SARS-CoV-2 and COVID-19 Research

CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest by analyzing lineage frequency dynamics and antigenic changes from GISAID data.

This study analyzes the structural and functional interactions of SARS-CoV-2 Nsp3 with the 5' UTR of the viral genome, identifying key domains involved in binding and translocation.

This paper shows that SARS-CoV-2 Omicron lineages replicate using a specific ACE2 pool that does not complex with TMPRSS2, unlike pre-Omicron variants.

This paper describes the discovery of S-892216, a potent SARS-CoV-2 3CLpro inhibitor with antiviral activity against multiple variants and low cross-resistance to existing drugs.

This paper develops a multi-epitope vaccine targeting conserved B- and T-cell epitopes from SARS-CoV-2, showing protection against Delta and Omicron variants in a mouse model.

The paper develops a kinetic model of the coronavirus main protease incorporating dimerization and ligand binding, showing how inhibitors and substrates affect enzyme activity differently.

This study optimizes a human monoclonal antibody to enhance its neutralization of SARS-CoV-2 variants, including subvariants XEC and LP.8.1, through structural analysis and engineering.

The paper examines how mutations and a deletion in the KP.3.1.1 SARS-CoV-2 spike protein affect ACE2 binding and antibody escape, revealing structural and functional insights into its evolution.

The paper investigates how aging and viral mutations affect pan-coronavirus immunity, finding reduced T cell responses in older individuals and mutation-driven impact on humoral immunity.

This study shows that Spike-specific IgG4 generated after BNT162b2 vaccination can inhibit effector functions when competing with other IgG subclasses, despite overall increased neutralization and effector activity.

The paper analyzes synonymous mutations in six SARS-CoV-2 Variants of Concern to assess their impact on RNA secondary structure and stability, finding minimal effects.

SARITA is a large language model that generates synthetic SARS-CoV-2 Spike S1 sequences, accurately predicting mutations in future variants like Delta and Omicron.

This paper characterizes the conjugation sites of a SARS-CoV-2 vaccine using LC-MS/MS and identifies 12 and 18 conjugation sites through different analytical strategies.

This study maps polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 vaccines using EMPEM, revealing the NTD supersite as an immunodominant epitope vulnerable to variant mutations.

This study shows that the proton-activated chloride channel inhibits SARS-CoV-2 entry by blocking endosomal acidification and the cathepsin-dependent pathway.

This study uses human iPSC-derived bronchial organoids to show SARS-CoV-2 causes prolonged infection, cilia destruction, and differential innate immune responses in healthy and COPD models.

This study compares early nasal cavity damage caused by SARS-CoV-2 D614G, Delta, and Omicron variants in Syrian hamsters, finding Delta causes more rapid viral spread and damage at 1 dpi.

This study introduces a back-projection model to improve inference from sparse genomic surveillance data by estimating infection times and accounting for sampling biases in SARS-CoV-2 variants.

This study investigates how Class 4 and Class 5 antibodies modulate the conformational dynamics and immune escape of SARS-CoV-2 spike protein through allosteric effects and mutational scanning.

This study examines T cell and antibody responses in vaccinated individuals over three years, finding stable T cell responses and increased regulatory T cells after multiple boosters.

This paper develops a three-in-one mucosal vaccine, 3Rs-NC, that elicits broad neutralizing antibodies against three ACE2-using sarbecovirus clusters and provides durable protection in mice.

This paper identifies Nsp14's role in activating pro-inflammatory pathways and downregulating IFN receptors, revealing broader immune evasion mechanisms in SARS-CoV-2.

This study compares host immune responses to SARS-CoV-2 Delta and Omicron variants using RNA-seq data, identifying distinct hub genes associated with different immune pathways and outcomes.

This study evaluates PI3K inhibitors against beta-coronaviruses, finding broad-spectrum antiviral activity and complex immunomodulatory effects.

The paper shows that the T9I mutation in the SARS-CoV-2 E protein confers autophagy resistance in Omicron variants, contributing to their spread.

This study shows that female mice tolerate low-dose MERS-CoV infection but experience severe inflammation with high dose, while male mice have uniformly lethal outcomes regardless of dose.

This study examines how rituximab and immune-checkpoint inhibitors affect immune responses to a COVID-19 booster vaccine, finding rituximab impairs interferon response and ICI maintains normal immune profiles.

This study shows that Poldip2 deficiency reduces lung inflammation and tissue damage in a mouse model of SARS-CoV-2 infection without affecting viral susceptibility.

The paper compares MERS-CoV variants from Arabian and African camels, showing Arabian viruses are more resistant to inhibition by human soluble DPP4 due to the Q1020R mutation in the spike protein.

This paper describes the optimization of a SARS-CoV-2 Mpro inhibitor to address genotoxic and metabolic liabilities, leading to improved in vivo efficacy and exposure.