A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations

Emerg Microbes Infect. 2021 Dec;10(1):994-997. doi: 10.1080/22221751.2021.1929504.

Abstract

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 are 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 1135 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey between late December 2020 and March 2021. Our data revealed dramatic increases in the frequencies of both E484K and N501Y over time, underscoring the need for continuous epidemiological monitoring.

Keywords: E484K; N501Y; SARS-CoV-2; molecular assay; screening; variants.

Publication types

  • Letter

MeSH terms

  • Antibodies, Neutralizing / immunology
  • Antibodies, Viral / immunology
  • COVID-19 / epidemiology
  • COVID-19 / virology*
  • Genotype
  • Humans
  • Mutation*
  • Nasopharynx / virology
  • New Jersey / epidemiology
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • SARS-CoV-2 / genetics*
  • Sensitivity and Specificity
  • Spike Glycoprotein, Coronavirus / genetics*
  • Whole Genome Sequencing

Substances

  • Antibodies, Neutralizing
  • Antibodies, Viral
  • RNA, Viral
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Grant support

This work was supported by the COVID Emergency Research Fund [Grant Number 61315]; Hackensack University Medical center, by funds provided to the CDI by Activision Publishing Inc; Suez North America; and by NJ Stands Up to COVID. The funders of this study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report. Whole-genome sequencing was performed at the New York Genome Center donors (NYGC) as part of the COVID-19 Genomic Research Network (CGRN) with funds generously provided by NYGC donors.