Investigation of SARS-CoV-2 Variants and Their Effect on SARS-CoV-2 Monoclonal Antibodies, Convalescent and Vaccine Plasma by a Novel Web Tool

(1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against monoclonal antibodies, convalescent, and vaccine plasma. (2) Methods: Strains isolated from COVID-19 cases in Turkey in April and September 2021 were involved. Illuma Nextera XT was processed for NGS, followed by virtual phenotyping (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). (3) Results: Among 211 strains, 79% were SARS-CoV-2 variants. B.1.1.7 (Alpha) was the most dominant, followed by B.1.617.2 (Delta), B.1.351 (Beta), and B.1.525 (Eta). Alpha and Delta were less susceptible to Etesevimab—Sotrovimab and Bamlanivimab—Etesevimab, respectively. Reduced efficacy was observed for convalescent plasma in Beta and Delta; AstraZeneca, Comirnaty plus AstraZeneca in Alpha; Comirnaty, Moderna, Novovax in Beta; Comirnaty in Delta. (4) Conclusion: CoV-RDB analysis is an efficient, rapid, and helpful web tool for SARS-CoV-2 variant detection and susceptibility analysis.