Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants

Abstract

We report that there is a recent global expansion of numerous independent severe acute respiratory syndrome coronavirus 2 (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 and December 2020, originally named CAL.20C and currently variant of interest epsilon. By PCR amplification and Sanger sequencing of a 541-base fragment coding for amino acids 414 to 583 of the 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 angiotensin-converting enzyme 2 (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.

Keywords: L452R; SARS-CoV-2; expansion; mutation.

FIG 1

Distribution of silent (green triangles) and amino acid (red triangles) mutations across region 414 to 583 of the spike protein. Dark red, receptor-binding domain (RBD); green, C-terminal domain 1 (CTD1) of S1 spike region; blue, receptor-binding ridge epitope residues; yellow, 443-to-450 loop epitope residues; black, 570-to-572 loop residues.

FIG 2

Phylogenetic trees of CAL.20A and the epsilon variant genomes. (A) nCoV strains identified in the tested samples. (B) nCoV strains deposited into GISAID database.

FIG 3

Nextstrain-generated radial cladogram of SARS-CoV-2 genetic variants (as of 12 June 2021). Showing 519 of 3,883 genomes randomly sampled between Jun 2020 and May 2021, belonging to 23 PANGO lineages. Circles tip branches containing genomes with any mutation in L452 (circles on branches without the mutations were manually removed for a visual clarity). Yellow circles, branches with L452R; blue, with L452Q; orange, with L452M. Black triangle tips the branch of lineage that includes CAL.20A. (At the date of analysis, CAL.20A strains were not among the sampled genomes in the Nextstrain database, and only three B.1.232 [all non-CAL.20A] lineages were found). Nomenclature: PANGO lineage followed by Nextstrain clade in parenthesis and the current VOC/VOI designation. In red, VOC/VOI with an omnipresent or nearly omnipresent L452 mutation (VOC beta is in black, as the L452 mutation is found only in few genomes of the variant).