoV-2 infections are done by RNA extraction and real-time RT-PCR (rRT ... of SARS-CoV-2 without RNA extraction were investigated. Nasopharyngeal and sputum samples were used ... PCR). However, the need for RNA extraction complicates testing due to increased processing time, high ...

Abstract	Standard diagnoses of SARS-CoV-2 infections are done by RNA extraction and real-time RT-PCR (rRT-PCR). However, the need for RNA extraction complicates testing due to increased processing time, high cost, and limited availability of commercial kits. Therefore, alternative methods for rRT-PCR detection of SARS-CoV-2 without RNA extraction were investigated. Nasopharyngeal and sputum samples were used to compare the sensitivity of three techniques: Trizol RNA extraction, thermal shock, and the direct use of samples with an RNase inhibitor. Direct, extraction-free use of primary samples plus the RNase inhibitor produced diagnostic values of 100 % sensitivity and specificity compared to standard protocols, and these findings were validated in a second, independent laboratory.
MeSH term(s)	COVID-19 ; COVID-19 Testing ; Humans ; Nasopharynx ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2 ; Sensitivity and Specificity ; Sputum
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-09-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114302
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Article ; Online: Point of care testing for detection of coronaviruses including SARS-CoV-2 from saliva without treating RNA in advance

Muraoka, Masaaki / Kawaguchi, Osamu / Mizukoshi, Mikio / Sejima, Shunsuke

medRxiv

Abstract: ... such as SARS-CoV-2, and thus needed to improve NAATs method. First, combining the mobile real-time RT-PCR (rRT ... At present, the routine confirmation of SARS-CoV-2 is based on detection of sequence unique in the virus RNA ... PCR) device PCR1100 with the appropriate rRT-PCR reagent, we found that it is possible to detect RNA ...

Abstract	Coronavirus disease 2019 (COVID-19) outbreak was reported to the WHO (World Health Organization) as an outbreak on end of 2019, afterwards pandemic on the worldwide in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has be reported it to cause COVID-19, and highly transmissible. Therefore, it is important that it is rapidly and continuously detected and monitored on site so that the infection is prevented. Namely, POCT (point of care testing) may be important to control cross infection of SARS-CoV-2. At present, the routine confirmation of SARS-CoV-2 is based on detection of sequence unique in the virus RNA by nucleic acid amplification tests (NAATs) such as rRT-PCR. Taking POCT into account, it is clear that it takes time and labour very much or much. Thus, it was our purpose this time to contribute to develop POCT for microbes such as SARS-CoV-2, and thus needed to improve NAATs method. First, combining the mobile real-time RT-PCR (rRT-PCR) device PCR1100 with the appropriate rRT-PCR reagent, we found that it is possible to detect RNA of SARS-CoV-2 for less 14 minutes with equivalent accuracy to conventional devices. Next, we found that the above method made it possible for us to detect coronaviruses by direct rRT-PCR without pre-treatments. Furthermore, it also made clear that coronaviruses in saliva could be detected by the similar direct rRT-PCR method. Hence, it was concluded that this method made it possible to detect virus in saliva without treating in advance (extraction, purification, concentration, etc.), and moreover, samples would be able to be collected with non-invasive. For this reason, we suggest that this method is useful for POCT of coronaviruses including SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2021-05-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.05.01.21256441
Database	COVID19

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Article ; Online: Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR

Parul Sinha / Sandeep Gupta / Megha Gupta / Dinesh Kumar Jain / Malvika Sharma / Kanika Sharma / Saroj Hooja / Nitya Vyas

Journal of Clinical and Diagnostic Research, Vol 15, Iss 9, Pp DC11-DC

2021 Volume 15

Abstract: ... the diagnostic value of four methods (that omit extraction step) for detection of SARS-CoV-2 against ... India, in October 2020. Ninety four SARS-CoV-2 RT-PCR positive samples and 20 negative samples were ... diagnostic accuracy of four methods for detection of SARS-CoV-2 by real-time ...

Abstract	Introduction: The emergence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been troublesome particularly for developing countries that lack infrastructure and capacities to produce the kits locally. Simplification of the method can increase diagnostic efficiency which can benefit patients and help in infection control, consequently saving time and lives. Aim: To evaluate the diagnostic value of four methods (that omit extraction step) for detection of SARS-CoV-2 against the traditional extraction method. Materials and Methods: This was a cross-sectional analysis for evaluating diagnostic accuracy of four methods for detection of SARS-CoV-2 by real-time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR), conducted in the Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India, in October 2020. Ninety four SARS-CoV-2 RT-PCR positive samples and 20 negative samples were taken for this study. Automated extraction system was used for Ribonucleic Acid (RNA) extraction and four different approaches were compared to the traditional extraction method for detection of SARS-CoV-2 by RT-PCR. Data was entered and analysed using Statistical Package for the Social Sciences (SPSS) statistical software version 24.0. Results: The automated RNA extraction method was compared to the method of direct addition of samples with (Heat processed Direct Viral transport medium Sample (HDVS)) and without heating (Direct Viral transport medium Sample (DVS)), directs addition of diluted (1:5) sample with (Heat processed diluted VTM sample (HdVS)) and without heating (Diluted VTM sample (dVS)) as well as after addition of Proteinse K (PK) to the diluted samples that came either negative/invalid. Out of four methods, the HdVS method gave the best results, considering extraction with Perkin Elmer as standard, this method showed sensitivity of 96.74%, specificity of 100%. Conclusion: In current pandemic, molecular testing is critically challenged by the limited supplies of reagents of nucleic ...
Keywords	coronavirus disease-19 ; molecular testing ; reverse transcriptase polymerase chain reaction ; viral transport media ; Medicine ; R
Subject code	630
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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