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

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.

Keywords: COVID-19; Delta variant; Diagnostic test; SARS-CoV-2; South Africa; Surveillance.

Fig. 1

Mean difference between RdRp and E-gene Ct values for samples tested by the Seegene Allplex 2019-nCoV assay (ΔCt). The mean ΔCt is shown for samples testing positive for both E and RdRp targets for each week of 2021 up to 31 July. Only samples tested in the Western Cape region of South Africa are included in the analysis. Error bars represent 1 standard deviation.

Fig. 2

Weekly frequency and distribution of SARS-CoV-2 variants circulating in the Western Cape region of South Africa between 1 January and 31 August 2021.