A Multiplexed SERS Microassay for Accurate Detection of SARS-CoV-2 and Variants of Concern

Severe acute respiratory syndrome coronavirus 2 variants play an important role in predicting patient outcome during postinfection, and with growing fears of COVID-19 reservoirs in domestic and wild animals, it is necessary to adapt detection systems for variant detection. However, variant-specific detection remains challenging. Surface-enhanced Raman scattering is a sensitive and multiplexing technique that allows the simultaneous detection of multiple targets for accurate identification. Here we propose the development of a multiplex SERS microassay to detect both the spike and nucleocapsid structural proteins of SARSCoV-2. The designed SERS microassay integrates gold-silver hollow nanobox barcodes and electrohydrodynamically induced nanomixing which in combination enables highly specific and sensitive detection of SARS-CoV-2 and the S-protein epitopes to delineate between ancestral prevariant strains with the newer variants of concern, Delta and Omicron. The microassay allows detection from as low as 20 virus/mu L and 50 pg/mL RBD protein and can clearly identify the virus among infected versus healthy nasopharyngeal swabs, with the potential to identify between variants. The detection of both S-and N-proteins of SARS-CoV-2 and the differentiation of variants on the SERS microassay can aid the early detection of COVID-19 to reduce transmission rates and lead into adequate treatments for those severely affected by the virus.

Automated summary

Variants of SARS-CoV-2 play a crucial role in predicting patient outcomes, hence the need for variant detection. This study proposes a multiplex SERS microassay for detecting both the spike and nucleocapsid structural proteins. The microassay combines gold-silver hollow nanobox barcodes and electrohydrodynamically induced nanomixing to achieve highly specific and sensitive detection of the virus and S-protein epitopes. The assay can detect as low as 20 virus/mu L and 50 pg/mL RBD protein in nasopharyngeal swabs and can differentiate between different variants.