Detection of SARS-CoV-2 in Clinical Samples: Target-specific Analysis of Qualitative Reverse Transcription-Polymerase Chain Reaction(RT-PCR) Diagnostic Kits

Ambica Rangaiah; Sathyanarayan Muthur Shankar; Shantala Gowdara Basawarajappa; Pritik A Shah; Aditya Chandrashekar; Asha Munegowda; Shashiraja Padukone

doi:10.1016/j.ijregi.2021.11.004

Detection of SARS-CoV-2 in Clinical Samples: Target-specific Analysis of Qualitative Reverse Transcription-Polymerase Chain Reaction(RT-PCR) Diagnostic Kits

IJID Reg. 2021 Dec:1:163-169. doi: 10.1016/j.ijregi.2021.11.004. Epub 2021 Nov 18.

Authors

Ambica Rangaiah^{1

2}, Sathyanarayan Muthur Shankar^{1

2}, Shantala Gowdara Basawarajappa^{1

2}, Pritik A Shah^{1

2}, Aditya Chandrashekar^{1

2}, Asha Munegowda², Shashiraja Padukone²

Affiliations

¹ Department of Microbiology, Bangalore Medical College and Research Institute, Bangalore, India.
² State Level Virus Research & Diagnostic Laboratory, Bangalore Medical College and Research Institute, Karnataka, India.

Abstract

Introduction: The Coronavirus disease 2019 pandemic caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the rise of many available modalities for diagnosis. One such modality is the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) kits which require evaluation amongst the many available commercial kits in the market.

Methods: We conducted a performance evaluation of twelve RT-PCR SARS-CoV-2 commercial kits. A total of 75 nasopharyngeal and oropharyngeal clinical samples were selected with their cycling threshold (Ct) values. Inclusion of 5 gene targets: E gene, N gene, S gene, RdRp and ORF1ab were assessed. Data was analyzed using R software version 4.1.1 and Microsoft Excel.

Results: We observe that, the positive sample's Ct values differs significantly across the 12 diagnostic kits. However, for gene-specific analysis, we observe that, positive sample's Ct values does not differ significantly across gene targets. There is significant difference in Ct values in Commercial kits targeting all genes except S-gene. All the commercial kits Altona (E and S genes), Thermo (ORF1ab and N genes), Multiplex (E, ORF1ab, RdRdp genes), Meril (N and ORF1ab genes), S D Biosensor (E and ORF1ab genes), Lab Gun (RdRp and N genes) and Lab systems (ORF1ab and E genes) scored a sensitivity of 100%. All other kits scored sensitivity above 95% and lowest sensitivity with the Genes2me (E gene) and Genes2me (RdRp) at 95.08% each. All kits were 100% specific.

Conclusion: This study provides an accurate comprehensive assessment of the different kits in the detection of SARS-CoV-2 which may promote standardization of testing across laboratories.

Keywords: Diagnostic Kits; ICMR, Indian Council of Medical Research; RT-PCR; RT-PCR, Reverse Transcriptase Polymerase Chain Reactions; SARS-CoV-2; SARS-CoV-2, Severe Acute Respiratory Syndrome CoronaVirus-2; VRDL, State-Level Virus Research and Diagnostics Laboratory; WHO, World Health Organisation; analysis.