key: cord-0736563-j3j6kfo3
authors: Peñarrubia, Luis; Ruiz, Maria; Porco, Roberto; Rao, Sonia N.; Vella, Stephen A.; Juanola-Falgarona, Martí; Manissero, Davide; López-Fontanals, Marta; Pareja, Josep
title: In Response to: Multiple assays in a real-time RT-PCR Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak
date: 2021-01-27
journal: Int J Infect Dis
DOI: 10.1016/j.ijid.2021.01.049
sha: 64460d996b5295a1a7b141da96d737e216882068
doc_id: 736563
cord_uid: j3j6kfo3

nan

Genomic analysis of these variants shows the highest mutation frequency occurring predominantly in the spike gene [3, 4] . Whether the expansion of these mutations is result of selection or genetic drift is still under investigation [5, 6] . However, the rapid spread of these variants has evoked public concern regarding the reliability of diagnostic RT-PCR assays.

We previously assessed the risk of sensitivity loss of different published assays by the emergence of genetic variability through week 21, 2020 [7] . We concluded that targeting more than one genomic region mitigates the risk of sensitivity loss by the accumulation of mutations in the primer binding regions. We also demonstrated that the QIAstat-Dx Respiratory SARS-CoV-2 panel successfully identified >99% of SARS-CoV-2 genomes with 100% oligonucleotide coverage. The remaining <1% of genomes exhibited a single variation in the annealing region of one of the oligonucleotides. From these, 0.02% sequences showed a mismatch in a critical position. In-vitro testing showed no effect on the Limit of Detection of the panel highlighting the robustness of its multi-target approach to maintain the nominal sensitivity [7] .

Following the described methodology, [7] we re-evaluated the impact on sensitivity of the The SARS-CoV-2 mutation rate will continue to increase the number of already numerous variants. Although reports of increased infectivity have appeared, no effect on COVID-19 virulence has been demonstrated this far. Here, our results confirm the conclusions of our J o u r n a l P r e -p r o o f previous work showing that multi-target real-time RT-PCR SARS-CoV-2 detection can mitigate the risk of loss of sensitivity. In this regard, continuous monitoring of genomic variants by assay manufacturers is essential to provide a rapid response in case assay re-design is needed.

Mutation (amino acid change)

Public Health Impact 

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-QPCR

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations

Mutant coronavirus in the United Kingdom sets off alarms, but its importance remains unclear

Fast-spreading UK virus variant raises alarms

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak

Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA. European Centre For Disease Preventation and Control

All authors are employees of QIAGEN;No ethical committee approval was required to the completion of this work.No external funding sources were used for the completion of this work.