1. Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests
- Author
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Ziyaad Valley-Omar, Gert Marais, Arash Iranzadeh, Michelle Naidoo, Stephen Korsman, Tongai Maponga, Hannah Hussey, Mary-Ann Davies, Andrew Boulle, Deelan Doolabh, Mariska Laubscher, Justyna Wojno, J.D. Deetlefs, Jean Maritz, Lesley Scott, Nokukhanya Msomi, Cherise Naicker, Houriiyah Tegally, Tulio de Oliveira, Jinal Bhiman, Carolyn Williamson, Wolfgang Preiser, Diana Hardie, and Nei-yuan Hsiao
- Subjects
VOCs, Variants of Concern ,Delta variant ,E, Envelope ,WGS, Whole Genome Sequencing ,GISAID, Global Initiative on Sharing All Influenza Data ,Article ,RT-PCR, reverse transcriptase polymerase chain reaction ,South Africa ,N, Nucleocapsid ,Virology ,RΔE, difference between the Ct values for RdRp and E-gene targets ,Humans ,AUC, Area Under the Curve ,Surveillance ,SARS-CoV-2 ,Diagnostic Tests, Routine ,COVID-19 ,SARS-CoV-2, Severe Acute respiratory Syndrome Coronavirus 2 ,NHLS, National Health Laboratory Service ,IQR, Interquartile range ,Diagnostic test ,RNA-Dependent RNA Polymerase ,S, Spike ,NGS-SA, Network for Genomic Surveillance South Africa ,GTF, Gene Target Failure ,COVID-19 Nucleic Acid Testing ,RNA ,RdRp, RNA-dependent-RNA-polymerase - Abstract
Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant. We investigated whether the reduced amplification efficiency denoted by an increased RT-PCR cycle threshold value (RΔE) can be used as an indirect measure of SARS-CoV-2 Delta variant prevalence. We found a significant increase in the median RΔE for patient samples tested from June 2021, which coincided with the emergence of the SARS-CoV-2 Delta variant within our sample set. Whole genome sequencing on a subset of patient samples identified a highly conserved G15451A, non-synonymous mutation exclusively within the RdRp gene of Delta variants, which may cause reduced RT-PCR amplification efficiency. While whole genome sequencing plays an important in identifying novel SARS-CoV-2 variants, monitoring RΔE value can serve as a useful surrogate for rapid tracking of Delta variant prevalence.
- Published
- 2022