Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.
J Virol Methods, 2022/04;302:114471.
Valley-Omar Z[1], Marais G[2], Iranzadeh A[3], Naidoo M[2], Korsman S[2], Maponga T[4], Hussey H[5], Davies MA[3], Boulle A[3], Doolabh D[3], Laubscher M[6], Wojno J[6], Deetlefs JD[7], Maritz J[8], Scott L[9], Msomi N[10], Naicker C[10], Tegally H[11], de Oliveira T[11], Bhiman J[12], Williamson C[2], Preiser W[13], Hardie D[2], Hsiao NY[2]
Affiliations
PMID: 35051442DOI: 10.1016/j.jviromet.2022.114471
Impact factor: 2.623
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
MeSH terms
COVID-19; COVID-19 Nucleic Acid Testing; Diagnostic Tests, Routine; Humans; RNA; RNA-Dependent RNA Polymerase; SARS-CoV-2
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