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Deep mutational scanning to understand the evolution of SARS-CoV-2 spike.
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Kugathasan-R-2023-PhD-Thesis.pdf | Thesis | 10.72 MB | Adobe PDF | View/Open |
Title: | Deep mutational scanning to understand the evolution of SARS-CoV-2 spike. |
Authors: | Kugathasan, Ruthiran |
Item Type: | Thesis or dissertation |
Abstract: | SARS-CoV-2 emerged as a zoonosis in 2019, causing a pandemic that led to significant global mortality, and devastating economic impact. SARS-CoV-2’s pathogenicity was related to its novelty in an immunologically naïve population. With increasing population immunity through vaccination and/or natural infection attenuating the disease, societies have been able to return to a semblance of normality, however SARS-CoV-2 has persisted to become endemic. With endemicity SARS-CoV-2 has continued to adapt and evolve, initially to optimise transmission and latterly to escape immune responses. To predict the future evolution, a deep mutagenesis scanning platform was developed. Deep mutagenesis scanning allows the phenotypic effects of thousands of mutations to be explored in a high-throughput manner. Using whole trimeric Alpha spike displayed on mammalian cells provided a physiologically relevant model and allowed the identification of mutations that increase ACE2 binding (the receptor for SARS-CoV-2 spike) and immune escape, which subsequently appeared in the Omicron lineages. Using this novel deep mutagenesis platform, the evolutionary trajectory of the SARS-CoV-2 receptor-binding domain can be seen to be restricted by epistasis. Vaccine induced immune responses against the receptor binding-domain are found to be remarkably focused on one or two residues despite being polyclonal and these residues have been repeatedly selected for in a variety of variants. From work exploring the antigenic effects of receptor-binding domain mutations, it becomes apparent the N-terminal domain contributes significantly to the immune escape seen with Delta and BA.1. This effect of the N-terminal domain does not appear to be mediated by escape from N-terminal domain directed antibodies, but by making the receptor-binding domain more difficult to neutralise. The plasticity of and focused immune response on the receptor-binding domain make further SARS-CoV-2 antigenic drift inevitable. Work described here suggests the most dramatic changes in antigenicity requires changes in both the N-terminal domain and receptor-binding domain. |
Content Version: | Open Access |
Issue Date: | Jan-2023 |
Date Awarded: | Jul-2023 |
URI: | http://hdl.handle.net/10044/1/105881 |
DOI: | https://doi.org/10.25560/105881 |
Copyright Statement: | Creative Commons Attribution NonCommercial Licence |
Supervisor: | Barclay, Wendy |
Sponsor/Funder: | Wellcome Imperial College Healthcare NHS Trust- BRC Funding Medical Research Council (Great Britain) |
Funder's Grant Number: | 216353/Z/19/Z RDA01 MR/W005611/1 |
Department: | Department of Infectious Disease |
Publisher: | Imperial College London |
Qualification Level: | Doctoral |
Qualification Name: | Doctor of Philosophy (PhD) |
Appears in Collections: | Department of Infectious Disease PhD Theses |
This item is licensed under a Creative Commons License