Comparison of the performance of RNA extraction kits used in the diagnosis of COVID-19 against TRIZOL-the gold standard for RNA extraction

Abstract

Background: During the COVID-19 pandemic, the Test-Trace-Isolate-Quarantine (TTIQ) strategy was used to break chains of transmission. Diagnosis is a key step in this strategy, and it is done using various RNA extraction techniques and Real-Time Reverse Transcription–Polymerase Chain Reaction (RT-PCR). Many commercial RNA extraction kits have been manufactured and released globally on the market however, due to growing demand, a shortage in kit supplies could be experienced in several labs. For these reasons, the use of different commercial or in-house protocols for RNA extraction may provide a basis for various labs to choose reliable extraction kits from the available pool and pave the way for seeking alternative procedures using reagents found in a basic molecular biology lab. Methods: This study compared the performance of different SARS-CoV-2 RNA extraction kits used in the diagnosis of SARS-CoV-2 in Uganda against the conventional TRIzol extraction method. SARS-CoV-2 positive nasopharyngeal swabs were retrieved from -80°C storage at the biobank-MakCHS. SARS-CoV-2 RNA was then extracted from the samples using four commercial kits and the TRIzol method. Results: The study demonstrated that there are significant variations in the performance of the different kits/methodologies; The TRIzol extraction method generated the highest concentration of RNA; however, its purity was significantly lower than that of the commercial kits. When comparing the CT values, there was no statistically significant difference between TRIzol and the commercial kits except one. Conclusion: This research demonstrated that although the TRIzol method recovered RNA with relatively lower purity, its performance in diagnosing SARS-CoV-2 using RT-PCR did not differ significantly from the tested commercial kits.