Biology subjects

Anthony, S. J.

Publications and source records attributed to Anthony, S. J..

11 recordsLinked to original sources

bioRxiv2026

Proteomic comparison of Marburg and Kasokero virus infection in natural host Egyptian rousette bat reveals distinct antiviral pathways

Bats are natural reservoir hosts for numerous zoonotic viruses, yet the molecular mechanisms enabling viral persistence without overt disease remain incompletely understood. The Egyptian rousette bat (Rousettus aegyptiacus, ERB) is the sole known natural reservoir of Marburg virus (MARV) and a key host in the enzootic cycle of the tick-borne Kasokero virus (KASV), providing a unique system to compare host responses to different RNA viruses within the same species. Here, we applied serial cross-sectional serum proteomics integrated with tissue-specific viral kinetics to characterize systemic host responses to experimental MARV and KASV infection in captive-reared bats. Nearly 16 % of detected proteins (67/419) were found exclusively in infected animals, yet canonical acute inflammatory signatures driving pathology in other susceptible hosts were absent (e.g., in humans and non-human primates). Differential abundance and detection analyses identified both shared and virus-dependent responses, with MARV infection eliciting limited and transient perturbations, while KASV induced broader and more sustained engagement of complement, lectin pathway, and hepatometabolic proteins. Network-based analysis uncovered coordinated proteasome modules, including circulating immunoproteasome complexes, consistent with enhanced antigen-processing capacity is a feature of these virus-host dynamics. Together, these findings reveal how ERBs mount structured, virus-dependent systemic responses, offering new insight into mechanisms underlying viral infection in natural reservoir hosts.

systems biology↗

bioRxiv2026

From receptor binding to biogeography: Multi-scale prediction of filovirus hosts in bats

Forecasting zoonotic risk requires identifying which host species are biologically susceptible to infection, yet susceptibility is rarely predicted using frameworks that integrate molecular mechanisms with macroecology. Filoviruses, a diverse group of bat-associated viruses that include Ebola and Marburg viruses, illustrate this challenge: viral entry depends on interactions between viral glycoproteins and the host receptor NPC1, and host ecology and distribution determine opportunity of viral entry. Additionally, receptor sequence data used for informing viral entry are available for only a small fraction of bat species. Here, we extend virus-specific susceptibility prediction across the global diversity of bats by integrating experimentally measured and physicochemically inferred virus-receptor binding strengths with phylogenetic, ecological, and environmental data. Using boosted regression models trained on binding assay labels, we generate predictions of NPC1-mediated binding strength for more than 1,300 bat species. Predicted susceptibility is strongly structured by evolutionary relationships, with high binding concentrated in particular bat lineages, but is further differentiated within clades by morphology, life-history strategy, and environmental context. Strikingly, macroevolutionary structure alone recovers interaction patterns originally derived from amino acid-level physicochemistry, indicating that information about receptor-mediated compatibility is recoverable from host evolutionary history and ecological traits. Predicted high binding strength extends well beyond historically recognized outbreak regions, suggesting that the fundamental host range of filoviruses may be substantially broader than their currently realized distribution. By scaling receptor biology to global host diversity, this multi-scale framework expands mechanistic susceptibility forecasting beyond species with available molecular data and provides a generalizable approach for integrating molecular and ecological information in zoonotic prediction.

ecology↗

bioRxiv2026

Generation-Establishment Tradeoffs Shape the Temporal Window of Recombinant Evolution

Recent viral coinfection experiments show that recombinant genomes are generated readily and depend strongly on infection timing and order, yet only a small fraction give rise to persistent lineages. We develop a hybrid deterministic-stochastic framework that resolves this discrepancy by coupling density-dependent recombinant generation with stochastic establishment of rare lineages. The resulting hazard of successful lineage formation is generically non-monotonic, increasing with parental abundance through enhanced generation while decreasing under competitive suppression, and exhibits a unique interior maximum in parental-density space. As parental populations evolve, their trajectory across this hazard landscape defines a sharply localized temporal window of evolutionary opportunity. These results reveal a general principle: evolutionary success is determined not only by intrinsic fitness, but by when variants arise within a dynamically changing ecological context.

biophysics↗

bioRxiv2021

Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae

As part of a broad One Health surveillance effort to detect novel viruses in wildlife and people, we report several paramyxoviruses sequenced primarily from bats during 2013 and 2014 in Brazil and Malaysia, including seven from which we recovered full-length genomes. Of these, six represent the first full-length paramyxovirus genomes sequenced from the Americas, including two sequences which are the first full-length bat morbillivirus genomes published to date. Our findings add to the vast number of viral sequences in public repositories that have been increasing considerably in recent years due to the rising accessibility of metagenomics. Taxonomic classification of these sequences in the absence of phenotypic data has been a significant challenge, particularly in the paramyxovirus subfamily Orthoparamyxovirinae, where the rate of discovery of novel sequences has been substantial. Using pairwise amino acid sequence classification (PASC), we describe a novel genus within this subfamily tentatively named Jeishaanvirus, which we propose should include as subgenera Jeilongvirus, Shaanvirus, and a novel South American subgenus Cadivirus. We also highlight inconsistencies in the classification of Tupaia virus and Mojiang virus using the same demarcation criteria and show that members of the proposed subgenus Shaanvirus are paraphyletic. Importantly, this study underscores the critical importance of sequence length in PASC analysis as well as the importance of biological characteristics such as genome organization in the taxonomic classification of viral sequences.

microbiology↗

bioRxiv2021

Zoonotic potential of a novel bat morbillivirus

Morbilliviruses are amongst the most contagious viral pathogens that infect mammals. Metagenomic surveys have identified numerous morbillivirus sequences in bats, but no full-length authentic morbillivirus has been isolated or characterized from bats. Here we detail the discovery of full-length Myotis Bat Morbillivirus (MBaMV) from a bat surveillance program in Brazil. After determining that MBaMV utilizes bat CD150 but not human CD150 as an entry receptor, we generated an infectious clone of MBaMV using reverse genetics. MBaMV exhibited features consistent with other morbilliviruses, including pleomorphic virions, P-editing and the rule-of-six. MBaMV replicated well in human epithelial cell lines in a nectin-4 dependent manner. Surprisingly, MBaMV was able to infect human macrophages in a CD150-independent manner. However, MBaMV was restricted by cross-neutralizing human sera and did not evade the human innate immune system, indicating that while zoonotic spillover into humans may be possible, MBaMV replication in humans would likely be restricted.

microbiology↗

bioRxiv2020

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus

SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

evolutionary biology↗

bioRxiv2020

Accounting for imperfect detection reveals role of host traits in structuring viral diversity of a wild bat community

Understanding how multi-scale host heterogeneity affects viral community assembly can illuminate ecological drivers of infection and host-switching. Yet, such studies are hindered by imperfect viral detection. To address this issue, we used a community occupancy model – refashioned for the hierarchical nature of molecular-detection methods – to account for failed detection when examining how individual-level host traits affect herpesvirus richness in eight species of wild bats. We then used model predictions to examine the role of host sex and species identity on viral diversity at the levels of host individual, population, and community. Results demonstrate that cPCR and viral sequencing failed to perfectly detect viral presence. Nevertheless, model estimates correcting for imperfect detection show that reproductively active bats, especially reproductively active females, have significantly higher viral richness, and host sex and species identity interact to affect viral richness. Further, host sex significantly affects viral turnover across host populations, as females host more heterogeneous viral communities than do males. Results suggest models of viral ecology benefit from integration of multi-scale host factors, with implications for bat conservation and epidemiology. Furthermore, by accounting for imperfect detection in laboratory assays, we demonstrate how statistical models developed for other purposes hold promising possibilities for molecular and epidemiological applications.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2020

A virion-based assay for glycoprotein thermostability reveals key determinants of filovirus entry and its inhibition

Ebola virus (EBOV) entry into cells is mediated by its spike glycoprotein (GP). Following attachment and internalization, virions traffic to late endosomes where GP is cleaved by host cysteine proteases. Cleaved GP then binds its cellular receptor, Niemann-Pick C1. In response to an unknown cellular trigger, GP undergoes conformational rearrangements that drive fusion of viral and endosomal membranes . The temperature-dependent stability (thermostability) of the pre-fusion conformers of Class I viral fusion glycoproteins, including those of filovirus GPs, has provided insights into their propensity to undergo fusion-related rearrangements. However, previously described assays have relied on soluble glycoprotein ectodomains. Here, we developed a simple ELISA-based assay that uses the temperature-dependent loss of conformational epitopes to measure thermostability of GP embedded in viral membranes. The base and glycan cap subdomains of all filovirus GPs tested suffered a concerted loss of pre-fusion conformation at elevated temperatures, but did so at different temperature ranges, indicating virus-specific differences in thermostability. Despite these differences, all of these GPs displayed reduced thermostability upon cleavage to GPCL. Surprisingly, acid pH enhanced, rather than decreased, GP thermostability, suggesting it could enhance viral survival in hostile endo/lysosomal compartments. Finally, we confirmed and extended previous findings that some small-molecule inhibitors of filovirus entry destabilize EBOV GP and uncovered evidence that the most potent inhibitors act through multiple mechanisms. We establish the epitope-loss ELISA as a useful tool for studies of filovirus entry, engineering of GP variants with enhanced stability for use in vaccine development, and discovery of new stability-modulating antivirals. ImportanceThough a vaccine for Ebola virus has been approved by the FDA within the past year, no FDA-approved therapeutics are available to treat infections by Ebola virus or other filoviruses. The development of such countermeasures is challenged by our limited understanding of the mechanism by which Ebola virus enters cells, especially at the final step of membrane fusion. The sole surface-exposed viral protein, GP, mediates key steps in virus entry, including membrane fusion, and undergoes major structural rearrangements during this process. The stability of GP at elevated temperatures (thermostability) can provide insights into its capacity to undergo these structural rearrangements. Here, we describe a new assay that uses GP-specific antibodies to measure GP thermostability under a variety of conditions relevant to viral entry. We show that proteolytic cleavage and acid pH have significant effects on GP thermostability that shed light on their respective roles in viral entry. We also show that the assay can be used to study how small-molecule entry inhibitors affect GP stability. This work provides a simple and readily accessible assay to engineer forms of GP with enhanced stability that could be useful as part of an antiviral vaccine and to discover and improve drugs that act by modulating the stability of GP.

microbiology↗

bioRxiv2019

Quantitative delineation of herpesviruses in bats for use in ecological studies

Public health concerns about recent viral epidemics have motivated researchers to seek transdisciplinary understanding of infection in wildlife hosts. With its deep history devoted to explaining the abundance and distribution of organisms, ecology can augment current methods for studying viral dynamics. However, datasets allowing ecological explorations of viral communities are lacking, and common methods for delineating viral operational taxonomic units (OTUs), or "species", are subjective. Here, we comprehensively sampled 1,086 bats from two Puerto Rican caves and tested them for infection with herpesviruses. Using percent identity of nucleotides and a machine learning algorithm, we categorized herpesviruses into 41 OTUs, representing approximately 80% of all herpesviruses in the host community. Although 13 OTUs were detected in multiple host species, OTUs generally exhibited host specificity by infecting a core host species at a significantly higher prevalence than in all other species combined. Only two OTUs showed significantly different prevalence between host sexes. This work is the first exploration of viral community ecology in a community of wildlife hosts.

ecology↗

bioRxiv2019

Trypsin treatment unlocks barrier for zoonotic coronaviruses infection

Traditionally, the emergence of coronaviruses (CoVs) has been attributed to a gain in receptor binding in a new host. Our previous work with SARS-like viruses argued that bats already harbor CoVs with the ability to infect humans without adaptation. These results suggested that additional barriers limit the emergence of zoonotic CoV. In this work, we describe overcoming host restriction of two MERS-like bat CoVs using exogenous protease treatment. We found that the spike protein of PDF2180-CoV, a MERS-like virus found in a Ugandan bat, could mediate infection of Vero and human cells in the presence of exogenous trypsin. We subsequently show that the bat virus spike can mediate infection of human gut cells, but is unable to infect human lung cells. Using receptor-blocking antibodies, we show that infection with the PDF2180 spike does not require MERS-CoV receptor DPP4 and antibodies developed against the MERS spike receptor-binding domain and S2 portion are ineffective in neutralizing the PDF2180 chimera. Finally, we found that addition of exogenous trypsin also rescues replication of HKU5-CoV, a second MERS-like group 2c CoV. Together, these results indicate that proteolytic cleavage of the spike, not receptor binding, is the primary infection barrier for these two group 2c CoVs. Coupled with receptor binding, proteolytic activation offers a new parameter to evaluate emergence potential of CoVs and offer a means to recover previously unrecoverable zoonotic CoV strains.\n\nImportanceOverall, our studies demonstrate that proteolytic cleavage is the primary barrier to infection for a subset of zoonotic coronaviruses. Moving forward, the results argue that both receptor binding and proteolytic cleavage of the spike are critical factors that must be considered for evaluating the emergence potential and risk posed by zoonotic coronaviruses. In addition, the findings also offer a novel means to recover previously uncultivable zoonotic coronavirus strains and argue that other tissues, including the digestive tract, could be a site for future coronavirus emergence events in humans.

microbiology↗

bioRxiv2018

Human antibody cocktail deploys multiple functions to confer pan-ebolavirus protection

During the unprecedented 2013-2016 Ebola virus disease (EVD) epidemic in Western Africa and in its aftermath, the passive administration of monoclonal antibodies (mAbs) emerged as a promising treatment approach1-7. However, all antibody-based therapeutics currently in advanced development are specific for a single member of the Ebolavirus genus, Ebola virus (EBOV), and ineffective against divergent outbreak-causing ebolaviruses, including Bundibugyo virus (BDBV) and Sudan virus (SUDV)2,3,5,7. Here we advance MBP134, a cocktail of two broadly neutralizing human mAbs targeting the filovirus surface glycoprotein, GP, as a candidate pan-ebolavirus therapeutic. One component of this cocktail is a pan-ebolavirus neutralizing mAb, ADI-15878, isolated from a human EVD survivor8,9. The second, ADI-23774, was derived by affinity maturation of a human mAb8,9 via yeast display to enhance its potency against SUDV. MBP134 afforded exceptionally potent pan-ebolavirus neutralization in vitro and demonstrated greater protective efficacy than ADI-15878 alone in the guinea pig model of lethal EBOV challenge. A second-generation cocktail, MBP134AF, engineered to effectively harness natural killer (NK) cells afforded additional, unprecedented improvements in protective efficacy against EBOV and SUDV in guinea pigs relative to both its precursor and to any mAbs or mAb cocktails tested previously. MBP134AF is a best-in-class mAb cocktail suitable for evaluation as a pan-ebolavirus therapeutic in nonhuman primates.

microbiology↗