Abstract
The study is aimed at establishing the optimal parameters for RNA purification of pooled specimens, in SARS-CoV-2 assay. This research work evaluates the difference of extracted RNA purity of pooled samples with and without treatment with isopropyl alcohol and its effect on real-time RT-PCR. As per the protocol of the Indian Council of Medical Research (ICMR), 5 sample pools were analysed using qRT-PCR. A total of 100 pooled samples were selected for the study by mixing 50 μL of one COVID-19 positive nasopharyngeal/oropharyngeal (NP/OP) specimen and 50 μL each of 4 known negative specimens. Pool RNA was extracted using the column-based method, and 1 set of pooled extracted RNA was tested as such, while RNA of the second set was treated additionally with chilled isopropyl alcohol (modified protocol). Further, the purity of extracted RNA in both the groups was checked using Microvolume Spectrophotometers (Nanodrop) followed by RT-PCR targeting E-gene and RNaseP target. The results showed that the purity index of extracted RNA of untreated pooled specimens was inferior to isopropyl alcohol-treated templates, which was observed to be 85% sensitivity and 100% specificity. The average Cq (E gene) in the unpurified and purified pool RNA group was 34.66 and 31.48, respectively. The nanodrop data suggested that purified RNA concentration was significantly increased with an average value of 24.73 ± 1.49 ng/uL, which might be the reason for high sensitivity and specificity. Thus, this group testing of SARS-CoV-2 cases using pools of 5 individual samples would be the best alternative for saving molecular reagents, personnel time, and can increase the overall testing capacity. However, purity of RNA is one of the important determinants to procure unfailing results, thus, this additional purification step must be included in the protocol after RNA has been extracted using commercially available kit before performing qRT-PCR.
Highlights
It is a very well-known fact that the global pandemic named COVID-19 caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hit the world in late December of 2019
Routine COVID-19 samples received in Viral Research and Diagnostic Laboratory (VRDL) from various health care centres of Varanasi, UP, India, were selected from July to August 2020
The results showed that the A260/A280 ratio in unpurified and purified RNA samples was 1:58 ± 0:06 and 2:02 ± 0:02, respectively
Summary
It is a very well-known fact that the global pandemic named COVID-19 caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hit the world in late December of 2019. It has enveloped major parts of the world resulting in a global emergency in most countries with more than 163,869,893 confirmed cases and 3,398,302 deaths as per the latest May 2021 COVID19 situation report of WHO [1]. Many diagnostic methods for COVID19 are available such as imaging (chest CT), Ag/Ab (ELISA based or RAPID kits), and RNA detection (next-generation sequencing, qRT-PCR (real-time reverse transcriptionpolymerase chain reaction), and LAMP assay) [2].
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