Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment

TLDR

SARS‑CoV‑2 vaccines and therapeutics are being developed using small‑molecule inhibitors and convalescent‑plasma antibodies, but the virus’s high mutation rate can drive genetic drift and immune escape, so sub‑strains and predicted B‑cell/T‑cell epitopes must be considered. The study aims to identify spike protein variants that could cause antigenic drift. Using epitope data and viral variants, the authors screened for mutations that alter B‑cell epitopes. The D614G (23403A>G) spike variant is common in Europe but rare in China, indicating geographic variation in potential drift.

Abstract

New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China.