Evaluation of boiling lysis method of genomic viral RNA isolation from SARS-CoV2 nasopharyngeal swabs for reverse transcriptase Polymerase Chain Reaction.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the COVID-19 pandemic. Despite the introduction of new diagnostic methods, the detection of viral genes in nasopharyngeal swabs using reverse-transcription real time-PCR (rRT-PCR) assays remains the gold standard and efficient Reverse-transcription real time-PCR (rRT-PCR) is a prerequisite for downstream performance of rRT-PCR assays and currently, several automatic methods that include RNA extraction are available. Herein, we compared the efficiency of RNA extraction of Zymo Quick RNA Viral kit and an in-house extraction protocol of boiling lysis method of SARS-CoV-2 in nasopharyngeal swabs from 80 samples. The mean Ct value for Zymo Quick RNA Viral kit and boiling lysis method was 23.24(SD = 5.216) and 29.43(SD=4.691) respectively. The results obtained were greatly significant using Spearman Rho correlation of nonparametric test, r = 0.689 p > 0.01 and BAc confidence interval [0.503, 0.828] and 100% specificity was observed in the tested negative samples. It was inferred that tested boiling lysis method can be used for the detection of the SARS-CoV-2 genome by rRT-PCR approaches in limited resource areas, although with low RNA yields. Overall, this boiling lysis method offers an alternative protocol to manually extract RNA that can be used for SARS-CoV-2 detection.