The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) emerged in late December 2019 in Wuhan, China, and is the causative agent for the worldwide COVID-19 pandemic. SARS-CoV-2 is a 29,811 nucleotides positive-sense single-stranded RNA virus belonging to the betacoronavirus genus. Due to inefficient proofreading ability of the viral RNA-dependent polymerase complex, coronaviruses are known to acquire new mutations following replication, which constitutes one of the main factors driving the evolution of its genome and the emergence of new genetic variants. In the last few months, the identification of new B.1.1.7 (UK), B.1.351 (South Africa) and P.1 (Brazil) variants of concern (VOC) highlighted the importance of tracking the emergence of mutations in the SARS-CoV-2 genome and their impact on transmissibility, infectivity, and neutralizing antibody escape capabilities. These VOC demonstrate increased transmissibility and antibody escape, and reduce current vaccine efficacy. Here we analyzed the appearance and prevalence trajectory of mutations that appeared in all SARS-CoV-2 genes from December 2019 to January 2021. Our goals were to identify which modifications are the most frequent, study the dynamics of their spread, their incorporation into the consensus sequence, and their impact on virus biology. We also analyzed the structural properties of the spike glycoprotein of the B.1.1.7, B.1.351 and P.1 variants. This study offers an integrative view of the emergence, disappearance, and consensus sequence integration of successful mutations that constitute new SARS-CoV-2 variants and their impact on neutralizing antibody therapeutics and vaccines.
Meta-Analysis of the Dynamics of the Emergence of Mutations and Variants of SARS-CoV-2