A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan

Three COVID-19 waves in Japan have been characterized by the presence of distinct PANGO lineages (B.1.1. 162, B.1.1.284, and B.1.1.214). Recently, in addition to the B.1.1.7 lineage, which shows 25% abundance, an R.1 lineage carrying the E484K mutation in the spike protein was found to show up to 40% predominance. E484K could be a pivotal amino acid substitution with the potential to mediate immune escape; thus, more attention should be paid to such potential variants of concern to avoid the emergence of mutants of concern. Such comprehensive real-time genome surveillance has become essential for the containment of COVID-19 clusters.

Automated summary

Three waves of COVID-19 in Japan have been characterized by distinct PANGO lineages, with the E484K mutation in the spike protein of the R.1 lineage showing up to 40% predominance. It is essential to pay attention to potential variants to prevent the emergence of mutants, highlighting the importance of real-time genome surveillance in containing COVID-19 clusters.