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 coronavirus disease 2019 (COVID-19). However, ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) can render monoclonal antibodies ineffective. Here, we completely map all of the 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 escapes LY-CoV016). In addition, 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 diversify the epitopes targeted by antibodies and antibody cocktails to make them more resilient to the antigenic evolution of SARS-CoV-2.

Keywords: SARS-CoV-2; antibody escape; bamlanivimab; deep mutational scanning.

Graphical abstract

Figure 1

Comprehensive escape maps for LY-CoV555, LY-CoV016, and a 1:1 cocktail of the 2 antibodies (A) Newly described escape maps for LY-CoV555 and LY-CoV555+LY-CoV016 cocktail, alongside our previously reported escape map for LY-CoV016. 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 magnified 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 affect ACE2 binding affinity (scale bar, bottom right), as measured in our prior deep mutational scan. See Figure S2 for escape maps colored by mutation effects on folded RBD expression and Data S1 for raw data. Note that the y axis is scaled differently for each antibody/cocktail. The sites shown in the logoplots are where mutations have an appreciable effect on either antibody, as well as site 406 (which is an escape mutation from the REGN-COV2 cocktail¹⁵). (B) Literature measurements of the effects of K417N, E484K, and N501Y on neutralization by LY-CoV555 and LY-CoV016. These measurements validate our maps, which suggest that K417N specifically escapes LY-CoV016, E484K specifically escapes LY-CoV555, and N501Y affects 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-CoV016¹⁵) study is plotted against the frequency of the mutation among all 679,454 high-quality human-derived SARS-CoV-2 sequences in GISAID as of March 15, 2021. Mutations with notable frequencies are labeled, and those discussed in the text are colored to key with (B) or to highlight observed cocktail escape mutations (Q493K/R). (B) The RBD mutations in 4 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 are described in the following references: B.1.1.7, B.1.351, P.1, and B.1.429.

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: 7C01²³); LY-CoV555 (PDB: 7KMG⁴); cocktail escape projected onto the 7KMG structure, with the LY-CoV016 Fab chain aligned from the 7C01 structure for reference.