Performing Department
(N/A)
Non Technical Summary
Swine influenza A Virus (IAV) is a highly contagious respiratory virus that is endemic in pigs worldwide. Swine IAV infections represent an enormous economic loss to producers and can result in acute respiratory disease and severe pathology when acting in concert with other pathogens. Zoonotic transmissions between pigs and humans are a threat to both human health and animal production, with spillover events and viral evolution leading to increased diversity. There are three major swine IAV subtypes (H1N1, H1N2, and H3N2) and ~10 distinct Hemagglutinin (HA) genes co-circulating within U.S. swine herds. Repeated outbreaks and rapid spread of genetically and antigenically distinct IAVs represent a considerable challenge for effective swine IAV control. The major problems with current commercially available swine IAV vaccines are 1) the challenge of updating vaccines faster than the rate of viral evolution, 2) the time needed for approval and licensing of updated vaccines, 3) maternal antibody interference, and 4) the lack of an adequate mucosal and cell-mediated immune response. There is an unmet need for closely matched efficacious vaccines that are updated and produced rapidly.The overall goal of this multi-phase SBIR project is to design, develop, validate, and commercialize a system for more-effective swine IAV control that can be utilized by veterinarians and producers. Genvax Technologies' Phase I project is designed to show it is feasible to develop the Genvax Sequence Database and Genvax Prescription self-amplifying RNA (saRNA) Vaccine Platform. Genvax will conduct swine IAV surveillance in production facilities and incorporate the collected sequence data into a centralized repository. The Genvax Sequence Database will be used to create predictive machine-learning (ML) models of viral evolution to improve vaccine design. We will create the first system that allows individual producers to have predictive analytics for viral changes within their farm. Using swine IAV HA sequences from Iowa Farms in 2018 as input, we could accurately predict sequences occurring for the following two years (2019-2020). We propose that with more producer-specific data, we could train customized ML models for individual production systems or farms and forecast the prevalence and diversity of swine IAV strains up to 12 months into the future. For Objective 2 we will attempt to prove the feasibility of the Genvax Prescriptive Vaccine Platform by creating a prescriptive saRNA nanoparticle vaccine that is designed based on producer-specific surveillance data within a 4 week turn-around time. Vaccine efficacy will be demonstrated with an in vivo study in pigs. Genvax has fully completed 5 preliminary swine IAV vaccine efficacy proof-of-concept studies in pigs. Briefly, pigs vaccinated with saRNA nanoparticle vaccines with HA as the gene of interest generated protective levels of immunity as demonstrated by high Hemagglutination Inhibition assay titers and protection from viral challenge.The Genvax team has a long history of entrepreneurship and innovative research. Co-investigator Hank Harris founded Harrisvaccines which developed innovative RNA particle technology that was a breakthrough in vaccine development. Genvax technology uses a cell-free encapsulation system based on nanoparticle saRNA vaccine delivery. Our goal is to help protect livestock from current and emerging infectious diseases by providing better solutions to veterinarians and producers by commercializing our innovative technologies. The global animal health market is projected to be over $13.6 billion by 2026, with swine vaccines representing $1.8 billion. A successful SBIR project and USDA approval of our vaccine platform will allow Genvax to pursue the $400 million U.S. swine vaccine market that includes targeting swine IAV and other important swine pathogens. The development and commercialization of our proposed technology will assist in protecting our nation's food supply, economic interests, and public health.
Animal Health Component
(N/A)
Research Effort Categories
Basic
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Applied
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Developmental
100%
Goals / Objectives
The Phase I goal is to establish the feasibility of surveying and predicting the HA gene sequences of circulating and future swine IAV specific to a production system. We will develop precise and efficacious prescriptive, self-amplifying RNA nanoparticle vaccines through two objectives:Technical Objective 1: Demonstrate the feasibility of a swine influenza A surveillance and viral evolution prediction platform. We will determine the HA gene sequences from swine IAV-positive nasal swabs monthly in Farrow to Wean Site 1 facilities and in 4-month-old growing pigs over 6 months. We will also implement ML models to predict the sequence and antigenic landscape of future swine IAV strains specific to a production system. To determine feasibility, we will collect nasal swabs from two production systems and will incorporate the collected HA gene sequences from swine IAV-positive samples into a central database. Using publicly available sequences and sequences collected during the study, we will implement and validate our ML-based viral evolution prediction algorithms to answer key Phase I questions:How do novel IAV strains emerge and circulate within production systems?What is the prevalence/diversity of circulating swine IAV within production systems?How do flu viruses persist on farms, and how do they move within/between systems?Is there significant overlap of related strains found in Farrow to Wean Site 1 facilities and 4-month-old growing pigs?What is the accuracy of various ML models and ensembles of models in predicting swine IAV evolution?Can we identify important metadata and ML feature sets to help improve the accuracy of swine IAV evolution predictions?To what extent does genetic diversity impact antigenic diversity?What is the antigenic diversity of circulating swine IAV and how can that help to inform us about possible protection offered from commercial vaccines and future efficacious vaccine design in possible Phase II projects?Can improved producer strain surveillance data be paired with vaccine strain data to prove vaccine efficacy?What improvements can be made to accelerate the turn-around time of sample collection, sequence deposition, and data analytics and ML outputs?What are the best methods for sequence deposition into the Genvax Sequence Database?Can we begin to formulate a plan to improve the process via APIs?Objective 1 milestone/metric: We will collect 50 nasal swabs from each site, each month, for a period of 6 months. Each sample will be tested for swine IAV and positive samples will be sequenced for the swine IAV HA gene and subsequently deposited into the Genvax Sequence Database. We expect that about 5% of the samples will be positive for swine IAV; thus, a milestone will be to deposit 60 new HA gene sequences into Genvax Sequence Database. We will begin to implement tools needed for tracking disease prevalence, homology charting, dendrogram assembly, and vaccine design. To predict viral evolution of circulating swine IAV strains, we will evaluate at least 4 different ML prediction models (XGboost, random forest, long short-term memory networks, and rough set techniques, along with ensemble approaches). The prediction models will be implemented and evaluated using K-fold cross-validation and backtesting using historical data. Results will be presented as a confusion matrix and evaluated using traditional ML assessment methods, including F1 score and ROC AUC. The best evaluated method will be implemented to predict future circulating swine IAV at production facilities to improve vaccine design and efficacy. The success metric for Objective 1 is achieving > 85% accuracy and precision with our ML models on predicting future changes in influenza evolution and prevalence. Some ML models also provide information about feature importance. We will utilize this information to identify important metadata and to create new relevant features to improve future data collection and prediction models.Technical Objective 2: Demonstrate the feasibility of a rapidly produced self-amplifying RNA nanoparticle vaccine designed from the surveillance and prediction of circulating swine IAV strains for a specific production system. Swine IAV mutates rapidly, and traditional vaccine production takes too long for effective swine IAV control. Also, no universal or broadly protective vaccine is available. The best protection is offered by vaccines that are highly matched to circulating virus strains. To demonstrate feasibility, we will incorporate the results of Objective 1 into a prescriptive vaccine design that is specific for a producer system. The vaccine will be injected into 3-week-old pigs and tested for protective antibody responses with hemagglutination inhibition (HI) assays. Objective 2 research questions are highlighted below:Can we design, develop, and deploy a vaccine once new producer-specific HA gene sequences have been added to the database in less than 4 weeks?Will the vaccine produce efficacious (HI titers >=1:40) immune responses?Does vaccination result in consistent and reproducible HI titers (All HI titers either >= 1:40 or < 1:40 in each experimental group and each timepoint)?Objective 2 milestone/metric: We will track the amount of time each stage of the vaccine creation process takes beginning with sample acquisition and ending with vaccine deployment. The success metric for total turn-around time will be 4 weeks. The deployed vaccine will be tested in no fewer than five 3-week-old pigs following a prime (day 0) and boost (day 28) vaccination strategy. Serum samples will be collected at minimum on days 42 and 56 post- prime-vaccination and sent to the Iowa State VDL for HI assay testing. The success metric for efficacy of the deployed vaccine will be HI titers >= 1:40 against an autologous swine IAV strain. Overall, vaccine efficacy will be considered successful if a majority of the piglets (Ex. 3/5) show HI titers >= 1:40 for at least one of the collection dates post-vaccination.
Project Methods
The overall objective of this multi-phase SBIR project is to design, develop, validate, and commercialize a system for more-effective swine IAV control that can be utilized by veterinarians/producers.Collection of nasal swab samples from Farrow to Wean Site 1 facilities and 4- month-old pigs. PI Lance Daharsh and co-investigator Hank Harris will coordinate sample collections with the two production facilities. During each collection, the production facility will collect 50 nasal swabs from Farrow to Wean Site 1 Facilities and 50 nasal swabs from 4-month- old pigs. Each facility will sample monthly for 6 months (July-Dec). All swabs will be labeled (location/date). Genvax will provide the BBL culture swabs and will arrange for shipping of the collected samples.Testing of collected nasal swab samples for swine IAV and sequencing positive samples. PI Daharsh will coordinate the shipment and storage of collected nasal swab samples. The samples will be submitted to the Iowa State Veterinary Diagnostic Lab (VDL). All samples will be screened for Influenza A by PCR. We assume there will be a positivity rate of 5% among samples. All PCR-positive samples will undergo full-length sequencing of the HA gene. The Iowa State VDL will generate and send results to Genvax via their online Client Portal. All newly generated HA sequencing data will be collected for sequential deposition into the Genvax Sequencing Database.Design and implementation of the Genvax Sequence Database. PI Daharsh, co- investigator Joel Harris, and Consultant Joe Webb will coordinate the design/implementation of the Genvax Sequence Database. Daharsh, Harris, and Webb will design a cloud computing database structure and implement it using Amazon AWS based tools. It will include associated services for database infrastructure (AWS DynamoDB), data storage (AWS S3), ML (AWS Sagemaker), and web app/website hosting (AWS API Gateway, Cloudfront, Route53).Aggregation and deposition of new sequence data and associated metadata into the Genvax Sequence Database. PI Daharsh and Lab Technician Naseer will design database protocols for adding sequences and metadata. Full-length swine IAV HA gene sequences and corresponding metadata from the past 10 years will be added to the database from online repositories, along with newly generated sequences from the Iowa State VDL Client Portal.Data analysis of gene sequences. PI Daharsh, Manager of Nanovaccines Dennis O'Neill, and Technician Naseer will perform data analysis on the sequences in the Genvax Sequence Database. We will summarize the prevalence/relatedness of swine IAV strains within Farrow to Wean Sites and 4-month-old pigs. This data will help to inform producers about the prevalence and possible spread of strains among sites. It will also provide clues about viral evolution and how often new strains are being introduced. Further, the Genvax team will conduct phylogenetic analyses on the collected sequences to see how they compare with historically collected data, including recently collected data from their surrounding region.Feature selection and ML predictions of viral evolution. The livestock sector needs a better way to manage sequencing data and potential genes of interest to aid in disease management. To provide added value to veterinarians/producers, the Genvax Sequence Database will be more than just a sequence repository. PI Daharsh and Consultant Webb will use the HA sequence and metadata information in the database to create predictive models of swine IAV evolution. The goal is to aid vaccine design by creating methods to help predict future circulating swine IAV strains within a specific producer facility or region. They will first evaluate the feature set from metadata using the Boruta algorithm to rank feature importance. Additional novel features may be created out of the existing metadata and evaluated for importance. At least 4 ML models will be tested using the highest-ranked features as input, including XGboost, random forest, neural networks, and rough set techniques. Additional ML models and ensemble approaches will also be tested. We will evaluate the feature set importance of each using SHAP values. The models will be implemented/evaluated using K-fold cross-validation and backtesting using historical data. Results will be presented as a confusion matrix and evaluated using traditional ML assessment methods, including F1 score and area under receiver-operating characteristic (AUROC).Production of the saRNA vaccine vector and insertion of the designed gene of interest. Manager O'Neill will coordinate production of the saRNA vaccine vector. Plasmid DNA is expanded in E. coli, these competent cells used for cloning are a DH5α derivative purchased from NEB. Antibiotic selection of the transformed cells with plasmid DNA is conducted with agar plates and LB broth containing carbenicillin. Plasmid DNA is extracted from the transformed cells using the endotoxin-free kit, ZymoPURE Plasmid Miniprep Kit. The restriction digest is purified with a column purification step to remove any residual E coli cells, so no living organism is present after this step in the saRNA production process. The carbenicillin selection gene is not part of the saRNA generated using the Promega RiboMAX Large Scale RNA Production System via the T7 promoter. The full-length saRNA is then 5'- Capped using the Vaccinia Capping Enzyme and mRNA Cap 2'-O-Methyltransferase with a One-Step capping Methyltransferase process.Design a 100% strain-matched gene of interest derived from a production facility. HA gene sequences from a production facility will be analyzed for predicted prevalence/ representation of circulating strains. PI Daharsh and co-investigator Hank Harris will choose the most prevalent and/or representative sequence for inclusion. Manager O'Neill will perform gene of interest integration with the vaccine vector by first conducting codon-optimization using the Integrated DNA Technologies (IDT) Codon Optimization Tool for expression within the Sus Scrofa pig genome. The optimized gene sequence will be ordered from IDT as a HiFidelity gBlock, which will be sequence-verified from the vendor. A seamless cloning strategy will be used for cloning all genes into the vector.In vivo vaccine trial in 3-week-old pigs. An in vivo study in pigs will be conducted at VRI-AMCV animal research facilities. The Genvax saRNA vaccine with the 100% strain- matched HA gene sequence and nanoparticle-delivery system will be injected intramuscularly into the ventral portion of the biceps femoris muscle. We will follow a prime boost vaccine strategy with a Day 1 prime injection followed by a boost injection 4 weeks later (Day 28). Each injection will use a 25-ug dose in 2 ml of volume. Animal well-being will be monitored throughout the study along with daily injection site monitoring. At minimum, a total of 5 animals will be injected with the vaccine along with a matched control animal group. Control animals will be injected with a similar volume of saline. Blood draws to collect serum samples will be performed on days 1, 14, 28, 42, and 56. All animals will be euthanized at the conclusion.Evaluation of vaccine efficacy. Serum samples collected during the in vivo vaccine trial will be submitted to the Iowa State VDL for HI testing. The assay will provide data on predicted protection provided by the vaccine against a homologous swine IAV strain. Titers >= 1:40 are considered to be protective. HI testing results from the VDL will be obtained via a client web portal by Genvax for further analysis and efficacy evaluation.Analysis of data from Objective 1 and 2, and Final Report. PI Daharsh will work with the other team members to assess Phase I results in terms of meeting or exceeding the feasibility metrics. A final report will be prepared that summarizes these results and provides recommendations for a follow-on Phase II project.