Location: Foreign Animal Disease Research
2025 Annual Report
Objectives
OBJECTIVE 1. Develop vaccines engineered for the control and eradication of Foot-and-Mouth Disease Virus (FMDV).
Sub-objective 1.A Determine the mechanisms of protective immunity to FMDV conferred by multiple Foot-and-Mouth Disease (FMD) vaccine platforms.
Sub-objective 1.B Determine the mechanisms mediating duration of immunity to FMDV.
Sub-objective 1.C Develop vaccine platforms that will provide cross-protective immunity against different FMDV subtypes.
Sub-objective 1.D Develop vaccines that reduce the incidence and accelerate clearance of persistent FMDV infections in cattle.
Sub-objective 1.E Develop vaccines that can be rapidly manufactured to respond to new FMDV outbreaks.
Objective 2. Develop biotherapeutics that can rapidly control the spread of FMD.
Sub-objective 2.A Develop biotherapeutic platforms that induce rapid onset of immunity as a companion to an effective FMD vaccination.
Sub-objective 2.B Develop biotherapeutics that alone or in vaccine formulations can reduce or abrogate FMDV persistence.
Objective 3. Elucidate the host-pathogen interactions of FMDV.
Sub-objective 3.A Identify viral determinants of FMD that control virulence in susceptible hosts.
Sub-objective 3.B Determine the virus/host interactions associated with FMDV persistence.
Objective 4. Characterize the ecology of FMDV in endemic regions.
Sub-objective 4.A Determine drivers of FMDV transmission and maintenance in endemic regions.
Sub-objective 4.B Determine factors that drive viral evolution and the mechanisms that lead to the emergence and spread of new FMDV strains.
Sub-objective 4.C Support the epidemiological analysis of data collected from countries with FMDV epidemics.
Approach
1. The development of intervention strategies to control and eradicate Foot-and-Mouth Disease Virus (FMDV) will be achieved through research on novel Foot-and-Mouth Disease (FMD) vaccine platforms including of marker modified live-attenuated FMDV vaccine candidates such as FMDV-LL3B3D, second–generation Recombinant adenovirus-5 vectored foot-and-mouth disease constructs (Ad5- FMD) vaccines, and cross-protective vaccines against multiple subtypes.
2. Combinations of vaccine and biotherapeutics / and or adjuvants will be investigated as a way to induce mucosal immunity necessary not only to prevent disease but also to decrease persistent infection. These vaccine/adjuvant formulations will be tested using alternate routes such as transdermal and by direct mucosal delivery.
3. The host-pathogen interactions of FMDV will be determined through: the identification of viral determinants of FMDV that control virulence in susceptible hosts, determining virus/host interactions associated with the FMDV life cycle, and determining the mechanisms of protective immunity to FMDV. The molecular basis for FMDV-host interactions that impact virulence and their specific contributions to virulence will be determined. In addition, the interactions of the virus with specific tissues at the primary infection sites will be studied by characterizing infected tissues at the cellular and subcellular level as well as utilizing transcriptomic analyses with micro arrays and next generation RNAsequencing. Bioinformatic analyses will be extensively applied in order to understand species specific factors mediating the establishment and maintenance of persistent infections. The withinhost FMDV genomic evolution will be characterized through an examination of sitespecific mutational pressure, genomic variation and potential adaption to the host.
The immune mechanisms affecting protective immunity against FMDV will be determined through the analysis of CD4 helper and CD8 cytotoxic T cell responses to FMDV vaccination and B-cell responses to FMDV in peripheral blood and lymphoid tissue.
4.The characterization of the ecology of FMDV in endemic regions, including determining drivers of FMDV transmission and maintenance in endemic regions, characterizing factors driving FMDV emergence and spread, and the characterization of the role of the Asian buffalo in the transmission and maintenance of FMDV in the context of tolerance to infection will be analyzed. Efforts will focus on the characterization of the ecology of FMDV in endemic regions in Asia and Africa, including determining the factors driving viral transmission and maintenance.
Factors driving FMDV emergence and spread of novel FMDV strains in endemic settings will be characterized. The role of Asian buffalo in maintenance and transmission of FMDV in endemic settings will be assessed.
Progress Report
In Objective 1, under Sub-objective 1B, progress involved the examination of transcriptomic signatures from circulating immune cells derived from vaccinated animals using a foot-and-mouth disease virus (FMDV) modified live attenuated vaccine. These evaluations employed both targeted and comprehensive transcriptomic platforms, utilizing Nanostring technologies and single cell RNA sequencing. For instance, in the case of circulating monocytes, our analysis showed the upregulation of genes associated with key immune functions, including antigen presentation, migration to tissues, inflammatory signaling, apoptosis regulation, and metabolic adaptation from those vaccinated and protected cattle. These transcriptional changes are likely critical for the monocytes to effectively respond to the vaccine and mediate a protective immune response.
This approach supports the overarching goal of refining vaccine development by elucidating the correlates of immunity. Preliminary findings have identified key factors critical for triggering innate immunity, which in turn can facilitate the development of a robust humoral response essential for effective FMD vaccine control in cattle.
In Objective 1, under Sub-objective 1C, substantial progress involved developing next generation foot-and-mouth disease (FMD) vaccines that display increase breadth of immunity. Through a partnership with domestic collaborators, we have produced novel leaderless (FMDLL3B3D) vaccine candidates that could offer broader protection in the event of an outbreak. We demonstrated efficient derivation of the mutant viruses and examined vaccine induced B and T cell responses in susceptible species. Importantly, cattle and pigs immunized with chemically-inactivated FMD vaccines were protected against heterologous FMD virus challenge at 21-days post vaccination. Progress was made at examining the efficacy of monovalent and polyvalent vaccines formulated with a commercial adjuvant for mutant viruses of the A, O and Asia serotypes.
In Objective 2, under Sub-objectives 2A and 2B, improved design of bovine IFN-lambda Fc construct was finalized, produced, purified and characterized in vitro using bovine cell lines. In vitro examination resulted in potent antiviral activity against FMDV. A subsequent cattle study was conducted to assess dose dependent efficacy. Preliminary findings indicate that treatment with bovine IFN-lambda Fc fusion shows partial protection against FMD. The animal group receiving the highest dose (166ug/kg) showed delayed onset of severe FMD, with one-third displaying only very mild FMD (score of 1 out of 5). A major limitation of this study is the lack of a reliable antiviral assay, which complicates understanding of the mechanism of action for this novel therapeutic. Current efforts are focused on determining whether increase dosing could enhance efficacy, but only if the limiting factor is bioavailability (not immunogenicity or receptor saturation). Additional refinements to the construct bovine IFN-lambda Fc, including optimization of post-translational modifications, linker size, and cross-species Fc compatibility are being explored.
In Objective 3, Sub-objective 3A substantial progress was made to understand host-pathogen interactions of FMDV. Immunophenotyping of T cells present in FMD-relevant tissues revealed an upregulation of Th1-related transcription factor in the nasopharynx as well as Th17-related transcription factor in both the nasopharynx and draining lymph node of animals that cleared the virulent virus compared to those that became persistently infected. This indicates that relative presence of T cell subsets with antiviral (Th1) and tissue remodeling (Th17) functions may be key to proper clearance of virus to avoid persistent infection. Single cell RNA sequencing analysis further supports the immunophenotyping findings, demonstrating antiviral responses present in T compartment of the nasopharynx. This feature could be exploited in the future to improve vaccine design and encourage T cell fate skewing towards Th17 and Th1. While modified live attenuated FMDV vaccines primarily drive protection through adaptive immune responses (i.e., humoral and cell mediated), insights from innate immune mechanisms such as those mediated by interferon stimulated gene (ISG) MCL-1(myeloid cell leukemia 1) can inform broader correlates of antiviral defenses. Our findings demonstrate that MCL-1 restriction of FMDV replication relies on mitochondrial dynamics and autophagy suppression, both critical for viral replication efficiency.
In Objective 4 progress was made in investigating FMDV evolution and recombination during serotype O persistent infection, with subsequent superinfection by a heterologous serotype O virus. It was concluded that although preceding infection with a within-serotype virus protected against clinical FMD upon heterologous virus exposure, most of the animals became silently infected following the second exposure. This finding highlights how sequential, overlapping FMDV infections may occur in absence of clinical signs of FMD, in areas where different variants of the virus are circulating. It further emphasizes how persistently infected carrier cattle may serve as mixing vessels for coinfecting viruses. Additional experimental work confirmed that sheep, although competent hosts of persistent FMDV infection, are not a source of recombinant FMDV strains following multi-strain coinfections. This phenomenon is likely explained by substantial differences in the anatomic sites of primary and persistent FMDV infection in sheep verses cattle.
Additional progress was made in In Objective 4 Sub-objectives 4A.1. and 4B.1, investigating the role of subclinical phase FMD transmission through simulation modeling. Preliminary results from simulation-based analysis aimed at quantifying the impacts of preclinical transmission in cattle show a substantial increase in disease spread rate and total affected geographic area. Simulations without incubation phase transmission impacted fewer farms and necessitated the depopulation of fewer cattle to contain disease spread. Extending the infectious subclinical phase to four days or more resulted in a significant rise in affected farms and the amount of depopulation needed to stop the outbreaks. This preliminary work highlights the importance of incorporating the subclinical infectious phase in epidemiologic models and emphasizes the impact of incubation phase transmission on FMD outbreak extent and duration. The modeling framework will be further refined to improve understanding of FMD infection dynamics and to support emergency preparedness.
Further progress was made under Objective 4, in assessing the potential for FMDV transmission between feral swine and domestic livestock. Extensive observational datasets of feral swine presence and behavior were compiled and standardized, and spatial modeling efforts were initiated to estimate the degree of geographic overlap and potential contact rates with livestock. A preliminary needs assessment identified data gaps in understanding feral swine ecology, which will guide the prioritization of future data collection efforts and inform the design of targeted models for FMD transmission. Additional progress was made through the application of predictive models to detect potential long-distance translocation events in feral swine. These events are characterized by individuals that are genetically distinct from local populations, suggesting human-mediated movement. This work is crucial for identifying regions at high risk of long-distance FMD dissemination and for informing surveillance strategies targeting unauthorized swine transport. Lastly, under Objective 4, initial modeling work was completed using African Swine Fever virus (ASFV) as a proxy system to inform future FMDV modeling. A spatially explicit simulation model was developed to evaluate the influence of epidemiological traits, including incubation period, infectious period, and duration of immunity, on outbreak dynamics across a range of feral swine host densities. This framework provides a foundation for adaptation to FMDV under comparable ecological conditions. These distinct forms of progress will help shape future strategies for monitoring and controlling FMD in livestock.
Accomplishments
1. Foot-and-mouth disease virus recombination leads to novel virus variants. Foot-and-mouth disease (FMD) is a serious virus infection of livestock with the potential of causing massive economic disruption to U.S livestock industries. One substantial challenge to FMD control is asymptomatic carriers FMD virus (FMDV). These are cattle that fail to fully clear the virus after recovering from acute FMD. Research done by ARS scientists at Orient Point, New York, has demonstrated that when these FMDV carriers are exposed to a different variant of FMDV, the overlapping old and new infections leads to development of novel recombinant viruses that have distinct parts derived from both of the original viruses. This research is important for cattle producers and regulators regarding the importance of appropriately managing persistently infected carrier animals in the event of an FMDV outbreak to prevent spread of new virus variants that may escape protection from current vaccines. This breakthrough was published in the Journal of Virology in 2025.
2. New discovery in fighting foot-and-mouth disease in animal cells. This research highlights a significant contribution to combating foot-and-mouth disease (FMD), a major threat to livestock worldwide. Scientists in ARS at Orient Point, New York, discovered that the gene named myeloid cell leukemia 1 (MCL-1) overexpression strongly suppresses FMD virus (FMDV) replication in pig-derived cells. MCL-1 works by boosting energy production in cells and preventing processes that the virus needs to multiply. Importantly, this antiviral effect is unrelated to cellular death or the cell cycle. The findings are important for the control of FMD outbreaks known to cause severe economic losses and can jeopardize food security. This discovery could lead to novel mechanisms to establish countermeasures in the protection of livestock, reducing outbreaks and improving animal health. By understanding how MCL-1 fights the virus, scientists are a step closer to developing improved biotherapeutics to protect U.S. livestock against FMD. This work was published in the Journal of Virology in 2025.
Review Publications
Gunasekera, U., Vanderwaal, K., Arzt, J., Perez, A. 2025. Foot-and-mouth disease reproduction number: A scoping review. Frontiers in Veterinary Science. 12. https://doi.org/10.3389/fvets.2025.1576974.
Stenfeldt, C., Fish, I., Rodriguez-Calzada, M., Richt, J., Arzt, J., Medina, G.N. 2025. Differential mosaicism of recombinant foot-and-mouth disease viruses associated with the order of exposure to two heterologous virus strains. Journal of Virology. 99(3). Article e02213-24. https://doi.org/10.1128/jvi.02213-24.
Mogulothu, A., Hickman, D., Attreed, S.E., Azzinaro, P.A., Rodriguez-Calzada, M., Dittmann, M., De Los Santos, T., Szczepanek, S., Medina, G.N. 2025. Interferon stimulated gene MCL-1 inhibits FMDV replication by modulating mitochondrial dynamics and blocking autophagy. Journal of Virology. Article e00581-25. https://doi.org/10.1128/jvi.00581-25.
Stenfeldt, C., Eschbaumer, M., Humphreys Jr, J.M., Medina, G.N., Arzt, J. 2025. The pathogenesis of foot-and-mouth disease virus: Current understandings and knowledge gaps. Veterinary Research. 56. Article 119. https://doi.org/10.1186/s13567-025-01545-5.
Humphreys Jr, J.M., Stenfeldt, C., King, D.P., Knight-Jones, T., Perez, A., Vanderwaal, K., Sanderson, M.W., Di Nardo, A., Temesgen, W., Pamornchainavakul, N., Arzt, J. 2025. Epidemiology and economics of foot-and-mouth disease: Current understanding and knowledge gaps. Veterinary Research. 56. Article 141. https://doi.org/10.1186/s13567-025-01561-5.
Imanbayeva, D., Perez-Aguirreburuald, M., Knauer, W., Tegzhanov, A., Yustyniuk, V., Arzt, J., Perez, A. 2025. A scoping review on progression towards freedom from Petits Ruminants (PPR) and the role of the PPR Monitoring and Assessment Tool (PMAT). Viruses. 17. Article 563. https://doi.org/10.3390/v17040563.