J. D. Bloom

Functional and antigenic landscape of the Nipah virus receptor binding protein

This study uses deep mutational scanning to analyze how mutations in the Nipah virus receptor-binding protein affect function, receptor binding, and antibody escape, revealing constrained regions and limited antigenic variation in natural strains.

Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination

This study compares IgG antibody responses from SARS-CoV-2 infection, vaccination, and hybrid immunity, finding that hybrid immunity retains the imprint of the initial exposure and enhances antibody breadth and affinity.

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

This paper computationally redesigns an antibody to restore potency against SARS-CoV-2 Omicron subvariants while maintaining efficacy against Delta and other variants.

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

This study develops a high-throughput sequencing-based neutralization assay to measure antibody titers against multiple influenza strains and finds that vaccination effects vary by individual and prior vaccination history.

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

The paper maps how HA mutations affect neutralization by serum from different age groups, showing age-dependent antigenic effects and implications for viral evolution.

Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades

This study uses deep mutational scanning to assess how mutations in SARS-CoV-2 spike proteins affect ACE2 binding, cell entry, and serum escape, linking these effects to clade growth rates.

The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies

This study identifies how single mutations in Zika virus envelope protein affect neutralization by broadly and narrowly specific antibodies, finding that broad antibodies are harder to escape.

Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market

The paper analyzes metagenomic data from the Huanan Seafood Market to assess the relationship between SARS-CoV-2 reads and animal species, finding no consistent correlation between viral reads and susceptible species.

Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking

This study identifies two antibodies that neutralize all SARS-CoV-2 variants by locking the spike protein in a down conformation, showing a novel mechanism and potential for prophylaxis.

Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning

This study maps the neutralizing specificity of human anti-HIV serum using deep mutational scanning to identify Env mutations affecting neutralization by polyclonal sera.

Fitness effects of mutations to SARS-CoV-2 proteins

The paper estimates fitness effects of SARS-CoV-2 mutations using phylogenetic data, finding most mutations are neutral or deleterious, with some accessory proteins under weak selection.

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection

This study identifies four broad, potent monoclonal antibodies against SARS-CoV-2 spike protein that neutralize multiple variants, including Omicron and XBB.1.5, targeting conserved regions with high functional constraint.

Evolution of the SARS-CoV-2 mutational spectrum

This study analyzes changes in the mutation spectrum of SARS-CoV-2 across millions of sequences, finding shifts in mutation rates, particularly a decrease in G[->]T mutations in Omicron compared to early clades.

A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike

This paper introduces a pseudovirus system for deep mutational scanning of SARS-CoV-2 spike protein mutations, showing how they affect antibody neutralization and infection.

Evolution of antibody immunity following Omicron BA.1 breakthrough infection

This study tracks antibody responses six months after Omicron BA.1 breakthrough infection and finds reduced neutralizing antibodies and memory B cells, with public clones dominating and predicting new sublineages.

Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains

This study uses deep mutational scanning to analyze how mutations in the Omicron BA.1 and BA.2 RBDs affect ACE2 binding, RBD folding, and antibody escape, identifying epistatic shifts and lineage-specific changes.

A biophysical model of viral escape from polyclonal antibodies

This paper introduces a biophysical model to predict viral escape from polyclonal antibodies by analyzing how mutations affect antibody activity against specific epitopes.

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

The paper maps how mutations in the SARS-CoV-2 Omicron BA.1 RBD affect antibody binding affinity through systematic analysis of 32,768 genotypes against four monoclonal antibodies.

Influenza virus transcription and progeny production are poorly correlated in single cells

This study measures both viral transcription and progeny production in single influenza-infected cells, finding they are poorly correlated.

Receptor binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2

This study shows that RBD antibodies contribute more to SARS-CoV-2 neutralization when target cells have high ACE2 expression, highlighting ACE2 levels as a critical experimental factor.

Molecular fate-mapping of serum antibodies reveals the effects of antigenic imprinting on repeated immunization

This study uses molecular fate-mapping to show that repeated immunization preferentially reuses initial B cell clones over recruiting new ones, with imprinting effects decreasing as antigenic distance increases.

Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1

This study identifies compensatory epistasis in SARS-CoV-2 Omicron BA.1 that maintains ACE2 affinity despite antibody-escape mutations.

Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models

This study designs mosaic RBD nanoparticles to elicit antibodies against conserved sarbecovirus epitopes, showing broader protection against SARS-CoV-2 variants and animal sarbecoviruses in animal models.

The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes

The paper examines the antibody response to the SARS-CoV-2 Delta variant, showing it targets class 1 and 2 epitopes more than class 3, and that mutations in these regions reduce antibody binding.

Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution

The paper analyzes epistatic shifts in SARS-CoV-2 RBD mutations across variants to understand how they influence ACE2 binding and future evolution.

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

This study investigates SARS-CoV-2 transmission on a fishing boat, finding low within-host viral diversity and limited viral evolution during the outbreak.

Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail

The paper examines structural changes in the SARS-CoV-2 spike E406W mutant that reduce neutralization by a monoclonal antibody cocktail and alters epitope recognition.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

An antibody-escape calculator for mutations to the SARS-CoV-2 receptor-binding domain

The paper develops an antibody-escape calculator to estimate the antigenic effects of mutations in the SARS-CoV-2 RBD, correlating with neutralization assays and highlighting Omicron's antigenic properties.