Abnormal Reverse Transcriptase-Polymerase Chain Reaction Amplification Curve as Possible Pre-Selection Tool for SARS-CoV-2 "English Variant" Sequencing

Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are rapidly spreading, and currently represent a consistent worldwide problem in containing coronavirus disease 2019 (COVID-19) pandemic.

Methods: We evaluated the Allplex™ SARS-CoV-2 Assay (Seegene) as a rapid pre-selection screening tool of viral variants by real-time polymerase chain reaction (PCR) amplification, before viral genome sequencing.

Results: The analytic platform targets envelope gene (E), ribonucleic acid (RNA)-dependent RNA polymerase (RdRp)/spike (S) gene and nucleocapsid (N) gene of SARS-CoV-2, and reveals the presence of an abnormal (non-sigmoidal) amplification curve in 130 of 1,000 positive samples obtained from nasopharyngeal swabs. Sequencing analysis of a percentage of non-sigmoidal samples confirmed the presence of the new variant B.1.1.7 of SARS-CoV-2.

Conclusions: Our results show the potential use of this reverse transcriptase-PCR (RT-PCR) pre-analysis to rapidly identify and track the new lineage B.1.1.7 of SARS-CoV-2, especially when sequencing analysis is not available, and consequently limiting its fast spreading among people.

Clin Infect Immun. 2021;6(2):47-50
doi: https://doi.org/10.14740/cii129