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

HIGHLIGHTS

• 5 gene targets were assessed: E gene, N gene, S gene, RdRp and ORF1ab

• Positive sample's Ct values differ significantly across the 12 diagnostic kits.

• Gene-specific analysis: positive sample's Ct values do not differ significantly.

• Comprehensive assessment of the different kits to promote standardization.

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.