SARS-CoV-2 mutations allow escape from clinical monoclonal antibodies

Monoclonal antibodies LY-CoV555 and LY-CoV016 are administered as a cocktail for the treatment and prevention of COVID-19. They target the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with high specificity, potentially neutralizing the virus. They have been shown to lessen viral load, and so have been approved for emergency use by the FDA in mild to moderate COVID-19 cases. However, the continuously changing genome of SARS-CoV-2 is likely to render such treatments ineffective eventually, meaning that new monoclonal antibodies specific to each strain may need to be developed.

A new research paper recently uploaded to the preprint server bioRxiv* by Jesse D. Bloom et al. (22nd Feb 2021) aims to map all of the currently circulating SARS-CoV-2 lineages with resistance towards LY-CoV555 and LY-CoV016, and document the specific mutations that confer resistance, ultimately suggesting that future monoclonal antibody cocktails should target a more diverse range of epitopes.

How was the study performed?

The research group from Fred Hutchinson Cancer Research Center and the University of Washington firstly generated yeast cells expressing nearly four thousand possible amino acid mutations of the receptor-binding domain (RBD) of wild-type SARS-CoV-2 and sorted to select mutants capable of binding with the angiotensin-converting enzyme 2 (ACE2) receptor. Tagged monoclonal antibodies LY-CoV555 and LY-CoV016 were then added, allowing the amino acid sequences with the greatest affinity to be identified and sorted based on the intensity of fluorescence. The mutant amino acid sequences of the RBDs that did not bind with the antibodies were then identified and compared with known mutant amino acid sequences in extant SARS-CoV-2 strains, assisting in identifying the specific mutations that grant monoclonal antibody evasion.

Which mutations allow escape from monoclonal antibodies?

LY-CoV555 and LY-CoV016 bind to opposite sides of the receptor binding ridge, a dynamic region of the RBD that interacts with the ACE2 receptor. LY-CoV555 in particular was evaded by E484 mutants, that is, a change from the wild-type sequence having a glutamic acid in the 484th position. E484K had previously been highlighted as a mutation that allowed escape from this antibody in previous work, and the group added L452R and S494P to this list. Interestingly, the group found that when assessing the affinity of mutants that escape LY-CoV555 towards the ACE2 receptor, there was little difference from wild-type, which is in-line with the observation that the expression of the conformation of the RBD is not altered.

Mutations that allow escape from LY-CoV016 were distinct from those that allowed evasion of  LY-CoV555, with K417N/T mutation being found to be most impactful to the binding affinity of LY-CoV016.

It was also noted that several single-site mutations allow escape from both monoclonal antibodies, including Q493, which is not located in the receptor binding ridge but in a region of overlap between LY-CoV555 and LY-CoV016 when they are bound. The group suggests that the replacement of the charge-neutral glutamine with a bulky positively charged residue such as lysine could negatively impact binding affinity towards the antibodies.

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.
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.

Which strains exhibit these mutations?

The B.1.351 SARS-CoV-2 variant, first identified in South Africa in October 2020, contains combinations of key mutations E484K and K417N, suggesting that the antibody cocktail is unlikely to be effective against this variant. Similarly, the P.1 (formerly B.1.1.28.1) variant identified in Tokyo, January 2021, bears E484K and K417T mutations. Additionally, the B.1.429 variant, found in California in July 2020, exhibits the L452R mutation, allowing it to evade LY-CoV555.

Importantly, several variants have been noted to adopt these mutations in cases of convergent evolution. The sporadic use of monoclonal antibodies is unlikely to generate a significant evolutionary pressure compared to vaccine or infection-induced immunity, and so the development of antibodies that target more conserved epitopes could prove a key strategy against the ever-changing SARS-CoV-2 virus.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Michael Greenwood

Written by

Michael Greenwood

Michael graduated from Manchester Metropolitan University with a B.Sc. in Chemistry in 2014, where he majored in organic, inorganic, physical and analytical chemistry. He is currently completing a Ph.D. on the design and production of gold nanoparticles able to act as multimodal anticancer agents, being both drug delivery platforms and radiation dose enhancers.

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