Jesse D. Bloom
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View article: Author response: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
Author response: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Open
View article: Functional and antigenic constraints on the Nipah virus fusion protein
Functional and antigenic constraints on the Nipah virus fusion protein Open
Nipah virus is a highly pathogenic virus in the family Paramyxoviridae that utilizes two distinct surface glycoproteins to infect cells. The receptor-binding protein (RBP) binds host receptors whereas the fusion protein (F) merges viral an…
View article: Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses
Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses Open
View article: Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants Open
SARS-CoV-2 is under strong evolutionary selection to acquire mutations in its spike protein that reduce neutralization by human polyclonal antibodies. Here, we use pseudovirus-based deep mutational scanning to measure how mutations to the …
View article: Combined crystallographic fragment screening and deep mutational scanning enable discovery of Zika virus NS2B-NS3 protease inhibitors
Combined crystallographic fragment screening and deep mutational scanning enable discovery of Zika virus NS2B-NS3 protease inhibitors Open
View article: Profiling of HIV-1 elite neutralizer cohort reveals a CD4bs bnAb for HIV-1 prevention and therapy
Profiling of HIV-1 elite neutralizer cohort reveals a CD4bs bnAb for HIV-1 prevention and therapy Open
View article: Identification of a broad and potent V3 glycan site bNAb targeting an N332<sub>gp120</sub> glycan-independent epitope
Identification of a broad and potent V3 glycan site bNAb targeting an N332<sub>gp120</sub> glycan-independent epitope Open
Broadly neutralizing antibodies (bNAbs) against HIV-1 can suppress viremia in vivo and inform vaccine development. Here, we characterized 007, a V3 glycan site bNAb exhibiting high levels of antiviral activity against multiclade pseudoviru…
View article: Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025 Open
The hemagglutinin of human influenza virus evolves rapidly to erode neutralizing antibody immunity. Twice per year, new vaccine strains are selected with the goal of providing maximum protection against the viruses that will be circulating…
View article: Profiling a large HIV-1 elite neutralizer cohort reveals remarkable CD4bs bNAb for HIV-1 prevention and therapy
Profiling a large HIV-1 elite neutralizer cohort reveals remarkable CD4bs bNAb for HIV-1 prevention and therapy Open
Administration of HIV-1 neutralizing antibodies can suppress viremia and prevent infection in vivo . However, clinical use is challenged by broad envelope sequence diversity and rapid emergence of viral escape 1–9 . Here, we performed sing…
View article: Fostemsavir analog BMS-818251 has enhanced viral neutralization potency and similar escape mutation profile
Fostemsavir analog BMS-818251 has enhanced viral neutralization potency and similar escape mutation profile Open
BMS-818251, a fostemsavir analog, is a next-generation HIV-1 attachment inhibitor with enhanced potency and a similar resistance profile. By using ex vivo viral outgrowth assays with HIV+ donor samples, we demonstrate here that BMS-818251 …
View article: Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins
Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins Open
Chikungunya virus (CHIKV) infects both humans and mosquitoes during its transmission cycle. How the virus’s envelope proteins mediate entry in cells from such different species is unclear. MXRA8 is a receptor for CHIKV in mammalian cells, …
View article: Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants Open
SARS-CoV-2 is under strong evolutionary selection to acquire mutations in its spike protein that reduce neutralization by human polyclonal antibodies. Here we use pseudovirus-based deep mutational scanning to measure how mutations to the s…
View article: Stabilization of H5 highly pathogenic avian influenza hemagglutinin improves vaccine-elicited neutralizing antibody responses
Stabilization of H5 highly pathogenic avian influenza hemagglutinin improves vaccine-elicited neutralizing antibody responses Open
Transmission of highly pathogenic avian influenza from H5 clade 2.3.4.4b has expanded in recent years to infect large populations of birds and mammals, heightening the risk of a human pandemic. Influenza viruses adapted to transmission in …
View article: Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics
Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics Open
The ability of coronaviruses to recombine and cross species barriers affects human and animal health globally and is a pandemic threat 1,2 . FCoV-23 is a recently emerged, highly pathogenic recombinant coronavirus responsible for a widespr…
View article: RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera
RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera Open
Vaccines and monoclonal antibodies targeting the respiratory syncytial virus (RSV) fusion protein (F) have recently begun to be widely used to protect infants and high-risk adults. Some other viral proteins evolve to erode polyclonal antib…
View article: Replaying germinal center evolution on a quantified affinity landscape
Replaying germinal center evolution on a quantified affinity landscape Open
Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition between GC B cells drives increased affin…
View article: Author response: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
Author response: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Open
View article: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Open
Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 H…
View article: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Open
Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 H…
View article: The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree
The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree Open
Several years ago, I published a paper that described the discrepancy between outgroup and date-based methods for rooting the SARS-CoV-2 phylogenetic tree, and proposed the discrepancy could arise from biases among the available early vira…
View article: The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure
The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure Open
RNA viruses like SARS-CoV-2 have high mutation rates, which contribute to their rapid evolution. Mutation rates depend on mutation type and can vary between sites in a virus’s genome. Understanding this variation can shed light on the muta…
View article: Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin
Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin Open
The evolution of human influenza virus hemagglutinin (HA) involves simultaneous selection to acquire antigenic mutations that escape population immunity while preserving protein function and stability. Epistasis shapes this evolution, as a…
View article: Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations
Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations Open
Rabies virus causes nearly 60,000 human deaths annually. Antibodies that target the rabies glycoprotein (G) are being developed as post-exposure prophylactics, but mutations in G can render such antibodies ineffective. Here, we use pseudov…
View article: A broad antibody with enhanced HIV-1 neutralization via bispecific antibody-mediated prepositioning
A broad antibody with enhanced HIV-1 neutralization via bispecific antibody-mediated prepositioning Open
View article: Comprehensive maps of escape mutations from antibodies 10-1074 and 3BNC117 for Envs from two divergent HIV strains
Comprehensive maps of escape mutations from antibodies 10-1074 and 3BNC117 for Envs from two divergent HIV strains Open
Antibodies capable of neutralizing many strains of HIV are being explored as prophylactic and therapeutic agents, but viral escape mutations pose a major challenge. Efforts have been made to experimentally define the escape mutations from …
View article: SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals
SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals Open
The immune response to viral infection is shaped by past exposures to related virus strains, a phenomenon known as imprinting. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), much of the population has been imprinted by a…
View article: Functional and antigenic landscape of the Nipah virus receptor-binding protein
Functional and antigenic landscape of the Nipah virus receptor-binding protein Open
Nipah virus recurrently spills over to humans, causing fatal infections. The viral receptor-binding protein (RBP or G) attaches to host receptors and is a major target of neutralizing antibodies. Here, we use deep mutational scanning to me…
View article: High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Open
Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 H…
View article: RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera
RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera Open
Vaccines and monoclonal antibodies targeting the respiratory syncytial virus (RSV) fusion protein (F) have recently begun to be widely used to protect infants and high-risk adults. Some other viral proteins evolve to erode polyclonal antib…
View article: Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern
Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern Open
The ongoing emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that ar…