Chengjin Ye

A bireporter recombinant SARS-CoV-2 Omicron BA.5 for in vitro and in vivo studies

This paper develops a bireporter recombinant SARS-CoV-2 Omicron BA.5 strain for tracking viral infections and testing antivirals and neutralizing antibodies in vitro and in vivo.

Scarless SARS-CoV-2 Genome Engineering and Variant Analysis

This paper develops a scarless genome engineering system for SARS-CoV-2 to study protease inhibitors and drug resistance mechanisms, showing improved antiviral potency when combined with drug efflux inhibitors.

Mutations in SARS-CoV-2 Nsp1 are critical determinants of viral pathogenicity in mice

This study identifies critical residues in SARS-CoV-2 Nsp1 that determine viral pathogenicity in mice by reducing replication and immune response severity.

Enhanced Pathogenicity and Contact Transmissibility of Human-origin Avian Influenza H5N1 Clade 2.3.4.4b Genotype B3.13 Compared to D1.1 in Ferrets

This study compares the pathogenicity and transmissibility of two H5N1 genotypes in ferrets, finding B3.13 is more pathogenic and transmissible than D1.1, while D1.1 acquires adaptive mutations rapidly.

Recovery of proofreading-impaired SARS-CoV-2 reveals a mutator phenotype and an ExoN activity threshold for viability

This paper shows SARS-CoV-2 can tolerate reduced proofreading activity but requires a minimal ExoN activity threshold for viability, leading to a mutator phenotype and reduced replication efficiency.

Development and characterization of mouse-adapted recombinant SARS-CoV-2 expressing reporter genes

This paper develops a recombinant SARS-CoV-2 virus expressing reporter genes to track viral infection in wild-type mice, showing it can be used for vaccine and antiviral research without needing transgenic models.

Identification and characterization of a SARS-CoV-2 Mpro G23 deletion ensitrelvir-resistant mutant

This study identifies and characterizes a SARS-CoV-2 Mpro G23 deletion mutant resistant to ensitrelvir but not to nirmatrelvir or remdesivir.

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

A single PA-X mutation in bovine-origin H5N1 influenza virus reduces pathogenicity in mice

This paper identifies a PA-X mutation in H5N1 influenza virus that reduces pathogenicity in mice by modulating immune responses rather than polymerase activity.

SARS-CoV-2 and MERS-CoV disrupt host protein synthesis via nsp1 with differential effects on the integrated stress response

This study compares how SARS-CoV-2 and MERS-CoV nsp1 proteins affect host protein synthesis and the integrated stress response, revealing differential impacts on eIF2 phosphorylation and stress granule formation.

SARS-CoV-2 Nonstructural Protein 3 Remodels the Phosphorylation of Target Proteins via Protein-Protein Interactions

This paper identifies NSP3 as a viral phosphatase that interacts with N protein and IRF3 to modulate host phosphorylation and suppress antiviral signaling during SARS-CoV-2 infection.

The ORF6 accessory protein contributes to SARS-CoV-2 virulence and pathogenicity in the naturally susceptible feline model of infection

This study shows that deleting ORF6 from SARS-CoV-2 reduces virulence and pathogenicity in cats, with decreased immune suppression and reduced viral replication.

A cocktail of SARS-CoV-2 spike stem helix domain and receptor binding domain human monoclonal antibodies prevent the emerge of viral escape mutants

This study shows that a combination of antibodies targeting both the SARS-CoV-2 spike protein's receptor binding domain (RBD) and stem helix (SH) domains prevents the emergence of viral escape mutants.

Identification of protective human monoclonal antibodies using a K18 hACE2 transgenic mouse SARS-CoV-2 challenge model

This study identifies protective human monoclonal antibodies against SARS-CoV-2 using a K18 hACE2 transgenic mouse model, showing that in vivo testing improves accuracy over in vitro assays.

A Human H5N1 Influenza Virus Expressing Bioluminescence for Evaluating Viral Infection and Identifying Therapeutic Interventions

This paper develops a bioluminescent H5N1 influenza virus to track infection and test antiviral drugs in vitro and in vivo.

A luminescent attenuated SARS-CoV-2 for the identification and validation of drug-resistant mutants

This paper develops an attenuated SARS-CoV-2 virus expressing nanoluciferase to identify and validate drug-resistant mutants to nirmatrelvir without using wild-type virus.

Targeting ROCK Signaling Mitigates Influenza Virus-Induced Fibrogenesis in Human Airway Organoids

This study shows that inhibiting the ROCK signaling pathway reduces influenza virus-induced fibrosis in human airway organoids.

Deletion of a KSF Motif Attenuates NSP1 Host Cell Translation Shutoff and Impairs SARS-CoV-2 Virulence

This study shows that a deletion in the NSP1 protein of SARS-CoV-2 variants reduces virulence by impairing host translation shutoff, suggesting NSP1 as a target for antiviral strategies.

Enhanced RNA replication and pathogenesis in recent SARS-CoV-2 variants harboring the L260F mutation in NSP6

This study identifies the L260F mutation in NSP6 as enhancing RNA replication and pathogenesis in recent SARS-CoV-2 variants, independent of Spike function.

A Live Attenuated Vaccine Candidate against Emerging Highly Pathogenic Cattle-Origin 2.3.4.4b H5N1 Viruses

This paper develops a live attenuated vaccine candidate, LPhTXdNS1, against H5N1 influenza viruses and shows it is safe, immunogenic, and protective in mice.

Identification of Amino Acid Residues Responsible for Differential Replication and Pathogenicity of Avian Influenza Virus H5N1 Isolated from Human and Cattle in Texas, US

This study identifies amino acid changes in the PB2 protein of H5N1 HPAIV that enhance replication and pathogenicity in human cells and mice.

Replication Kinetics, Pathogenicity and Virus-induced Cellular Responses of Cattle-origin Influenza A(H5N1) Isolates from Texas, United States

This study compares replication and pathogenicity of cattle-origin H5N1 influenza viruses in mammals and birds, finding higher replication efficiency and pathogenicity in human-adapted isolates.

Potent neutralization by a receptor binding domain monoclonal antibody with broad specificity for SARS-CoV-2 JN.1 and other variants

This study develops a monoclonal antibody that broadly neutralizes multiple SARS-CoV-2 variants, including JN.1, and shows its protective efficacy in mice.

Cellular N-myristoyl transferases Are Required for Mammarenavirus Multiplication

This study shows that NMT inhibition reduces mammarenavirus replication by impairing Z protein budding and GP2 fusion activity.

Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories

The paper systematically analyzes proteomic and genomic data of SARS-CoV-2 variants to identify how mutations affect viral gene expression, host interactions, and immune evasion.