J. D. Bloom

The paper recovers deleted SARS-CoV-2 sequences from the early Wuhan epidemic, showing that market sequences are not representative and the progenitor had three mutations closer to bat coronaviruses.

This paper designs stabilized SARS-CoV-2 RBD variants using deep mutational scanning and structure-based design, showing improved thermal stability and manufacturability for vaccine applications.

This study maps all single-amino-acid mutations in avian PB2 conferring resistance to pimodivir, identifying known and novel mutations in multiple domains.

The paper compares the specificity of antibodies from the mRNA-1273 vaccine and natural infection, finding vaccine antibodies are more RBD-focused but have broader epitope coverage within the RBD.

The paper maps mutations in SARS-CoV-2 spike RBD that escape binding by three antibody classes and finds that plasma escape maps closely resemble those of a single antibody class targeting site E484.

This study characterizes the development of a V3-specific broadly neutralizing antibody from an HIV superinfection case, revealing unique epitope recognition and escape mechanisms.

This study identifies a class of broadly neutralizing antibodies targeting a conserved membrane-proximal epitope on influenza HA, showing their induction by a chimeric HA vaccine.

The paper maps SARS-CoV-2 RBD mutations that escape LY-CoV555 and its cocktail with LY-CoV016, identifying escape mutations in circulating variants and suggesting epitope diversification for improved antibody resilience.

This study maps mutations in the SARS-CoV-2 RBD that affect recognition by polyclonal human serum antibodies, identifying key sites like E484 that significantly reduce neutralization.

This study shows that human coronavirus 229E evolves antigenically to escape antibody immunity, suggesting the need for periodic vaccine updates.

The paper maps viral mutations in SARS-CoV-2 that escape two therapeutic antibodies, identifying escape mutations present in circulating strains.

This study maps the neutralizing and binding specificities of polyclonal rabbit serum against HIV Env trimers using mutational antigenic profiling and EMPEM.

This study maps mutations in the SARS-CoV-2 spike RBD that escape antibody recognition, revealing escape mutation patterns and enabling the design of antibody cocktails.

This paper describes an influenza-based vaccine for SARS-CoV-2 that induces neutralizing antibodies in mice comparable to natural infection.

The paper experimentally measures the effects of all amino-acid mutations in the SARS-CoV-2 RBD on protein folding and ACE2 binding, identifying constrained regions and tolerated mutations.

Phage-DMS combines immunoprecipitation of phage peptide libraries with deep mutational scanning to fine map antibody epitopes, refining known epitopes for HIV monoclonal antibodies.

This study shows that anti-NA antibodies can neutralize influenza viruses that use NA for receptor binding, enabling sensitive detection and escape mutant selection.

This paper provides a protocol for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein to measure neutralizing antibody activity in a luciferase-based assay.

The paper shows that synthetic tandem domain APOBEC3C proteins create more potent antiviral factors against HIV-1 than native A3C, with increased resistance to viral antagonism.

The paper develops a statistical mechanical model to predict antibody mixture activity based on epitope interactions and validates it using EGFR antibodies and engineered multidomain antibodies.

The paper evaluates genetic barriers to resistance against broadly neutralizing antibodies targeting the stem region of influenza H3 and H1 hemagglutinins, finding H3 has lower resistance barriers.

This study identifies HIV-1 Env mutations that enhance entry into macaque cells using deep mutational scanning, finding mutations that increase entry up to 38-fold and affect antibody sensitivity.

This study links influenza virus evolution within and between human hosts, finding that synonymous mutations accumulate globally while nonsynonymous mutations are purged, except at antigenic sites where selection favors them.

This study uses deep mutational scanning to map how Zika virus envelope protein mutations affect viral growth and antibody escape, revealing detailed functional and antigenic constraints.

This study identifies H3N2 HA RBS-targeting antibodies in humans, showing some can be broadly reactive despite sensitivity to substitutions near the RBS.

The paper maps how amino-acid mutations in influenza's hemagglutinin affect neutralization by polyclonal human sera, showing individual variation in escape mutations not observed in ferrets.

This study maps amino-acid mutations in avian influenza PB2 polymerase that enhance growth in human cells, identifying new adaptive mutations and their evolutionary constraints.

This study examines how genetic variation in influenza viruses contributes to heterogeneous immune responses in infected cells.

This study identifies additional resistance mutations to enfuvirtide using deep mutational scanning, expanding the known mechanisms of resistance.

This study characterizes two influenza B virus variants with NAI resistance, finding H273Y reduces fitness more than D197N in vivo, while D197N remains prevalent in surveillance.