key: cord-0907281-ih2op4up
authors: Zhao, Y.; Lee, A.; Composto, K.; Cunninghan, M. H.; Mediavilla, J. R.; Fennessey, S.; Corvelo, A.; Chow, K. F.; Zody, M. C.; Chen, L.; Kreiswirth, B. N.; Perlin, D. S.
title: A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations
date: 2021-03-29
journal: nan
DOI: 10.1101/2021.03.26.21253712
sha: cdce2ad50fb0766555fbe3ec3c1bec015cdd5932
doc_id: 907281
cord_uid: ih2op4up

Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. While the concerning variants are fast spreading in various geographical areas, identification and monitoring of these variants is lagging far behind, due in large part to the slow speed and insufficient capacity of viral sequencing. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. Using this tool, we screened a total of 435 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey. While B.1.351 and P.1 variants were absent from the current study, our data revealed a dramatic increase in the frequency of E484K over time, underscoring the need for continuous epidemiological monitoring.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-34

CoV-2) has plagued human society causing immeasurable losses in an unprecedented way. In 35 the circumstances, many monoclonal and polyclonal antibodies have been approved for clinical 36 use and several vaccines have been licensed with two mRNA vaccines and one viral vectored 37 vaccine being rolled out for population vaccination in various countries and geographical areas. 38

Opposed to these encouraging progresses and facts, this virus has quickly adapted to various 39 pressures from antiviral therapy and host immunity and evolved independently into several 40 SARS-CoV-2 variants of concern (VOC). These variants, including B. York (B.1.526) also carries the E484K mutation, and alarmingly, fast-spreading over the past 49 two months [9, 10]. Another key spike mutation, N501Y, present in all three VOCs is considered 50 to enhance the binding between spike and the ACE2 receptor in human cells, thus contributing 51 to increased transmissibility and possibly virulence as well [11, 12, 13]. As we continue to 52 understand the impact of these variants on the mode of the ongoing pandemic, efficient and 53 continuous monitoring of these variants is critical to implementation of fast and effective 54 countermeasures to eventually defeat this devastating disease. The closer this genotyping can 55 happen to the testing, the quicker the data can be used and actioned. To this end, we 56 developed a novel molecular diagnostic assay capable of identifying the signature mutations 57 within 2.5 h from sample preparation to report, and used this tool to screen clinical 58 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Using this tool, we next accessed to SARS-CoV-2 positive NS specimens through the HMH 84

institutional Biorepository under an HMH-IRB approved protocol Pro2018-1022, to screen the 85 signature mutations. This study also accessed de-identified data for time and location of sample 86 collection through the HMH-IRB approved protocol, Pro2020-0342. A total of 435 samples 87 (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. screening tool that can be used in a high-throughput fashion to increase the capacity of SARS-122

CoV-2 variant detection in real-time. Herein, we demonstrate that a novel and easy molecular 123 diagnostic assay can be used as a convenient tool for large scale of SARS-CoV-2 variant 124 screening, thus, to enable highly efficient epidemiological monitoring. Not only the assay is 125 proved to be highly accurate in our clinical screening, notably, it is also sensitive to new 126 mutations within the probe binding site. This has been well exemplified by our discovery of the 127 N501T mutation from the clinical specimens. To our knowledge, this is the first report of using 128 novel screening tool to identify key mutation harboring SARS-CoV-2 variants in NJ hospitals. 129 B.1.351 and P.1 variants were absent from the current study, however our data revealed a 130 dramatic increase in the frequency of E484K over time, underscoring the need for continuous 131 epidemiological monitoring. 132

A couple of limitations of this study need to be noted. Firstly, this novel screening assay is 134 slightly less sensitive than the widely used RT-PCR COVID diagnostic assay. Therefore, 135 All rights reserved. No reuse allowed without permission.

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

The localized rise of a B

SARS-CoV-2 variant containing an E484K mutation in New York State

MMWR Morbidity and 190 mortality weekly report

PubMed Central PMCID: PMCPMC7821772 Journal Editors 192 form for disclosure of potential conflicts of interest. No potential conflicts of interest were 193 disclosed. eng

Covid-19: New UK variant may be linked to increased death rate, early data 195 indicate

Genomic epidemiology identifies 198 emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 199 medRxiv : the preprint server for health sciences

Diagnosis, clinical characteristics, and 203 outcomes of COVID-19 patients from a large healthcare system in northern New Jersey

Scientific reports

Platform to Enhance SARS-CoV-2 Testing Capacity. Med

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted March 29, 2021. ; https://doi.org/10.1101/2021.03.26.21253712 doi: medRxiv preprint All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted March 29, 2021. ; https://doi.org/10.1101/2021.03.26.21253712 doi: medRxiv preprint