Cargando…
Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype
New variants of SARS-CoV-2 are continually emerging with mutations in spike associated with increased transmissibility and immune escape. Phenotypic maps can inform the prediction of concerning mutations from genomic surveillance, however most of these maps currently derive from studies using monome...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10426949/ https://www.ncbi.nlm.nih.gov/pubmed/37535672 http://dx.doi.org/10.1371/journal.ppat.1011545 |
_version_ | 1785090146289319936 |
---|---|
author | Kugathasan, Ruthiran Sukhova, Ksenia Moshe, Maya Kellam, Paul Barclay, Wendy |
author_facet | Kugathasan, Ruthiran Sukhova, Ksenia Moshe, Maya Kellam, Paul Barclay, Wendy |
author_sort | Kugathasan, Ruthiran |
collection | PubMed |
description | New variants of SARS-CoV-2 are continually emerging with mutations in spike associated with increased transmissibility and immune escape. Phenotypic maps can inform the prediction of concerning mutations from genomic surveillance, however most of these maps currently derive from studies using monomeric RBD, while spike is trimeric, and contains additional domains. These maps may fail to reflect interdomain interactions in the prediction of phenotypes. To try to improve on this, we developed a platform for deep mutational scanning using whole trimeric spike. We confirmed a previously reported epistatic effect within the RBD affecting ACE2 binding, that highlights the importance of updating the base spike sequence for future mutational scanning studies. Using post vaccine sera, we found that the immune response of vaccinated individuals was highly focused on one or two epitopes in the RBD and that single point mutations at these positions can account for most of the immune escape mediated by the Omicron BA.1 RBD. However, unexpectedly we found that the BA.1 RBD alone does not account for the high level of antigenic escape by BA.1 spike. We show that the BA.1 NTD amplifies the immune evasion of its associated RBD. BA.1 NTD reduces neutralistion by RBD directed monoclonal antibodies, and impacts ACE2 interaction. NTD variation is thus an important mechanism of immune evasion by SARS-CoV-2. Such effects are not seen when pre-stabilized spike proteins are used, suggesting the interdomain effects require protein mobility to express their phenotype. |
format | Online Article Text |
id | pubmed-10426949 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-104269492023-08-16 Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype Kugathasan, Ruthiran Sukhova, Ksenia Moshe, Maya Kellam, Paul Barclay, Wendy PLoS Pathog Research Article New variants of SARS-CoV-2 are continually emerging with mutations in spike associated with increased transmissibility and immune escape. Phenotypic maps can inform the prediction of concerning mutations from genomic surveillance, however most of these maps currently derive from studies using monomeric RBD, while spike is trimeric, and contains additional domains. These maps may fail to reflect interdomain interactions in the prediction of phenotypes. To try to improve on this, we developed a platform for deep mutational scanning using whole trimeric spike. We confirmed a previously reported epistatic effect within the RBD affecting ACE2 binding, that highlights the importance of updating the base spike sequence for future mutational scanning studies. Using post vaccine sera, we found that the immune response of vaccinated individuals was highly focused on one or two epitopes in the RBD and that single point mutations at these positions can account for most of the immune escape mediated by the Omicron BA.1 RBD. However, unexpectedly we found that the BA.1 RBD alone does not account for the high level of antigenic escape by BA.1 spike. We show that the BA.1 NTD amplifies the immune evasion of its associated RBD. BA.1 NTD reduces neutralistion by RBD directed monoclonal antibodies, and impacts ACE2 interaction. NTD variation is thus an important mechanism of immune evasion by SARS-CoV-2. Such effects are not seen when pre-stabilized spike proteins are used, suggesting the interdomain effects require protein mobility to express their phenotype. Public Library of Science 2023-08-03 /pmc/articles/PMC10426949/ /pubmed/37535672 http://dx.doi.org/10.1371/journal.ppat.1011545 Text en © 2023 Kugathasan et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Kugathasan, Ruthiran Sukhova, Ksenia Moshe, Maya Kellam, Paul Barclay, Wendy Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype |
title | Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype |
title_full | Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype |
title_fullStr | Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype |
title_full_unstemmed | Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype |
title_short | Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype |
title_sort | deep mutagenesis scanning using whole trimeric sars-cov-2 spike highlights the importance of ntd-rbd interactions in determining spike phenotype |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10426949/ https://www.ncbi.nlm.nih.gov/pubmed/37535672 http://dx.doi.org/10.1371/journal.ppat.1011545 |
work_keys_str_mv | AT kugathasanruthiran deepmutagenesisscanningusingwholetrimericsarscov2spikehighlightstheimportanceofntdrbdinteractionsindeterminingspikephenotype AT sukhovaksenia deepmutagenesisscanningusingwholetrimericsarscov2spikehighlightstheimportanceofntdrbdinteractionsindeterminingspikephenotype AT moshemaya deepmutagenesisscanningusingwholetrimericsarscov2spikehighlightstheimportanceofntdrbdinteractionsindeterminingspikephenotype AT kellampaul deepmutagenesisscanningusingwholetrimericsarscov2spikehighlightstheimportanceofntdrbdinteractionsindeterminingspikephenotype AT barclaywendy deepmutagenesisscanningusingwholetrimericsarscov2spikehighlightstheimportanceofntdrbdinteractionsindeterminingspikephenotype |