[HTML][HTML] Omicron variant (B. 1.1. 529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2?

M Dhawan, ARA Saied, S Mitra, FA Alhumaydhi… - Biomedicine & …, 2022 - Elsevier
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been
reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid …

COVID-19: challenges of viral variants

JL Jacobs, G Haidar, JW Mellors - Annual Review of Medicine, 2023 - annualreviews.org
The COVID-19 pandemic has been accompanied by SARS-CoV-2 evolution and
emergence of viral variants that have far exceeded initial expectations. Five major variants of …

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ. 1.1 variant

J Ito, R Suzuki, K Uriu, Y Itakura, J Zahradnik… - Nature …, 2023 - nature.com
In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These
variants convergently acquired amino acid substitutions at critical residues in the spike …

Deep-learning-enabled protein–protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution

G Wang, X Liu, K Wang, Y Gao, G Li… - Nature Medicine, 2023 - nature.com
Host–pathogen interactions and pathogen evolution are underpinned by protein–protein
interactions between viral and host proteins. An understanding of how viral variants affect …

Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA. 1 and BA. 2 receptor-binding domains

TN Starr, AJ Greaney, CM Stewart, AC Walls… - PLoS …, 2022 - journals.plos.org
SARS-CoV-2 continues to acquire mutations in the spike receptor-binding domain (RBD)
that impact ACE2 receptor binding, folding stability, and antibody recognition. Deep …

Contributions of adaptation and purifying selection to SARS-CoV-2 evolution

RA Neher - Virus Evolution, 2022 - academic.oup.com
Continued evolution and adaptation of SARS-CoV-2 has led to more transmissible and
immune-evasive variants with profound impacts on the course of the pandemic. Here I …

Omicron Spike protein has a positive electrostatic surface that promotes ACE2 recognition and antibody escape

HH Gan, J Zinno, F Piano, KC Gunsalus - Frontiers in Virology, 2022 - frontiersin.org
High transmissibility is a hallmark of the Omicron variant of SARS-CoV-2. Understanding the
molecular determinants of Omicron's transmissibility will impact development of intervention …

Coordinated evolution at amino acid sites of sars-cov-2 spike

AD Neverov, G Fedonin, A Popova, D Bykova… - Elife, 2023 - elifesciences.org
SARS-CoV-2 has adapted in a stepwise manner, with multiple beneficial mutations
accumulating in a rapid succession at origins of VOCs, and the reasons for this are unclear …

Exploring and learning the universe of protein allostery using artificial intelligence augmented biophysical and computational approaches

S Agajanian, M Alshahrani, F Bai, P Tao… - Journal of chemical …, 2023 - ACS Publications
Allosteric mechanisms are commonly employed regulatory tools used by proteins to
orchestrate complex biochemical processes and control communications in cells. The …

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants

Q Yan, X Gao, B Liu, R Hou, P He, Y Ma… - Nature …, 2024 - nature.com
Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity
established by infection and vaccination. A connection between population immunity and …