In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives

MS Sohail, SF Ahmed, AA Quadeer… - Advanced drug delivery …, 2021 - Elsevier
Growing evidence suggests that T cells may play a critical role in combating severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, COVID-19 vaccines that can …

Protein engineering strategies for rational immunogen design

TM Caradonna, AG Schmidt - npj Vaccines, 2021 - nature.com
Antibody immunodominance refers to the preferential and asymmetric elicitation of
antibodies against specific epitopes on a complex protein antigen. Traditional vaccination …

Learning the language of viral evolution and escape

B Hie, ED Zhong, B Berger, B Bryson - Science, 2021 - science.org
The ability for viruses to mutate and evade the human immune system and cause infection,
called viral escape, remains an obstacle to antiviral and vaccine development …

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

J Rodriguez-Rivas, G Croce, M Muscat… - Proceedings of the …, 2022 - pnas.org
The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) is a major concern given their potential impact on the transmissibility and …

GEMME: a simple and fast global epistatic model predicting mutational effects

E Laine, Y Karami, A Carbone - Molecular biology and evolution, 2019 - academic.oup.com
The systematic and accurate description of protein mutational landscapes is a question of
utmost importance in biology, bioengineering, and medicine. Recent progress has been …

Map** mutational effects along the evolutionary landscape of HIV envelope

HK Haddox, AS Dingens, SK Hilton, J Overbaugh… - Elife, 2018 - elifesciences.org
The immediate evolutionary space accessible to HIV is largely determined by how single
amino acid mutations affect fitness. These mutational effects can shift as the virus evolves …

Relationship between latent and rebound viruses in a clinical trial of anti–HIV-1 antibody 3BNC117

YZ Cohen, JCC Lorenzi, L Krassnig… - Journal of Experimental …, 2018 - rupress.org
A clinical trial was performed to evaluate 3BNC117, a potent anti–HIV-1 antibody, in infected
individuals during suppressive antiretroviral therapy and subsequent analytical treatment …

Direct-acting antiviral resistance of Hepatitis C virus is promoted by epistasis

H Zhang, AA Quadeer, MR McKay - Nature communications, 2023 - nature.com
Direct-acting antiviral agents (DAAs) provide efficacious therapeutic treatments for chronic
Hepatitis C virus (HCV) infection. However, emergence of drug resistance mutations (DRMs) …

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

M Li, D Oliveira Passos, Z Shan, SJ Smith, Q Sun… - Science …, 2023 - science.org
HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is
mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors …