Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-CoV-2 variants

Tchesnokova, Veronika; Kulasekara, Hemantha; Larson, Lydia; Bowers, Victoria; Rechkina, Elena; Kisiela, Dagmara; Sledneva, Yulia; Choudhury, Debarati; Maslova, Iryna; Deng, Kai; Kutumbaka, Kirthi; Geng, Hao; Fowler, Curtis; Greene, Dina; Ralston, James; Samadpour, Mansour; Sokurenko, Evgeni

We report that there is a recent global expansion of numerous independent SARS-CoV-2 variants with mutation L452R in the receptor-binding domain (RBD) of the Spike protein. The massive emergence of L452R variants was first linked to lineage B.1.427/B.1.429 (clade 21C) that has been spreading in California since November-December 2020, originally named CAL.20C and currently variant of interest Epsilon. By PCR amplification and Sanger sequencing of a 541 base fragments coding for amino acids 414-583 of RBD from a collection of clinical specimens, we identified a separate L452R variant that also recently emerged in California but derives from the lineage B.1.232, clade 20A (named CAL.20A). Notably, CAL.20A caused an infection in gorillas in the San Diego Zoo, reported in January 2021. Unlike the Epsilon variant that carries two additional mutations in the N-terminal domain of Spike protein, L452R is the only mutation found in the Spike proteins of CAL.20A. Based on genome-wide phylogenetic analysis, emergence of both viral variants was specifically triggered by acquisition of L452R, suggesting a strong positive selection for this mutation. Global analysis revealed that L452R is nearly omnipresent in a dozen independently emerged lineages, including the most recent variants of concern/interest Delta, Kappa, Epsilon and Iota, with the Lambda variant carrying L452Q. L452 is in immediate proximity to the ACE2 interaction interface of RBD. It was reported that the L452R mutation is associated with immune escape and could result in a stronger cell attachment of the virus, with both factors likely increasing viral transmissibility, infectivity and pathogenicity.