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

Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. Valley-Omar, Z., Marais, G., Iranzadeh, A., Naidoo, M., Korsman, S., Maponga, T., Hussey, H., Davies, M., Boulle, A., Doolabh, D., Laubscher, M., Wojno, J., Deetlefs, J., Maritz, J., Scott, L., Msomi, N., Naicker, C., Tegally, H., de Oliveira, T., Bhiman, J., Williamson, C., Preiser, W., Hardie, D., & Hsiao, N. Journal of Virological Methods, 302:114471, Elsevier, apr, 2022.

Paper doi abstract bibtex

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

@article{Valley-Omar2022,
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 (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, 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 R$\Delta$E value can serve as a useful surrogate for rapid tracking of Delta variant prevalence.},
author = {Valley-Omar, Ziyaad and Marais, Gert and Iranzadeh, Arash and Naidoo, Michelle and Korsman, Stephen and Maponga, Tongai and Hussey, Hannah and Davies, Mary-Ann and Boulle, Andrew and Doolabh, Deelan and Laubscher, Mariska and Wojno, Justyna and Deetlefs, J.D. and Maritz, Jean and Scott, Lesley and Msomi, Nokukhanya and Naicker, Cherise and Tegally, Houriiyah and de Oliveira, Tulio and Bhiman, Jinal and Williamson, Carolyn and Preiser, Wolfgang and Hardie, Diana and Hsiao, Nei-yuan},
doi = {10.1016/j.jviromet.2022.114471},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Valley-Omar et al. - 2022 - Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SA.pdf:pdf},
issn = {01660934},
journal = {Journal of Virological Methods},
keywords = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {apr},
pages = {114471},
pmid = {35051442},
publisher = {Elsevier},
title = {{Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0166093422000180},
volume = {302},
year = {2022}
}

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