Comparative analysis of different RNA extraction kits used in detection of COVID-19 virus

Abhishek Jhajharia; Riya Bhargava; Bharti Malhotra; Amit Tak; Parul Gupta

doi:10.18203/2320-6012.ijrms20243709

Authors

Abhishek Jhajharia Sawai Man Singh Medical College, Jaipur, Rajasthan, India
Riya Bhargava Department of Microbiology, Fortis Escorts Hospital, Jaipur, Rajasthan, India
Bharti Malhotra Department of Microbiology, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
Amit Tak Department of Preventive and Social Medicine, RVRS Medical College, Bhilwara, Rajasthan, India
Parul Gupta Department of Microbiology, Bharatpur Medical College, Bharatpur, Rajasthan, India

DOI:

https://doi.org/10.18203/2320-6012.ijrms20243709

Keywords:

COVID-19, RT-PCR, Sensitivity, Specificity

Abstract

Background: COVID-19, caused by SARS-CoV-2, was first reported in December 2019 and declared a Public Health Emergency of International Concern by the WHO. While various diagnostic methods exist, rRT-PCR remains the gold standard for detecting viral genes (N gene for SARS-CoV-2 and the E gene for all sarbecoviruses). Thus, ample RNA should be extracted for the efficient performance of the RT-PCR.

Methods: We compared the specificity, sensitivity, and efficiency of three automated nucleic acid extraction kits: Perkin Elmer®, HiPurA, and Zybio. A total of 96 known NP/OP samples from a biorepository were processed using these kits according to their respective protocols. Magnetic Bead method was employed for the same, followed by rRT-PCR using Quantiplus Multiplex COVID-19 detection kit. The JASP version 0.16.2 and MATLAB 2019a were used for statistical analysis.

Results: Both Perkin Elmer® and Zybio kits demonstrated 100% sensitivity, while the HiPurA kit showed 97.9% sensitivity compared to the original results. All three kits exhibited 100% specificity.

Conclusions: Based on the comparison of sensitivity, specificity, efficiency, cost, turnaround time etc. Perkin Elmer® followed by Zybio are recommended as the preferred extraction kits. Both Perkin Elmer® and Zybio performed well with 100% sensitivity. This study provides alternatives in high demands during surge and in places of limited resources.

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