In this work, we report a new approach for detecting SARS-CoV-2 RBD protein (RBD) using the surface-enhanced Raman spectroscopy (SERS) technique. The optical enhancement was obtained thanks to the preparation of nanostructured Ag/Au substrates. Fabricated Au/Ag nanostructures were used in the SERS experiment for RBD protein detection. SERS substrates show higher capabilities and sensitivity to detect RBD protein in a short time (3 s) and with very low power. We were able to push the detection limit of proteins to a single protein detection level of 1 pM. The latter is equivalent to 1 fM as a detection limit of viruses. Additionally, we have shown that the SERS technique was useful to figure out the presence of RBD protein on antibody functionalized substrates. In this case, the SERS detection was based on protein-antibody recognition, which led to shifts in the Raman peaks and allowed signal discrimination between RBD and other targets such as Bovine serum albumin (BSA) protein. A perfect agreement between a 3D simulated model based on finite element method and experiment was reported confirming the SERS frequency shift potential for trace proteins detection. Our results could open the way to develop a new prototype based on SERS sensitivity and selectivity for rapid detection at a very low concentration of virus and even at a single protein level.

Summary: The Middle East respiratory syndrome coronavirus (MERS‐CoV) emerged in late 2012 in Saudi Arabia. For this study, we conducted a large‐scale comparative genome study of MERS‐CoV from both human and dromedary camels from 2012 to 2019 to map any genetic changes that emerged in the past 8 years. We downloaded 1309 submissions, including 308 full‐length genome sequences of MERS‐CoV available in GenBank from 2012 to 2019. We used bioinformatics tools to describe the genome structure and organization of the virus and to map the most important motifs within various regions/genes throughout the genome over the past 8 years. We also monitored variations/mutations among these sequences since its emergence. Our phylogenetic analyses suggest that the cluster within African camels is derived by S gene. We identified some prominent motifs within the ORF1ab, S gene and ORF‐5, which may be used for barcoding the African camel lineages of MERS‐CoV. Furthermore, we mapped some sequence patterns that support the zoonotic origin of the virus from dromedary camels. Other sequences identified selection pressures, particularly within the N gene and the 5′ UTR. Further studies are required for careful monitoring of the MERS‐CoV genome to identify any potential significant mutations in the future.

Controlling contagious diseases necessitates using diagnostic techniques that can detect infection in the early stages. Although different diagnostic tools exist, there are still challenges related to accuracy, rapidity, cost-effectiveness, and ease of use. Surface-enhanced Raman spectroscopy (SERS) is a rapid, simple, less expensive, and accurate method. We continue our previous work published on SERS detection of the SARS-CoV-2 receptor-binding domain (RBD) in water. In this work, we replace water with saliva to detect SARS-CoV-2 proteins at very low concentrations and during a very short time. We prepared a very low concentration of 10⁻⁹ M SARS-CoV-2 spike protein (S) and SARS-CoV-2 receptor-binding domain (RBD) in saliva to mimic a real case scenario. Then, we drop them on a SERS substrate. Using modified SERS measurements on the control and the sample containing the biomolecules, confirmed the sensitivity of the target identification. This technique provides different diagnostic solutions that are fast, simple, non-destructive and ultrasensitive. Simulation of the real-world of silicon wire covered with silver and gold, were performed using an effective and accurate tool, COMSOL Multiphysics software, for the enhancement properties study.