Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach
Matthew M. Hernandez,
Ana S. Gonzalez-Reiche,
Adriana van de Guchte,
Luz Helena Patiño,
Juan David Ramírez,
Melissa R. Gitman,
Michael D. Nowak,
Ted E. Schutzbank,
Harm van Bakel,
Emilia M. Sordillo,
Alberto E. Paniz Mondolfi
Posted 16 Sep 2021
medRxiv DOI: 10.1101/2021.09.09.21263348
Posted 16 Sep 2021
The COVID-19 pandemic sparked rapid development of SARS-CoV-2 diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY SARS-CoV-2 Panel combines RT-PCR and MALDI-TOF mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified dataset of 1,262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 through April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly-specific for the alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.
- Downloaded 192 times
- Download rankings, all-time:
- Site-wide: 144,133
- In infectious diseases: 5,955
- Year to date:
- Site-wide: 60,715
- Since beginning of last month:
- Site-wide: 15,724
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!