Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

SARS-CoV-2: Genetic variability, mutations and variants of concern for the global world

Since emerging from Wuhan, China, in December of 2019, the novel coronavirus named SARS-CoV-2 has been causing devastating severe respiratory infections in human population worldwide. The new emerging disease was called COVID-19 and, as early as the beginning of 2020, the world found itself in a COVID 19 pandemic. Despite the slow evolutionary rate of SARS-CoV-2 relative to other RNA viruses, its massive and rapid transmission during the COVID-19 pandemic has enabled it to acquire significant genetic diversity since it first entered the human population. This led to the emergence of numerous variants, some of them recently being labeled, "variants of concern" (VOC). Emerging SARS-CoV-2 variants can be problematic if one or more of the independent mutations result in changes that make the virus more pathogenic, resistant to treatment, able to escape vaccines, or able to evade diagnostic tests. So far, four VOCs have been globally recognized (Alpha or B.1.1.7, Beta or B.1.351, Gamma or P.1 and newly recognized as VOC Delta or lineage B.1.617.2), and areas of the emerging variant of concern first time observed are United Kingdom, South Africa, Brazil, and India, respectively. Notable variants are those that contain mutations within the S gene, particularly within the region that codes for the receptor-binding domain (RBD) that recognize and attach the specific ACE2 cell receptor. These mutations are responsible for increased viral transmission and influence disease severity, reliability of clinical tests as well as vaccine and therapy efficacy. The characteristics of VOCs and their mutational patterns indicate the necessity of permanent close monitoring on a global level.

[Genomics and epidemiology of SARS-CoV-2 lineage]

Coronavirus disease 2019（COVID-19）is a newly emerging human infectious disease caused by severe acute respiratory syndrome coronavirus 2（SARS-CoV-2）．It had been first identified in Wuhan at the end of 2019 and the spread of SARS-CoV-2 variants has become a crucial issue worldwide. WHO categorized SARS-CoV-2 variants as "Variants of Concern; VOCs" and "Variants of Interest; VOIs" based on transmissibility, disease severity or their susceptibility to vaccines. Especially, the spread of SARS-CoV-2 variant categorized in VOCs, such as B.1.1.7 and B.1.617.2, has been a serious concern worldwide. In Japan, in addition to the B.1.1.214/B.1.1.284 variants, the B.1.1.7 variant has been rapidly spreading in Osaka and Tokyo. The B.1.617 variant was first identified in April 2021 in a patient who was under domestic quarantine and cases of community-acquired infections of the B.1.617.2 variant were first observed in May 2021. Amino acid changes in the spike protein, such as the N501Y, E484K or L452R mutations mainly observed in VOCs in addition to the D614G mutation are thought to affect the transmissibility and immune escape of the virus as well as the disease severity and this may be contributory to the rapid spread of SARS-CoV-2 variants. Now, several SARS-CoV-2 variants with additional mutations are continuously emerging worldwide and the prevailing SARS-CoV-2 variants are rapidly changing.