ABSTRACT
BACKGROUND AND AIM: Existing real-time reverse transcriptase PCR (RT-qPCR) has certain limitations for the point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since it requires sophisticated instruments, reagents and skilled laboratory personnel. In this study, we evaluated an assay termed the reverse transcriptase-polymerase spiral reaction (RT-PSR) for rapid and visual detection of SARS-CoV-2. METHODS: The RT-PSR assay was optimized using RdRp gene and evaluated for the detection of SARS-CoV-2. The time of 60min and a temperature of 63°C was optimized for targeting the RNA-dependent RNA polymerase gene of SARS-CoV-2. The sensitivity of the assay was evaluated by diluting the in-vitro transcribed RNA, which amplifies as low as ten copies. RESULTS: The specific primers designed for this assay showed 100% specificity and did not react when tested with other lung infection-causing viruses and bacteria. The optimized assay was validated with 190 clinical samples in two phases, using automated RTPCR based TrueNat test, and the results were comparable. CONCLUSIONS: The RT-PSR assay can be considered for rapid and sensitive detection of SARS-CoV-2, particularly in resource-limited settings. To our knowledge, there is as yet no RT-PSR-based kit developed for SARS-CoV-2.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19 Testing , RNA-Directed DNA Polymerase/genetics , Clinical Laboratory Techniques/methods , Sensitivity and Specificity , Reverse Transcriptase Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction , RNA, Viral/geneticsSubject(s)
COVID-19/complications , Kidney Failure, Chronic/complications , Pancreatitis/complications , Pancreatitis/therapy , Peritoneal Dialysis/methods , SARS-CoV-2 , Automation , Biomarkers , COVID-19/diagnosis , COVID-19/virology , Disease Management , Female , Humans , Middle Aged , Symptom Assessment , Tomography, X-Ray Computed , Treatment OutcomeABSTRACT
OBJECTIVES: Due to the surge in demand for N95 masks during the Covid-19 pandemic, and considering the situation in countries grappling with acute shortages of N95 masks, this study investigated the possibilities of decontamination and reuse of masks. METHODS: Three N95 masks of different makes (A, B and C) were subjected to six decontamination methods: ultraviolet (UV) irradiation, isopropyl alcohol (IPA) dip, plasma sterilization (Sterrad®), ethylene oxide (ETO, 3M®), dry heat sterilization, and moist heat sterilization (autoclaving). The integrity of the N95 masks was assessed by measuring their particle filtering efficiency at particle sizes ranging 0.3-0.5 microns. RESULTS: All the masks decontaminated with ETO and plasma sterilization retained over 95% particle filtering efficiency. Masks decontaminated using IPA dip and autoclaving showed a drop, and UV irradiation showed variations in particle size efficiency degradation after decontamination. CONCLUSIONS: Plasma sterilization is recommended for decontamination of N95 masks in low-resource settings. ETO is not recommended due to hazards associated with handling of ethylene oxide, although the filtering efficiency was retained. Since the UV irradiation method showed variations in results, evaluation of UV decontamination for N95 masks needs to be performed on a case-by-case basis.
Subject(s)
COVID-19/prevention & control , Decontamination/methods , N95 Respirators , SARS-CoV-2 , Equipment Reuse , Ethylene Oxide/pharmacology , Health Resources , Humans , India/epidemiology , Ultraviolet RaysABSTRACT
The envelope glycoprotein (E) is the smallest structural component of SARS-CoVs; plays an essential role in the viral replication starting from envelope formation to assembly. The in silico analysis of 2086 whole genome sequences from India performed in this study provides the first observation on the extensive deletion of amino acid residues in the C-terminal region of the envelope glycoprotein in 34 Indian SARS-CoV-2 genomes. These amino acid deletions map to the homopentameric interface and PDZ binding motif (PBM) present in the C-terminal region of E protein as well as immediately after the reverse primer binding region as per Charité protocol in 26 of these genomes, hence, their detection through RT-qPCR may not be hampered and therefore E gene-based RT-qPCR would still detect these isolates. Eight genomes from the State of Odisha had deletion even in the primer binding site. It is possible that the deletions in the C-terminal region of E protein of these genomes are a result of adapting to a newer geographical area and host. The information on the clinical status was available only for 9 out of 34 cases and these were asymptomatic. However, further studies are indispensable to understand the functional consequences of amino acid deletion in the C terminal region of SARS-CoV-2 envelope protein in the viral pathogenesis and host adaptation.
Subject(s)
Coronavirus Envelope Proteins/genetics , SARS-CoV-2/genetics , Adult , Amino Acid Sequence , Computer Simulation , Coronavirus Envelope Proteins/immunology , Epitopes, B-Lymphocyte , Female , Gene Deletion , Genome, Viral , Humans , India , Male , Middle Aged , Real-Time Polymerase Chain Reaction , SARS-CoV-2/isolation & purificationABSTRACT
The new pandemic of SARS-CoV-2 has shown stark differences in number of affected patients between countries in the tropics and those with temperate environments. Though there have been many theories on reasons for these differences, we hypothesise that this could be due to differences in the fate of respiratory droplets in the two environments. A simple understanding of the mechanics of droplet size, dispersion and displacement could help infection control and public health measures to minimize spread and mitigate the risk of people getting infected especially in hotspots like hospital environments or other closed spaces. This paper discusses the possibility of differences in number of infections and spread between different countries based on the spread of droplets.