key: cord-0705127-yxo2cooa
authors: Ramírez, Juan D.; Muñoz, Marina; Patiño, Luz H.; Ballesteros, Nathalia; Paniz‐Mondolfi, Alberto
title: Will the emergent SARS‐CoV2 B.1.1.7 lineage affect molecular diagnosis of COVID‐19?
date: 2021-02-09
journal: J Med Virol
DOI: 10.1002/jmv.26823
sha: fba9a188a93615d3f36205ad150e67d23d893bb9
doc_id: 705127
cord_uid: yxo2cooa

As the coronavirus disease 2019 pandemic keep tackling global public health systems worldwide. The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV2) genome keeps mutating. In that regard, the recent emergence of the B.1.1.7 lineage in the UK has called the attention of global authorities. One point of concern is that if this lineage can be detected by traditional molecular schemes for SARS‐CoV‐2 detection. Herein, we showed that this lineage does not affect the Berlin–Charité protocol but can challenge the available commercial kits directed to the Spike (S) gene. All efforts should be made to continue to monitor SARS‐CoV‐2 genomes for potential variants that can impair diagnostic testing and lead to false negative results.

this lineage can be detected by traditional molecular schemes for SARS-CoV-2 detection. Herein, we showed that this lineage does not affect the Berlin-Charité protocol but can challenge the available commercial kits directed to the Spike (S) gene. All efforts should be made to continue to monitor SARS-CoV-2 genomes for potential variants that can impair diagnostic testing and lead to false negative results. Even though diagnostic detection of SARS-CoV-2 by RT-PCR using Berlin-Charité does not involve the spike (S) protein-encoding-gene as a target, the fact that 8 out of the 17 mutations defining the novel UK variant involve the S gene is a matter of concern that deserves further comments. In a recent press note dated December 22nd, DiaSorin Molecular has stated that an in silico analysis evaluating the multiple spike (S) and ORF1a/b mutations present in the emerging variant will not affect performance of the Simplexa™ COVID19 Direct assay, given that none of the reported mutations locate at the primers/probes targeted regions included in their assay. 8 Conversely, Thermo Fisher Scientific has already announced that the 69-70del mutation (S gene) will result in a "drop-out" of the S gene target, as this region is targeted through their TaqPath COVID-19 assay. 9 However, because TaqPath is a 3-gene target assay covering different regions on the S and N genes, it is unlikely that this will affect overall test performance. Moreover, S gene "drop out" may prove beneficial from an epidemiological standpoint as it may serve as a proxy indicator for detection of the emerging B.1.1.1.7 lineage. In fact, the European CDC has stated that for multitarget RT-PCR assays including the S gene, 'Spike drop out" maybe used as a surrogate marker for the 69-70del for variant detection in testing limited settings. 10 In conclusion, it is expected that an increase in the frequency of variants could eventually impact testing of SARS-CoV-2 RT-PCRs assays for both in-house and commercially available assays. Such has been the case for the emerging UK variant which has accumulated an unprecedented repertoire of mutations in a very brief timeframe. This emphasizes the need to follow a multi-target approach interrogating different regions of the viral genome to build-in redundancy and increase test sensitivity. All efforts should be made to continue to monitor SARS-CoV-2 genomes for potential variants that can impair diagnostic testing and lead to false negative results.

The peer review history for this article is available at https://publons. 

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