SARS-CoV-2 and COVID-19 Research

The paper uses molecular dynamics simulations to analyze water-glycan interactions in SARS-CoV-2 spike protein states, revealing structural and dynamic differences that impact immune evasion.

This study isolates and characterizes SARS-CoV-2 from Kenya, showing its growth in Vero CCL-81 cells and identifying mutations in two isolates.

The paper predicts synthetic lethal antiviral targets by analyzing omics data and CRISPR KO screens, finding common targets across SARS-CoV-2 and influenza infections.

This paper generates and characterizes three monoclonal antibodies against SARS-CoV-2 RBD, showing varying efficacy in neutralization and detection assays.

CompCorona compares host transcriptome responses to SARS-CoV-2, SARS-CoV, and MERS-CoV using pre-processed datasets and provides functional analysis tools.

The paper shows JN.1 outcompetes BA.2.86 and other variants by evading antibodies more effectively, despite reduced ACE2 binding.

This study uses AlphaFold2 and molecular simulations to analyze how mutations in SARS-CoV-2 Spike protein variants balance ACE2 binding and antibody resistance through epistatic interactions.

This study uses computational methods to identify drugs targeting ACE2 and AT1R to mitigate cytokine storm in COVID-19, highlighting Lomefloxacin and Fostamatinib as promising candidates.

The paper uses long-read sequencing with a 2x tiled primer set to identify SARS-CoV-2 mutations and subtypes in Seoul, Korea, showing improved variant detection and genotype-patient characteristic correlation.

The paper identifies RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs, revealing new host factors involved in viral replication and antiviral defense.

This study uses ML to design diverse VHH antibodies that neutralize SARS-CoV-1 and SARS-CoV-2 variants, including Delta and Omicron BA.1.

This paper develops a pseudotyped HSV-1 virus expressing SARS-CoV-2 Spike protein to study its fusogenic activity and antibody neutralization.

This study identifies 51 direct interactions between SARS-CoV-2 proteins and human kinases, revealing altered kinase activity patterns and highlighting FER kinase inhibition by ORF6.

The paper uses phylogenetic analysis of coronavirus genomes to estimate the time and likely host reservoir of SARS-CoV-2 spillover into humans.

This study predicts binding affinity between SARS-CoV-2 variants BA.2.86 and JN.1 and antibodies/ACE2 using in silico modeling, finding minor reductions in affinity but no significant immune escape.

The paper designs an intranasal pan-coronavirus vaccine using epitopes from SARS-CoV-2 and zoonotic coronaviruses, showing immune responses in mice but needing further cross-reactivity testing.

This study shows a gorilla adenovirus-based vaccine provides durable immunity against SARS-CoV-2 in both airways of non-human primates, with enhanced protection from aerosol delivery and prime-boost regimens.

This study identifies sequence and structural similarities between SARS-CoV-2 helicase and human UPF1, suggesting interference with NMD pathway and potential pathogenic effects.

The paper identifies tissue-specific host proteins and miRNA networks influenced by SARS-CoV-2 ORF3a in lung, heart, and brain, suggesting potential drug targets.

The paper identifies immunological epitopes and receptor binding determinants of SARS-CoV spike protein using the Qubevirus platform, revealing key regions for ACE2 binding and antibody recognition.

This study uses mathematical modeling to analyze B cell and antibody dynamics against SARS-CoV-2 variants, showing reduced neutralization against Omicron and enhanced secondary response.

The paper assesses the virulence of the SARS-CoV-2 BA.2.86 variant in hamsters and finds it is attenuated compared to BA.2.75.

This study evaluates a multivalent mRNA vaccine against SARS-CoV-2 variants in mice, showing broad protection against multiple strains.

The paper develops a structure-based computational model to predict virus fitness by analyzing mutations in the SARS-CoV-2 spike protein's binding to ACE2 and antibodies.

This study shows that T-type calcium channel blockers reduce SARS-CoV-2 spread via apoptotic bodies and limit cytokine storms in macrophages.

This paper introduces a framework using genomic sequence data to predict the threat of novel SARS-CoV-2 lineages by analyzing co-evolving motifs and evaluates its performance across multiple lineages and countries.

GenSLMs use large language models to analyze SARS-CoV-2 genomes, enabling rapid identification of variants of concern and providing insights into evolutionary dynamics.

This study investigates how the P2' proline residue affects SARS-CoV-2 PLpro catalytic efficiency using molecular dynamics and substrate analysis.

This study shows ivermectin reduces SARS-CoV-2 viral burden in vitro but at concentrations that also cause cytotoxicity, suggesting its antiviral effect may be due to nonspecific membrane perturbation rather than specific antiviral activity.

This study identifies a bioactive peptide from a pearl oyster that inhibits SARS-CoV-2 infection and enhances ACE2 activity to treat related complications.