Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests

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 (R Delta E) can be used as an indirect measure of SARS-CoV-2 Delta variant prevalence. We found a significant increase in the median R Delta E 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, nonsynonymous 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 R Delta E value can serve as a useful surrogate for rapid tracking of Delta variant prevalence.

Automated summary

Routine surveillance in the Western Cape region of South Africa found reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. Increased RT-PCR cycle threshold values (R Delta E) could serve as an indirect measure of SARS-CoV-2 Delta variant prevalence. Whole genome sequencing identified a mutation exclusively within the RdRp gene of Delta variants, which may cause reduced RT-PCR amplification efficiency. Monitoring R Delta E value can be a useful surrogate for rapid tracking of Delta variant prevalence.