Effect of Disinfectants on SARS-CoV-2 RNA Detection in Swabs from Various Surfaces

2021 ◽  
Vol 37 (4) ◽  
pp. 78-84
Author(s):  
E.A. Lazareva ◽  
S.P. Yatsentyuk
Keyword(s):  
Hydrogen Peroxide ◽  
Uv Irradiation ◽  
Sodium Salt ◽  
Viral Rna ◽  
Rt Pcr ◽  
Rna Detection ◽  
The World ◽  
Porous Surfaces ◽  
Rna Fragments ◽  
Dichloroisocyanuric Acid

The COVID-19 pandemic has spread rapidly around the world, and some countries have introduced controls on imported products, including testing for viral nucleic acids. In this work, the influence of disinfectants for treatment of various SARS-CoV-2-contaminated surfaces on the detection of viral RNA fragments in swabs from these surfaces was analyzed using quantitative RT-PCR. The effect of disinfectants based on quaternary ammonium salt, hydrogen peroxide, 1-propanol, sodium salt of dichloroisocyanuric acid and ultraviolet radiation was investigated. Our results show that without the exposure to disinfectants, viral RNA can be detected on the surface of all examined materials for at least three days. UV irradiation or irrigation with a disinfectant containing 0.2% active chlorine had the greatest effect on the decontamination of non-porous surfaces as measured by RT-PCR of swabs from these surfaces. Irrigation of porous surfaces (cardboard) with disinfectants had practically no effect on the detection of SARS-CoV-2 RNA by RT-PCR. Key words: SARS-CoV-2, viral RNA, RT-PCR, disinfectants, UV irradiation, surface swabs Funding - This work was supported by the Federal Service of Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor).

scholarly journals Management of oncology patients receiving anti-cancer treatment in the COVID-19 pandemic

2020 ◽  
Author(s):  
Esat Namal ◽  
Nur Dinc ◽  
Sezer Saglam ◽  
Ali Vefa Ozturk ◽  
Safiye Koculu ◽  
...  
Keyword(s):  
Cancer Treatment ◽  
World Health ◽  
Rt Pcr ◽  
Oncology Patients ◽  
Rna Detection ◽  
Recommended Treatment ◽  
Anti Cancer ◽  
The World ◽  
Oropharyngeal Swab ◽  
Health Organization

Abstract Background/Aim: Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has deeply affected life all over the World. The World Health Organization named this disease as COVID-19. The most important factor in the transmission of the disease is asymptomatic carriers. We’ve tested all oncology patients, that receive anti-cancer therapy, for COVİD-19 to prevent asymptomatic oncology patients from spreading infection and to make the decision to postpone chemotherapy in infected patients. Then, we analyzed the clinical and radiological findings of infected patients.Materials and Methods: Oncology patients who have indications of receiving anti-cancer treatment in the hospital were tested for COVID-19, two day prior to their treatment even if they were asymptomatic by collecting nasopharyngeal and oropharyngeal swab specimens for RT-PCR for viral RNA detection. Positive patients, underwent inspiratory phase of chest computed tomography (CT) examination. Infected patients were given the recommended treatment for COVID-19. Anti-cancer treatment of all patients that had positive PCR results was delayed for 14 days.Results: PCR test was positive in 28 of 312 patients that we tested, and the positivity rate was 8.9%. Three patients (10.7%) had symptoms; 2 of whom had dyspnea and cough, and 1 had headache, and 25 patients (89.3%) had no symptoms.Conclusion: In oncology patients, who are receiving anti-cancer treatment, we have to recognize the asymptomatic COVID-19 infection. We recommend testing for COVID-19 in oncology patients receiving chemotherapy, periodically or before each anti-cancer treatment, in order to continue their treatment without any problems and to prevent the risk of transmission.

scholarly journals Viral RNA load quantification as helpful tool to arbitrate SARS–CoV-2 detection results in respiratory samples

2020 ◽  
Author(s):  
Flora Marzia Liotti ◽  
Giulia Menchinelli ◽  
Simona Marchetti ◽  
Grazia Angela Morandotti ◽  
Maurizio Sanguinetti ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
False Negative ◽  
Negative Association ◽  
Viral Rna ◽  
N Gene ◽  
Rt Pcr ◽  
Rna Detection ◽  
Direct Assay ◽  
Future Clinical Practice ◽  
Oropharyngeal Swab

Abstract Purpose: The increasing COVID-19 widespread has created the necessity to assess the diagnostic accuracy of newly introduced (RT-PCR based) assays for SARS–CoV-2 RNA detection in respiratory tract samples.Methods: We compared the results of the Allplex™ 2019-nCoV assay with those of the Simplexa™ COVID-19 Direct assay, both performed on 125 nasal/oropharyngeal swab samples of patients with COVID-19 suspicion.Results: Fifty-four samples tested positive (CT below 40) and 71 negative (CT above 40) with the Allplex™ 2019-nCoV assay, whereas 47 of 54 samples were also positive with the Simplexa™ COVID-19 Direct assay. Eight results were discordant, resulting in 93.6% agreement between the assays. We used the Quanty COVID-19 assay—developed to detect and quantify SARS–CoV-2 in respiratory tract samples—to arbitrate these results. One Allplex™ 2019-nCoV negative (but Simplexa™ COVID-19 positive) and seven Simplexa™ COVID-19 negative samples were truly false negative. Interestingly, a Spearman’s negative association was found between the viral RNA loads quantified by the Quanty COVID-19 assay and the CT values of RT PCRs performed with either the Allplex™ 2019–nCoV assay or the Simplexa™ COVID-19 Direct assay. However, the strength of this association was higher for the Allplex™ 2019–nCoV assay (N gene, ρ = −0.92; RdRP gene, ρ = −0.91) than for the Simplexa™ COVID-19 Direct assay (ORF1ab gene, ρ = −0.65; S gene, ρ = −0.80).Conclusion: The Allplex™ 2019–nCoV and Simplexa™ COVID-19 Direct assays yielded comparable results. However, the role these assays might play in future clinical practice warrants larger comparison studies.

scholarly journals SARS-CoV-2 RNA detection in nasal mid-turbinate swabs

2020 ◽  
Author(s):  
Laura Dioni ◽  
Benedetta Albetti ◽  
Federica Rota ◽  
Valentina Bollati
Keyword(s):  
Rna Extraction ◽  
Positive Control ◽  
Viral Rna ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Rna Detection ◽  
Nasal Swabs ◽  
Internal Positive Control ◽  
Polymerase Chain ◽  
Genomic Regions

Abstract In this protocol, we describe a method to investigate the presence of SARS-CoV-2 RNA in nasal swabs, using a commercially available high-throughput Real-Time Polymerase Chain Reaction (RT-PCR) assay (TaqPath™ Covid-19 kit, ThermoFisher Scientific) in a 384-Well Plate. After Viral RNA extraction with QIAamp Viral RNA Mini kit, reverse transcription and cDNA amplification, all samples are assessed for the presence of three specific SARS-CoV-2 viral genomic regions and an internal positive control (IPC), in one Multiplex RT-PCR reaction.

scholarly journals Rapid processing of SARS-CoV-2 containing specimens for direct RT-PCR

2020 ◽  
Author(s):  
Piotr Chomczynski
Keyword(s):  
Room Temperature ◽  
Diagnostic Testing ◽  
Viral Rna ◽  
Rt Pcr ◽  
Purification Step ◽  
Biological Specimen ◽  
Rna Detection ◽  
Rna Purification ◽  
Rapid Processing ◽  
Effect Of Inhibitors

Widespread diagnostic testing is needed to reduce transmission of COVID-19 and manage the pandemic. Effective mass screening requires robust and sensitive tests that reliably detect the SARS-CoV-2 virus, including asymptomatic and pre-symptomatic infections with a low viral count. Currently, the most accurate tests are based on detection of viral RNA by RT-PCR. We developed a method to process COVID-19 specimens that simplifies and increases the sensitivity of viral RNA detection by direct RT-qPCR, performed without RNA purification. In the method, termed Alkaline-Glycol Processing (AG processing), a SARS-CoV-2-containing biological specimen, such as saliva or a swab-collected suspension, is processed at pH 12.2 to 12.8 for 5 min at room temperature. An aliquot of the AG-processed specimen is used for detection of SARS-CoV-2 RNA by direct RT-qPCR. AG processing effectively lyses viruses and reduces the effect of inhibitors of RT-PCR that are present in biological specimens. The sensitivity of detecting viral RNA using AG processing is on par with methods that include a viral RNA purification step. One copy of SARS-CoV-2 virus per reaction, equivalent to 300 copies per ml of saliva, is detectable in the AG-processed saliva. The LOD calculated following U.S. FDA guidelines is 600 viral copies per ml of initial saliva specimen. AG processing works with saliva specimens or swab specimens collected into Universal Transport Medium (UTM), is compatible with heat treatment, and was confirmed to work with a range of CDC-approved RT-qPCR products and kits. Detection of SARS-CoV-2 RNA using AG processing with direct RT-qPCR provides a reliable and scalable diagnostic test for COVID-19 that can be integrated into a range of workflows, including automated settings.

scholarly journals Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

2020 ◽  
Author(s):  
Ozlem Akgun Dogan ◽  
Betsi Kose ◽  
Nihat Bugra Agaoglu ◽  
Jale Yildiz ◽  
Gizem Alkurt ◽  
...  
Keyword(s):  
Gold Standard ◽  
Viral Rna ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Standard Samples ◽  
Rna Detection ◽  
Detection Rates ◽  
Gold Standard Method ◽  
Non Invasive ◽  
Isolation Period

The gold standard method in the diagnosis of SARS-CoV-2 infection is the detection of viral RNA in nasopharyngeal sample by RT-PCR. Recently, saliva samples has been suggested as an alternative due to being fast, reliable and non-invasive, rather than nasopharyngeal samples. We compared RT-PCR results in nasopharyngeal, oro-nasopharyngeal and saliva samples of COVID-19 patients. 98 of 200 patients were positive in RT-PCR analysis performed before the hospitalization. In day 0, at least one sample was positive in 67% of 98 patients. Positivity rate was 83% for both oro-nasopharyngeal and nasopharyngeal samples, while it was 63% for saliva samples (p<0.001). On day 5, RT-PCR was performed in 59 patients, 34% had at least one positive result. The positivity rate was 55% for saliva and nasopharyngeal samples, while it was 60% for oro-nasopharyngeal samples. Our study shows that the sampling saliva does not increase the sensitivity of RT-PCR tests at early stages of infection. However, on 5th day, viral RNA detection rates in saliva were similar to nasopharyngeal and oro-nasopharyngeal samples. In conclusion, we suggest that, in patients receiving treatment, virus presence in saliva, in addition to the standard samples, is important to determine the isolation period and to control the transmission.

scholarly journals A Viral Fragmentation Signature for SARS-CoV-2 in Clinical Samples Correlating with Contagiousness

2021 ◽  
Author(s):  
Yukti Choudhury ◽  
Chae Yin Cher ◽  
Zi Yi Wan ◽  
Chao Xie ◽  
Jing Shan Lim ◽  
...  
Keyword(s):  
Viral Load ◽  
Disease Onset ◽  
Viral Rna ◽  
Clinical Samples ◽  
Quantitative Detection ◽  
Rt Pcr ◽  
Subgenomic Rna ◽  
Rna Fragments ◽  
Novel Method ◽  
Next Generation Sequencing Ngs

AbstractThe viral load of SARS-CoV-2 in clinical samples as measured by the primary diagnostic tool of RT-PCR is an imperfect readout for infection potential as most targeted assays designed for sensitivity, indiscriminately detect short and long RNA fragments, although infectivity is embodied only in the whole virus and its intact genome. Here, we used next-generation sequencing (NGS) to characterize 155 clinical samples and show sensitive and quantitative detection of viral RNA which confirmed subgenomic RNA in 57.6% of samples and provided a novel method to determine relative integrity of viral RNA in samples. The relative abundance of long fragments quantified as a viral fragmentation score was positively associated with viral load and inversely related to time from disease onset. An empirically determined score cut-off for presence of substantially fragmented RNA was able to identify 100% of samples collected after 8 days of illness with poor infection potential in line with current clinical understanding of infectiousness of SARS-CoV-2. The quantification of longer fragments in addition to existing short targets in an NGS or RT-PCR-based assay could provide a valuable readout of infection potential simultaneous to the detection of any fragments of SARS-CoV-2 RNA in test samples.

scholarly journals Rapid processing of SARS-CoV-2 containing specimens for direct RT-PCR

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246867
Author(s):  
Piotr Chomczynski ◽  
Peter W. Chomczynski ◽  
Amy Kennedy ◽  
Michal Rymaszewski ◽  
William W. Wilfinger ◽  
...  
Keyword(s):  
Room Temperature ◽  
Diagnostic Testing ◽  
Viral Rna ◽  
Rt Pcr ◽  
Purification Step ◽  
Biological Specimen ◽  
Rna Detection ◽  
Rna Purification ◽  
Rapid Processing ◽  
Effect Of Inhibitors

Widespread diagnostic testing is needed to reduce transmission of COVID-19 and manage the pandemic. Effective mass screening requires robust and sensitive tests that reliably detect the SARS-CoV-2 virus, including asymptomatic and pre-symptomatic infections with a low viral count. Currently, the most accurate tests are based on detection of viral RNA by RT-PCR. We developed a method to process COVID-19 specimens that simplifies and increases the sensitivity of viral RNA detection by direct RT-qPCR, performed without RNA purification. In the method, termed Alkaline-Glycol Processing (AG Processing), a SARS-CoV-2-containing biological specimen, such as saliva or a swab-collected suspension, is processed at pH 12.2 to 12.8 for 5 min at room temperature. An aliquot of the AG-processed specimen is used for detection of SARS-CoV-2 RNA by direct RT-qPCR. AG processing effectively lyses viruses and reduces the effect of inhibitors of RT-PCR that are present in biological specimens. The sensitivity of detecting viral RNA using AG processing is on par with methods that include a viral RNA purification step. One copy of SARS-CoV-2 virus per reaction, equivalent to 300 copies per ml of saliva, is detectable in the AG-processed saliva. The LOD is 300 viral copies per ml of initial saliva specimen. AG processing works with saliva specimens or swab specimens collected into Universal Transport Medium, is compatible with heat treatment of saliva, and was confirmed to work with a range of CDC-approved RT-qPCR products and kits. Detection of SARS-CoV-2 RNA using AG processing with direct RT-qPCR provides a reliable and scalable diagnostic test for COVID-19 that can be integrated into a range of workflows, including automated settings.

scholarly journals TaffiX® nasal powder spray forms an effective barrier against infectious new variants of SARS-CoV-2 (Alpha, Beta and Delta)

2021 ◽  
Author(s):  
Michal Mandelboim ◽  
Ella Mendelson ◽  
Yaron Drori ◽  
Nofar Atari ◽  
Tair Lapidot ◽  
...  
Keyword(s):  
Infectious Virus ◽  
Preventive Measures ◽  
Low Ph ◽  
Viral Rna ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Protective Measures ◽  
Effective Barrier ◽  
The World ◽  
Alpha Beta

Abstract While vaccination efforts against SARS-CoV-2 around the world are ongoing, new highly infectious virus variants continue to evolve. The protection provided by the available vaccines against some of the new variants is weaker. Additional preventive measures will therefore be needed to protect the population until effective vaccinations are widely available. TaffiX® is an anti-viral nasal powder spray comprised of low-pH hypromellose, which forms a protective mechanical barrier that prevents viruses from engaging with nasal cells. The current study aimed to test the protective effect of Taffix against Alpha (B.1.1.7; hCoV-19/Israel/CVL-46879-ngs/2020), Beta, (B.1.351; hCoV-19/Israel/CVL-2557-ngs/2020) and Delta (B.1.617.2; hCoV-19/Israel/VVL-12806/2021), three highly infectious and pathogenic SARS-CoV-2 strains. A nylon filter was treated with Taffix® gel, after which SARS-CoV-2 Alpha, Beta or Delta was seeded. After a 10-min incubation, the downstream side of each filter was washed, and the rinse was collected and placed over Vero-E6 cells. After 5 days of incubation, viral RNA was extracted and subjected to SARS-CoV-2 RT-PCR analysis. Taffix® fully blocked passage of all three tested SARS-CoV-2 variants, as demonstrated by a 100% reduction of recoverable viral RNA from Vero-E6 cells treated with filter rinse. These results support its use as an effective barrier against new variants of SARS-CoV-2 in conjunction with other protective measures.

Sign in / Sign up

Export Citation Format

Share Document