[HTML][HTML] Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades

B Dadonaite, J Brown, TE McMahon, AG Farrell… - bioRxiv, 2023 - ncbi.nlm.nih.gov
SARS-CoV-2 variants acquire mutations in spike that promote immune evasion and impact
other properties that contribute to viral fitness such as ACE2 receptor binding and cell entry …

The SARS-CoV-2 Spike mutation D614G increases entry fitness across a range of ACE2 levels, directly outcompetes the wild type, and is preferentially incorporated …

WA Michaud, GM Boland, SA Rabi - bioRxiv, 2020 - biorxiv.org
Early in the current pandemic, the D614G mutation arose in the Spike protein of SARS-CoV-
2 and quickly became the dominant variant globally. Mounting evidence suggests D614G …

[HTML][HTML] Deep mutational scans of XBB. 1.5 and BQ. 1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution

AL Taylor, TN Starr - PLoS Pathogens, 2023 - journals.plos.org
Substitutions that fix between SARS-CoV-2 variants can transform the mutational landscape
of future evolution via epistasis. For example, large epistatic shifts in mutational effects …

Predictive profiling of SARS-CoV-2 variants by deep mutational learning

JM Taft, CR Weber, B Gao, RA Ehling, J Han, L Frei… - BioRxiv, 2021 - biorxiv.org
The continual evolution of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-
2) and the emergence of variants that show resistance to vaccines and neutralizing …

[PDF][PDF] Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain

JM Taft, CR Weber, B Gao, RA Ehling, J Han, L Frei… - Cell, 2022 - cell.com
The continual evolution of SARS-CoV-2 and the emergence of variants that show resistance
to vaccines and neutralizing antibodies threaten to prolong the COVID-19 pandemic …

[HTML][HTML] Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype

R Kugathasan, K Sukhova, M Moshe, P Kellam… - PLoS …, 2023 - journals.plos.org
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 …

[HTML][HTML] Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility

JA Plante, Y Liu, J Liu, H Xia, BA Johnson… - BioRxiv, 2020 - ncbi.nlm.nih.gov
A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19
pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to …

[HTML][HTML] Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies

M Alenquer, F Ferreira, D Lousa, M Valério… - PLoS …, 2021 - journals.plos.org
Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19
pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin …

[HTML][HTML] Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA. 1

A Moulana, T Dupic, AM Phillips, J Chang… - Nature …, 2022 - nature.com
The Omicron BA. 1 variant emerged in late 2021 and quickly spread across the world.
Compared to the earlier SARS-CoV-2 variants, BA. 1 has many mutations, some of which …

[HTML][HTML] Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs

HK Haddox, JG Galloway, B Dadonaite, JD Bloom… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Deep mutational scanning (DMS) is a high-throughput experimental technique that
measures the effects of thousands of mutations to a protein. These experiments can be …