Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

Abstract

Monoclonal antibodies and antibody cocktails are a promising therapeutic and prophylaxis for COVID-19. However, ongoing evolution of SARS-CoV-2 can render monoclonal antibodies ineffective. Here we completely map all mutations to the SARS-CoV-2 spike receptor binding domain (RBD) that escape binding by a leading monoclonal antibody, LY-CoV555, and its cocktail combination with LY-CoV016. Individual mutations that escape binding by each antibody are combined in the circulating B.1.351 and P.1 SARS-CoV-2 lineages (E484K escapes LY-CoV555, K417N/T escape LY-CoV016). Additionally, the L452R mutation in the B.1.429 lineage escapes LY-CoV555. Furthermore, we identify single amino acid changes that escape the combined LY-CoV555+LY-CoV016 cocktail. We suggest that future efforts should diversify the epitopes targeted by antibodies and antibody cocktails to make them more resilient to antigenic evolution of SARS-CoV-2.

Figure 1.. Comprehensive escape maps for LY-CoV555, LY-CoV016, and a 1:1 cocktail of the two antibodies.

(A) Newly described escape maps for LY-CoV555 and LY-CoV555+LY-CoV016 cocktail, alongside our previously reported escape map for LY-CoV016 [15]. Line plots at left show the total escape (sum of per-mutation escape fractions) at each RBD site. Sites indicated by pink lines on the x-axis are then shown in zoomed in form in the logoplots at right. In these logoplots, the height of each letter indicates the escape fraction for that mutation (larger letters mean stronger escape from antibody binding). Letters are colored by how mutations impact ACE2 binding affinity (scale bar bottom right), as measured in our prior deep mutational scan [20]. See Fig. S2 for escape maps colored by mutation effects on folded RBD expression. Note that y-axis is scaled differently for each antibody / cocktail. The sites shown in the logoplots are those where mutations have an appreciable effect on either antibody, as well as site 406 (which is an escape mutation from the REGN-COV2 cocktail [15]). (B) Literature measurements of the effects of K417N, E484K, and N501Y on neutralization by LY-CoV555 and LY-CoV016 [14]. These measurements validate our maps, which suggest that K417N specifically escapes LY-CoV016, E484K specifically escapes LY-CoV555, and N501Y impacts neither antibody.

Figure 2.. Mutations present in sequenced SARS-CoV-2 isolates that escape antibody binding.

(A) For each mutation, the escape fraction measured in the current (LY-CoV555) or prior (LY-CoV016 [15]) study is plotted against the mutation’s frequency among all 405,692 high-quality human-derived SARS-CoV-2 sequences in GISAID as of February 6, 2021. Mutations with notable frequencies are labeled, and those discussed in the text are colored to key with panel (B) or to highlight observed cocktail escape mutations (Q493K/R). (B) The RBD mutations in four emerging viral lineages, categorized by their effect on binding by LY-CoV555 and LY-CoV016. The B.1.351 and P.1 lineages contain combinations of mutations that escape each component of the LY-CoV555+LY-CoV016 cocktail. Lineages described in the following references: B.1.1.7, [11]; B.1.351, [10]; P.1, [12]; B.1.429, [13].

Figure 3.. Escape maps projected onto structures of the RBD bound by LY-CoV555 or LY-CoV016.

In each structure, the RBD surface is colored by escape at each site (white = no escape, red = strongest site-total escape for antibodies or strongest per-mutation escape for cocktail, gray = no escape because no mutations functionally tolerated). Sites of interest in each structure are labeled. The structures are as follows: LY-CoV016 (PDB 7C01 [22]); LY-CoV555 (PDB 7KMG [4]); cocktail escape projected onto the 7KMG structure, with the LY-CoV016 Fab chain aligned from the 7C01 structure for reference.