key: cord-0281040-b1q6zt0o
authors: Valley-Omar, Z.; Marais, K.; Iranzadeh, A.; Naidoo, M.; Korsman, S.; Maponga, T.; Hussey, H.; Davies, M.-A.; Boulle, A.; Doolabh, D.; Laubscher, M.; Deetlefs, J.; Maritz, J.; Scott, L.; Msomi, N.; Tegally, H.; de Oliveira, T.; Bhiman, J.; Williamson, C.; Preiser, W.; Hardie, D. R.; Hsiao, N.-y.
title: Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests
date: 2021-10-01
journal: nan
DOI: 10.1101/2021.10.01.21264408
sha: 081e8f8a9b3a1faa02e1af5b2c9673a817cd24f2
doc_id: 281040
cord_uid: b1q6zt0o

Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. ; https://doi.org/10.1101/2021.10.01.21264408 doi: medRxiv preprint

The Study 42 Genomic surveillance of the severe acute respiratory syndrome coronavirus 2 43 (SARS-CoV-2) by whole genome sequencing (WGS) has played a critical role in 44 identifying and monitoring the dissemination of variants of concern (VOCs) [1, 2] . 45 However, WGS is costly and time-consuming, and not all countries have the 46 resources to do this at scale to get detailed VOC epidemiological information. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Table 1) . is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. increased to 4 and 4.5 cycles, the specificity was improved to 96.5% and 98% 132 respectively but the sensitivity was reduced to 86.7% and 80% respectively. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. ; https://doi.org/10.1101/2021.10.01.21264408 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted October 1, 2021. ; https://doi.org/10.1101/2021.10.01.21264408 doi: medRxiv preprint

New SARS-CoV-2 Variants -Clinical, Public Health, and Vaccine 164

Tracking SARS-CoV-2 variants

WHO inhouse assays

SARS-CoV-2 Isolates in the Greater Toronto Area

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in 171

Network for Genomic Surveillance in South Africa writing g. A 173 genomics network established to respond rapidly to public health threats in South Africa

Detection of a SARS-CoV-2 variant of concern in South 176

Detection of 2019 novel coronavirus (2019-nCoV) by real-178

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European 179 communicable disease bulletin 2020

Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in 181

Clinical infectious diseases : an official publication of the Infectious Diseases 182 Society of

SARS-CoV-2 PCR cycle threshold at hospital admission 184 associated with patient mortality

It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted October 1, 2021. ; https://doi.org/10.1101/2021.10.01.21264408 doi: medRxiv preprint