The potential of antiviral agents to control classical swine fever: a modelling study

Structure of the recombinant RNA polymerase from African Swine Fever Virus

African Swine Fever Virus is a Nucleo-Cytoplasmic Large DNA Virus that causes an incurable haemorrhagic fever in pigs with a high impact on global food security. ASFV replicates in the cytoplasm of the infected cell and encodes its own transcription machinery that is independent of cellular factors, however, not much is known about how this system works at a molecular level. Here, we present methods to produce recombinant ASFV RNA polymerase, functional assays to screen for inhibitors, and high-resolution cryo-electron microscopy structures of the ASFV RNAP in different conformational states. The ASFV RNAP bears a striking resemblance to RNAPII with bona fide homologues of nine of its twelve subunits. Key differences include the fusion of the ASFV assembly platform subunits RPB3 and RPB11, and an unusual C-terminal domain of the stalk subunit vRPB7 that is related to the eukaryotic mRNA cap 2´-O-methyltransferase 1. Despite the high degree of structural conservation with cellular RNA polymerases, the ASFV RNAP is resistant to the inhibitors rifampicin and alpha-amanitin. The cryo-EM structures and fully recombinant RNAP system together provide an important tool for the design, development, and screening of antiviral drugs in a low biosafety containment environment.

Modelling infectious viral diseases in swine populations: a state of the art

Mathematical modelling is nowadays a pivotal tool for infectious diseases studies, completing regular biological investigations. The rapid growth of computer technology allowed for development of computational tools to address biological issues that could not be unravelled in the past. The global understanding of viral disease dynamics requires to account for all interactions at all levels, from within-host to between-herd, to have all the keys for development of control measures. A literature review was performed to disentangle modelling frameworks according to their major objectives and methodologies. One hundred and seventeen articles published between 1994 and 2020 were found to meet our inclusion criteria, which were defined to target papers representative of studies dealing with models of viral infection dynamics in pigs. A first descriptive analysis, using bibliometric indexes, permitted to identify keywords strongly related to the study scopes. Modelling studies were focused on particular infectious agents, with a shared objective: to better understand the viral dynamics for appropriate control measure adaptation. In a second step, selected papers were analysed to disentangle the modelling structures according to the objectives of the studies. The system representation was highly dependent on the nature of the pathogens. Enzootic viruses, such as swine influenza or porcine reproductive and respiratory syndrome, were generally investigated at the herd scale to analyse the impact of husbandry practices and prophylactic measures on infection dynamics. Epizootic agents (classical swine fever, foot-and-mouth disease or African swine fever viruses) were mostly studied using spatio-temporal simulation tools, to investigate the efficiency of surveillance and control protocols, which are predetermined for regulated diseases. A huge effort was made on model parameterization through the development of specific studies and methodologies insuring the robustness of parameter values to feed simulation tools. Integrative modelling frameworks, from within-host to spatio-temporal models, is clearly on the way. This would allow to capture the complexity of individual biological variabilities and to assess their consequences on the whole system at the population level. This would offer the opportunity to test and evaluate in silico the efficiency of possible control measures targeting specific epidemiological units, from hosts to herds, either individually or through their contact networks. Such decision support tools represent a strength for stakeholders to help mitigating infectious diseases dynamics and limiting economic consequences.

Meeting report: 32nd International Conference on Antiviral Research

The 32nd International Conference on Antiviral Research (ICAR), sponsored by the International Society for Antiviral Research (ISAR), was held in Baltimore, Maryland, USA, on May 12-15, 2019. This report gives an overview of the conference on behalf of the Society. It provides a general review of the meeting and awardees, summarizing the presentations, and their main conclusions from the perspective of researchers active in many different areas of antiviral research and development. As in past years, ICAR promoted and showcased the most recent progress in antiviral research, and continued to foster collaborations and interactions in drug discovery and development. The 33rd ICAR will be held in Seattle, Washington, USA, March 30th-April 3rd, 2020.

African swine fever

The continuing spread of African swine fever (ASF) outside Africa in Europe, the Russian Federation, China and most recently to Mongolia and Vietnam, has heightened awareness of the threat posed by this devastating disease to the global pig industry and food security. In this review we summarise what we know about the African swine fever virus (ASFV), the disease it causes, how it spreads and the current global situation. We discuss current control methods in domestic and wild pigs and prospects for development of vaccines and other tools for control.

Control fast or control smart: When should invading pathogens be controlled?

The intuitive response to an invading pathogen is to start disease management as rapidly as possible, since this would be expected to minimise the future impacts of disease. However, since more spread data become available as an outbreak unfolds, processes underpinning pathogen transmission can almost always be characterised more precisely later in epidemics. This allows the future progression of any outbreak to be forecast more accurately, and so enables control interventions to be targeted more precisely. There is also the chance that the outbreak might die out without any intervention whatsoever, making prophylactic control unnecessary. Optimal decision-making involves continuously balancing these potential benefits of waiting against the possible costs of further spread. We introduce a generic, extensible data-driven algorithm based on parameter estimation and outbreak simulation for making decisions in real-time concerning when and how to control an invading pathogen. The Control Smart Algorithm (CSA) resolves the trade-off between the competing advantages of controlling as soon as possible and controlling later when more information has become available. We show-using a generic mathematical model representing the transmission of a pathogen of agricultural animals or plants through a population of farms or fields-how the CSA allows the timing and level of deployment of vaccination or chemical control to be optimised. In particular, the algorithm outperforms simpler strategies such as intervening when the outbreak size reaches a pre-specified threshold, or controlling when the outbreak has persisted for a threshold length of time. This remains the case even if the simpler methods are fully optimised in advance. Our work highlights the potential benefits of giving careful consideration to the question of when to start disease management during emerging outbreaks, and provides a concrete framework to allow policy-makers to make this decision.

Epidemiology, diagnosis and control of classical swine fever: Recent developments and future challenges

Classical swine fever (CSF) represents a major health and trade problem for the pig industry. In endemic countries or those with a wild boar reservoir, CSF remains a priority for Veterinary Services. Surveillance as well as stamping out and/or vaccination are the principle tools of prevention and control, depending on the context. In the past decades, marker vaccines and accompanying diagnostic tests allowing the discrimination of infected from vaccinated animals have been developed. In the European Union, an E2 subunit and a chimeric live vaccine have been licensed and are available for the use in future disease outbreak scenarios. The implementation of commonly accepted and globally harmonized concepts could pave the way to replace the ethically questionable stamping out policy by a vaccination-to-live strategy and thereby avoid culling of a large number of healthy animals and save food resources. Although a number of vaccines and diagnostic tests are available worldwide, technological advancement in both domains is desirable. This work provides a summary of an analysis undertaken by the DISCONTOOLS group of experts on CSF. Details of the analysis can be downloaded from the web site at http://www.discontools.eu/.

Simulation of Spread of African Swine Fever, Including the Effects of Residues from Dead Animals

To study the spread of African swine fever (ASF) within a pig unit and the impact of unit size on ASF spread, a simulation model was created. In the model, an animal can be in one of the following stages: susceptible, latent, subclinical, clinical, or recovered. Animals can be infectious during the subclinical stage and are fully infectious during the clinical stage. ASF virus (ASFV) infection through residues of dead animals in the slurries was also modeled in an exponentially fading-out pattern. Low and high transmission rates for ASFV were tested in the model. Robustness analysis was carried out in order to study the impact of uncertain parameters on model predictions. The results showed that the disease may fade out within the pig unit without a major outbreak. Furthermore, they showed that spread of ASFV is dependent on the infectiousness of subclinical animals and the residues of dead animals, the transmission rate of the virus, and importantly the unit size. Moreover, increasing the duration of the latent or the subclinical stages resulted in longer time to disease fade out. The proposed model is a simple and robust tool simulating the spread of ASFV within a pig house taking into account dynamics of ASFV spread and the unit size. The tool can be implemented in simulation models of ASFV spread between herds.

A thiazepino[4,5-a]benzimidazole derivative hampers the RNA replication of Eurasian serotypes of foot-and-mouth disease virus

The stamping-out policy for the control of foot-and-mouth disease virus (FMDV) in countries that are free from FMD without vaccination has a dramatic socio-economic impact, huge animal welfare issues and may result in the loss of farm animal genetic resources. As an alternative to pre-emptive culling or emergency vaccination we further explore the possibility to use antiviral drugs in the event of an FMD outbreak. In the present study, we tested the in vitro cytotoxicity and anti-FMDV activity of 1,2,4,5-tetrahydro-[1,4]thiazepino[4,5-a]benzimidazole. The molecule was shown to inhibit the replication of reference strains of the Eurasian FMDV serotypes O, A, C and Asia but not the FMDV serotypes from the South African Territories (SAT) neither a related picornavirus, i.e. swine vesicular disease virus. The molecule can be added until 2h post inoculation in a 'single replication cycle experiment' without losing its antiviral activity. The genetic characterization of progressively selected resistant FMD viruses shows that the molecule presumably interacts with the non-structural 2C protein of FMDV. Further studies are required on the use of this molecule in vivo.

Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases?

The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.

Potential applications for antiviral therapy and prophylaxis in bovine medicine

Viral disease is one of the major causes of financial loss and animal suffering in today's cattle industry. Increases in global commerce and average herd size, urbanization, vertical integration within the industry and alterations in global climate patterns have allowed the spread of pathogenic viruses, or the introduction of new viral species, into regions previously free of such pathogens, creating the potential for widespread morbidity and mortality in naïve cattle populations. Despite this, no antiviral products are currently commercially licensed for use in bovine medicine, although significant progress has been made in the development of antivirals for use against bovine viral diarrhea virus (BVDV), foot and mouth disease virus (FMDV) and bovine herpesvirus (BHV). BVDV is extensively studied as a model virus for human antiviral studies. Consequently, many compounds with efficacy have been identified and a few have been successfully used to prevent infection in vivo although commercial development is still lacking. FMDV is also the subject of extensive antiviral testing due to the importance of outbreak containment for maintenance of export markets. Thirdly, BHV presents an attractive target for antiviral development due to its worldwide presence. Antiviral studies for other bovine viral pathogens are largely limited to preliminary studies. This review summarizes the current state of knowledge of antiviral compounds against several key bovine pathogens and the potential for commercial antiviral applications in the prevention and control of several selected bovine diseases.

In vitro surrogate models to aid in the development of antivirals for the containment of foot-and-mouth disease outbreaks

Foot-and-mouth disease virus (FMDV) is a highly pathogenic member of the genus Aphthovirus (family Picornaviridae) that is only to be manipulated in high-containment facilities, thus complicating research on and discovery of antiviral strategies against the virus. Bovine rhinitis B virus (BRBV) and equine rhinitis A virus (ERAV), phylogenetically most closely related to FMDV, were explored as surrogates for FMDV in antiviral studies. Although no efficient cell culture system has been reported so far for BRBV, we demonstrate that infection of primary bovine kidney cells resulted in an extensive but rather poorly-reproducible induction of cytopathic effect (CPE). Madin-Darby bovine kidney cells on the other hand supported viral replication in the absence of CPE. Antiviral tests were developed for ERAV in Vero A cells employing a viral RNA-reduction assay and CPE-reduction assay; the latter having a Z' factor of 0.83±0.07. The BRBV and ERAV models were next used to assess the anti-aphthovirus activity of two broad-spectrum antiviral agents 2'-C-methylcytidine (2CMC) and ribavirin, as well as of the enterovirus-specific inhibitor enviroxime. The effects of the three compounds in the CPE-reduction (ERAV) and viral RNA-reduction assays (BRBV and ERAV) were comparable. Akin to 2CMC, compound A, a recently-discovered non-nucleoside pan-serotype FMDV inhibitor, also inhibited the replication of both BRBV and ERAV, whereas enviroxime was devoid of activity. The BRBV and ERAV surrogate models reported here can be manipulated in BSL-2 laboratories and may facilitate studies to unravel the mechanism of action of novel FMDV inhibitors.