E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

The COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people since its beginning in 2019. The propagation of new lineages and the discovery of key mechanisms adopted by the virus to overlap the immune system are central topics for the entire public health policies, research and disease management. Since the second semester of 2020, the mutation E484K has been progressively found in the Brazilian territory, composing different lineages over time. It brought multiple concerns related to the risk of reinfection and the effectiveness of new preventive and treatment strategies due to the possibility of escaping from neutralizing antibodies. To better characterize the current scenario we performed genomic and phylogenetic analyses of the E484K mutated genomes sequenced from Brazilian samples in 2020. From October 2020, more than 40% of the sequenced genomes present the E484K mutation, which was identified in three different lineages (P.1, P.2 and B.1.1.33 -posteriorly renamed as N.9) in four Brazilian regions. We also evaluated the presence of E484K associated mutations and identified selective pressures acting on the spike protein, leading us to some insights about adaptive and purifying selection driving the virus evolution.

Automated summary

The COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people since 2019, with new lineages propagating and the virus adopting mechanisms to evade the immune system. The E484K mutation has been progressively found in Brazil since the second half of 2020, raising concerns about reinfection risk and vaccine effectiveness. Genomic and phylogenetic analyses showed over 40% of sequenced genomes in October 2020 from Brazilian samples had the E484K mutation, leading to insights about adaptive and purifying selection driving virus evolution.