Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, South Africa, and other COVID-19-devastated countries
Recently, the SARS-CoV-2 variants from the United Kingdom (UK), South Africa, and Brazil have received much attention for their increased infectivity, potentially high virulence, and possible threats to existing vaccines and antibody therapies. The question remains if there are other more infectious variants transmitted around the world. We carry out a large-scale study of 252,874 SARS-CoV-2 genome isolates from patients to identify many other rapidly growing mutations on the spike (S) protein receptor-binding domain (RDB). We reveal that 88 out of 95 significant mutations that were observed more than 10 times strengthen the binding between the RBD and the host angiotensin-converting enzyme 2 (ACE2), indicating the virus evolves toward more infectious variants. In particular, we discover new fast-growing RBD mutations N439K, L452R, S477N, S477R, and N501T that also enhance the RBD and ACE2 binding. We further unveil that mutation N501Y involved in United Kingdom (UK), South Africa, and Brazil variants may moderately weaken the binding between the RBD and many known antibodies, while mutations E484K and K417N found in South Africa and Brazilian variants can potentially disrupt the binding between the RDB and many known antibodies. Among three newly identified fast-growing RBD mutations, L452R, which is now known as part of the California variant B.1.427, and N501T are able to effectively weaken the binding of many known antibodies with the RBD. Finally, we hypothesize that RBD mutations that can simultaneously make SARS-CoV-2 more infectious and disrupt the existing antibodies, called vaccine escape mutations, will pose an imminent threat to the current crop of vaccines. A list of most likely vaccine escape mutations is given, including N501Y, L452R, E484K, N501T, S494P, and K417N.