Biology subjects

McCarthy, K. R.

Publications and source records attributed to McCarthy, K. R..

13 recordsLinked to original sources

bioRxiv2026

Antibody feedback limits specific B-cell entry and alters germinal center repertoires by antibody-antigen complexes

Antibody (Ab) feedback impacts germinal center (GC) responses. Mice given IgG1 or IgG2c recombinant Ab (rAb) specific for the receptor binding site (RBS) of H3 hemagglutinin (HA) and later immunized with the H3 HA trimer exhibited altered GC repertoires. Passive RBS rAb had no effect on the magnitude of ensuing primary GC responses but reduced the numbers of RBS-specific GC B cells. These losses were matched by increases in "unspecific" B cells which did not bind the HA immunogen, with no changes in B cells specific for distal epitopes. These effects were independent of IgG subclass. Higher doses of passive rAb resulted in reduced epitope-specific affinity maturation and clonal proliferation in GCs. Passive rAb generated Ab:HA complexes and favored recruitment of rare HA-specific GC B cells with enhanced avidity for the rAb:HA immune complex (IC). We show that some no- and low-affinity GC B cells represent responses to local ICs.

immunology↗

bioRxiv2026

Determinants in gammaretroviral Env dictate the production of neutralizing antibodies

Protective immune responses are shaped by the nature of the infectious pathogen. Some viral infections are self-limiting and stimulate lasting immunity, while others activate poor responses that fail to control the infection or prevent development of disease. Little is known concerning the specific viral determinants that control whether a given viral infection will result in protective immunity. Here, we demonstrate that strains of the gammaretrovirus, murine leukemia virus, differ in their ability to stimulate neutralizing antibody production via a noncanonical pathway. Additionally, we show that virus-specific production of neutralizing immune responses is unique to infection, suggesting that the activation of alternative antibody responses is triggered by the infectious process rather than the unique nature of specific viral antigens. Viral chimeras indicate that activation of neutralizing antiviral antibody production is determined by the receptor-binding domain, and that the surface subunit controls binding to and infection of various cell types. The ability of specific viral factors to determine the outcome of infection and the induction of distinctive immune responses between closely related retroviral strains provides an ideal model for the dissection of both host and viral determinants underlying the control of viral infection and the production of neutralizing antibodies. SUMMARYWe report here that retroviral envelope glycoprotein determines stimulation of GC B cell responses and the production of neutralizing antibodies in the absence of IFN{gamma}-signaling, thus defining the factors that stimulate non-canonical immune responses and further developing the knowledge required for vaccine development.

immunology↗

bioRxiv2025

Dairy cattle herds mount a characteristic antibody response to highly pathogenic H5N1 avian influenza viruses

An unprecedented outbreak of a highly pathogenic avian influenza virus, H5 clade 2.3.4.4b, was reported in United States dairy cattle during the spring of 2024. It has now spread to hundreds of herds across multiple states. In humans, antibodies to the hemagglutinin (HA) protein confer the strongest protection against infection. Human herd immunity limits viral spread but also drives the emergence of antigenic variants that escape dominant antibody responses. We used store-bought milk to profile the collective H5N1 antibody response of dairy cattle herds. We detected HA binding antibodies in specific samples from states with recent/ongoing outbreaks. These antibodies present in milk neutralized replicating virus expressing dairy cattle HA and neuraminidase (NA). Despite originating from independent vendors, dairies/plants, geographic regions, and time, antibodies present in these samples are remarkably similar in activity and HA binding specificity. The dominant antibody response was clade 2.3.4.4b HA specific, followed by cross-reactivity with other H5s. Whether the uniformity of the response is a pathway to achieve herd immunity or an avenue for antigenic variants to rapidly escape remains to be seen. SIGNIFICANCEEstablishing human herd immunity ends pandemics. For influenza viruses, this immunity drives continued antigenic evolution that enables viruses to infect once-immune individuals. An outbreak of highly pathogenic avian influenza virus was detected in dairy cattle in 2024 and has spread rapidly across herds and states. We report approaches to assess dairy cattle herd immunity using store-bought milk samples. Across samples separated by geography and time we find dairy cattle mount a strikingly similar antibody response that is strongest to the dairy cattle virus. Benchmarking immunity at this phase of the outbreak is important to understand either eradication or the emergence of antigenic variants that enable reinfection.

microbiology↗

bioRxiv2025

A replicating recombinant vesicular stomatitis virus model for dairy cattle H5N1 influenza virus glycoprotein evolution

A panzootic of highly pathogenic avian influenza (HPAI) H5N1 viruses from clade 2.3.4.4b has triggered a multistate outbreak in United States dairy cattle and an unknown number of human infections. HPAI viruses are handled in specialized biocontainment facilities. Ethical considerations limit certain experimental evolution experiments aimed at assessing viral resistance to potential therapeutics. We have developed a replicating recombinant vesicular stomatitis virus (rVSV) where we replaced its glycoprotein with the hemagglutinin (HA) and neuraminidase (NA) genes of a 2.3.4.4b H5N1 virus (rVSV-H5N1dc2024), which is free of these constraints. This virus grows to high titers and encodes a fluorescent reporter to track infection. We demonstrate the utility of rVSV-H5N1dc2024 in neutralization experiments, evaluating antibody escape and characterization of resistance mutations to NA inhibitors. rVSV-H5N1dc2024 or similar viruses may accelerate efforts to develop and evaluate interventions against this emerging threat to human and animal health. IMPORTANCEHighly pathogenic avian influenza H5 viruses have spread globally, established sustained transmission in mammals and caused human infections. Research on these viruses is restricted to high biocontainment laboratories. We report the characterization and utility of a surrogate, replicating virus that displays the two key influenza glycoproteins, hemagglutinin and neuraminidase, that can be safely handled in most research laboratories. This virus is amenable for the evaluation of antiviral antibodies and small molecule inhibitors and the evolution of viral resistance to these agents. This virus can enable a wider range of researchers to study H5 viruses of pandemic concern.

microbiology↗

bioRxiv2024

Pre-existing H1N1 immunity reduces severe disease with bovine H5N1 influenza virus

The emergence of highly pathogenic H5N1 avian influenza in dairy cattle herds across the United States has caused multiple mild human infections. There is an urgent need to understand the risk of spillover into humans. Here, we show that pre-existing immunity from the 2009 H1N1 pandemic influenza virus provided protection from mortality and severe clinical disease to ferrets intranasally infected with bovine H5N1. H1N1 immune ferrets exhibited a differential tissue tropism with little bovine H5N1 viral dissemination to organs outside the respiratory tract and significantly less H5N1 virus found in nasal secretions and the respiratory tract. Additionally, ferrets with H1N1 prior immunity produced antibodies that cross-reacted with H5N1 neuraminidase protein. Taken together, these results suggest that mild disease in humans may be linked to prior immunity to human seasonal influenza viruses.

microbiology↗

bioRxiv2024

Potential pandemic risk of circulating swine H1N2 influenza viruses

Influenza A viruses in swine have considerable genetic diversity and continue to pose a pandemic threat to humans. They were the source of the most recent influenza pandemic, and since 2010, novel swine viruses have spilled over into humans more than 400 times in the United States. Although these zoonotic infections generally result in mild illness with limited onward human transmission, the potential for sustained transmission of an emerging influenza virus between individuals due to lack of population level immunity is of great concern. Compiling the literature on pandemic threat assessment, we established a pipeline to characterize and triage influenza viruses for their pandemic risk and examined the pandemic potential of two widespread swine origin viruses. Our analysis revealed that a panel of human sera collected from healthy adults in 2020 has no cross-reactive neutralizing antibodies against an -H1 clade strain but do against a {gamma}-H1 clade strain. Swine H1N2 virus from the -H1 clade (-swH1N2) replicated efficiently in human airway cultures and exhibited phenotypic signatures similar to the human H1N1 pandemic strain from 2009 (H1N1pdm09). Furthermore, -swH1N2 was capable of efficient airborne transmission to both naive ferrets and ferrets with prior seasonal influenza immunity. Ferrets with H1N1pdm09 pre-existing immunity had reduced -swH1N2 viral shedding from the upper respiratory tract and cleared the infection faster. Despite this, H1N1pdm09-immune ferrets that became infected via the air could still onward transmit -swH1N2 with an efficiency of 50%. Taken together, these results indicate that this -swH1N2 strain has a higher pandemic potential, but a moderate level of impact since there is reduced replication fitness in animals with prior immunity.

microbiology↗

bioRxiv2023

A broad antibody class engages the influenza virus hemagglutinin head at its stem interface

Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to "universal" influenza immunity.

microbiology↗

bioRxiv2023

A class of antibodies that overcome a steric barrier to cross-group neutralization of influenza viruses

Antibody titers that inhibit the influenza virus hemagglutinin (HA) from engaging its receptor are the accepted correlate of protection from infection. Many potent antibodies with broad, intra-subtype specificity bind HA at the receptor binding site (RBS). One barrier to broad H1-H3 cross-subtype neutralization is an insertion (133a) between positions 133 and 134 on the rim of the H1 HA RBS. We describe here a class of antibodies that overcome this barrier. These genetically unrestricted antibodies are abundant in the human B-cell memory compartment. Analysis of the affinities of selected members of this class for historical H1 and H3 isolates suggest that they were elicited by H3 exposure and broadened or diverted by later exposure(s) to H1 HA. RBS mutations in egg-adapted vaccine strains cause the new H1 specificity of these antibodies to depend on the egg adaptation. The results suggest that suitable immunogens might elicit 133a-independent, H1-H3 cross neutralization by RBS-directed antibodies.

microbiology↗

bioRxiv2021

Deletion disrupts a conserved antibody epitope in a SARS-CoV-2 variant of concern

Multiple SARS-CoV-2 variants with altered antigenicity have emerged and spread internationally. In one lineage of global concern, we identify a transmitted variant with a deletion in its receptor binding domain (RBD) that disrupts an epitope which is conserved across sarbecoviruses. Overcoming antigenic variation by selectively focusing immune pressure on this conserved site may, ultimately, drive viral resistance.

microbiology↗

bioRxiv2020

A prevalent focused human antibody response to the influenza hemagglutinin head interface

Novel animal influenza viruses emerge, initiate pandemics and become endemic seasonal variants that have evolved to escape from prevalent herd immunity. These processes often outpace vaccine-elicited protection. Focusing immune responses on conserved epitopes may impart durable immunity. We describe a focused, protective antibody response, abundant in memory and serum repertoires, to a conserved region at the influenza hemagglutinin head interface. Structures of eleven examples, eight reported here, from seven human donors demonstrate the convergence of responses on a single epitope. The eleven are genetically diverse, with one class having a common, IG{kappa}V1-39, light chain. All of the antibodies bind HAs from multiple serotypes. The lack of apparent genetic restriction and potential for elicitation by more than one serotype may explain their abundance. We define the head interface as a major target of broadly protective antibodies with the potential to influence the outcomes of influenza infection.

immunology↗

bioRxiv2020

Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Zoonotic pandemics, like that caused by SARS-CoV-2, can follow the spillover of animal viruses into highly susceptible human populations. Their descendants have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire substitutions more slowly than other RNA viruses, due to a proofreading polymerase. In the spike glycoprotein, we find recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. They frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

microbiology↗

bioRxiv2020

The ancient fusogen EnvP(b)1 is expressed in human tissues and its structure informs the evolution of gammaretrovirus envelope proteins

Host genomes have acquired diversity from viruses through the capture of viral elements, often from endogenous retroviruses (ERVs). These viral elements contribute new transcriptional control elements and new protein encoding genes, and their refinement through evolution can generate novel physiological functions for the host. EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We show that EnvP(b)1 arose very early in the evolution of primates, i.e. at least 40-47 million years ago, but has nevertheless retained its ability to fuse primate cells. We have detected similar sequences in the genome of a lemur species, suggesting that a progenitor virus may have circulated 55+ million years ago. We demonstrate that EnvP(b)1 protein is expressed in multiple human tissues and is fully processed, rendering it competent to fuse cells. This activated fusogen is expressed in multiple healthy human tissues and is under purifying selection, suggesting that its expression is selectively advantageous. We determined a structure of the inferred receptor binding domain of human EnvP(b)1, revealing close structural similarities between this Env protein and those of currently circulating leukemia viruses, despite poor sequence conservation. This observation highlights a common scaffold from which novel receptor binding specificities have evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses and coopted elements alike. The function of EnvP(b)1 in primates remains unknown. SIGNIFICANCE STATEMENTOrganisms can access genetic and functional novelty by capturing viral elements within their genomes, where they can evolve to drive new cellular or organismal processes. We demonstrate that a retrovirus envelope gene, EnvP(b)1, has been maintained as a functional protein for 40 to [≥]55 million years and is expressed as a protein in multiple healthy human tissues. We believe it has an unknown function in primates. We determined the structure of its inferred receptor binding domain and compared it with the same domain in modern viruses. We find a common conserved architecture that underlies the varied receptor binding activity of divergent Env genes. The modularity and versatility of this domain may underpin the evolutionary success of this clade of fusogens.

microbiology↗

bioRxiv2018

Reconstruction of the cell entry pathway of an extinct virus

Endogenous retroviruses (ERVs), remnants of ancient germline infections, comprise 8% of the human genome. The most recently integrated includes human ERV-K (HERV-K) where several envelope (env) sequences remain intact. Viral pseudotypes decorated with one of those Envs are infectious. Using a recombinant vesicular stomatitis virus encoding HERV-K Env as its sole attachment and fusion protein (VSV-HERVK) we conducted a genome-wide haploid genetic screen to interrogate the host requirements for infection. This screen identified 11 genes involved in heparan sulfate biosynthesis. Genetic inhibition or chemical removal of heparan sulfate and addition of excess soluble heparan sulfate inhibit infection. Direct binding of heparin to soluble HERVK Env and purified VSV-HERVK defines it as critical for viral attachment. Cell surface bound VSV-HERVK particles are triggered to infect on exposure to acidic-pH, whereas acid pH pretreatment of virions blocks infection. Testing of additional endogenous HERV-K env sequences reveals they bind heparin and mediate acid pH triggered fusion. This work reconstructs and defines key steps in the infectious entry pathway of an extinct virus.\n\nAuthor SummaryThe genomes of all vertebrates are littered with the remains of once exogenous retroviruses. The properties of these ancient viruses that fostered germline colonization and their subsequent inheritance as genetic elements are largely unknown. The viral envelope protein (Env) dictates the cell entry pathway. Here we define host factors involved in the cell-entry of the youngest human ERV, HERV-K. Using a forward genetic screen, we identified heparan sulfate as a critical mediator of productive cell-entry. The abundance of this carbohydrate on almost all cells in the body suggests that HERV-K endogenization was a consequence of a broad tropism and not a specific targeting of germ cells. We demonstrate that multiple HERV-K Env protein encoded in the genome bind heparin. As HERV-K Envs are expressed in some transformed and virus-infected cells as well as during inflammation, it is tempting to speculate that this heparan sulfate binding property could be physiologically relevant during disease.

microbiology↗