A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations

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 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.

Post-vaccination SARS-COV-2 among healthcare workers in New Jersey: a genomic epidemiological study

“…To further characterize the SARS-CoV-2 genotypes recovered from the post-vaccinated individuals, we examined the spread of key mutations underlying VOCs (i.e., B.1.1.7) in New Jersey using a high-throughput molecular beacon assay designed to screen for polymorphisms N501Y/T and E484K/Q in the RBD region (10). Among 138 HCPs, 83 swabs were available for rapid screening providing 76 genotypic results (60 from partial and 16 from fully vaccinated).…”

“…SARS-CoV-2 positive swabs collected from seven HMH network hospitals were shipped to CDI on a weekly basis and stored at -80 o C. 1,404 swabs collected during the same time frame as the vaccinated samples were randomly selected and subjected to a molecular beacon-based real-time asymmetric PCR and melting curve analysis to identify the SARS-CoV-2 E484K/Q and 13 N501Y mutations, as previously described (10). In brief, µl aliquots of SARS-CoV-2 swab specimens were treated by proteinase K and heated at 95°C for 5 min.…”

“…N501Y mutations, as previously described (10). In brief, µl aliquots of SARS-CoV-2 swab specimens were treated by proteinase K and heated at 95°C for 5 min.…”