AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between …

N Raisinghani, M Alshahrani, G Gupta… - The Journal of …, 2024 - ACS Publications
In this study, we combined AlphaFold-based atomistic structural modeling, microsecond
molecular simulations, mutational profiling, and network analysis to characterize binding …

[HTML][HTML] Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency

E Abousamra, M Figgins, T Bedford - Medrxiv, 2023 - ncbi.nlm.nih.gov
Genomic surveillance of pathogen evolution is essential for public health response,
treatment strategies, and vaccine development. In the context of SARS-COV-2, multiple …

[HTML][HTML] Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and …

N Raisinghani, M Alshahrani, G Gupta… - International Journal of …, 2024 - mdpi.com
In this study, we performed a computational study of binding mechanisms for the SARS-CoV-
2 spike Omicron XBB lineages with the host cell receptor ACE2 and a panel of diverse class …

[HTML][HTML] Rapid spread of the SARS-CoV-2 JN. 1 lineage is associated with increased neutralization evasion

L Zhang, A Dopfer-Jablonka, A Cossmann, MV Stankov… - Iscience, 2024 - cell.com
Summary In July/August 2023, the highly mutated severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) BA. 2.86 lineage emerged and its descendant JN. 1 is on track …

[HTML][HTML] Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern

AA Rubio, VA Baharani, B Dadonaite, M Parada… - bioRxiv, 2024 - ncbi.nlm.nih.gov
The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the
effectiveness of antibody therapeutics necessitates development of next-generation …

[HTML][HTML] Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

CR Carr, KHD Crawford, M Murphy, JG Galloway… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Lassa virus is estimated to cause thousands of human deaths per year, primarily due to
spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody …

Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN. 1

F Jian, J Wang, A Yisimayi, W Song, Y Xu, X Chen… - bioRxiv, 2024 - biorxiv.org
The continuous evolution of SARS-CoV-2, particularly the emergence of the BA. 2.86/JN. 1
lineage replacing XBB lineages, necessitates a re-evaluation of current vaccine strategies …

Reverse mutational scanning of spike BA. 2.86 identifies the epitopes contributing to immune escape from polyclonal sera

N Bdeir, T Lüddecke, H Maaß, S Schmelz, H Jacobsen… - medRxiv, 2024 - medrxiv.org
The recently detected Omicron BA. 2.86 lineage contains more than 30 amino acid
mutations relative to BA. 2. Here, we identify the epitopes driving immune escape of BA. 2.86 …

[HTML][HTML] Concepts and methods for predicting viral evolution

M Meijers, D Ruchnewitz, J Eberhardt, M Karmakar… - ArXiv, 2024 - ncbi.nlm.nih.gov
The seasonal human influenza virus undergoes rapid evolution, leading to significant
changes in circulating viral strains from year to year. These changes are typically driven by …

Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission

M Benlarbi, S Ding, E Belanger, A Tauzin, R Poujol… - bioRxiv, 2024 - biorxiv.org
The continued evolution of SARS-CoV-2 requires persistent monitoring of its subvariants.
Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections …