Source: NORTH CAROLINA STATE UNIV submitted to
PREDICT AND PROTECT AGAINST PRRSV: COMBINE PRRSV FORECASTING TECHNOLOGY WITH VACCINE EFFICACY PREDICTION TO PREVENT PRRSV OUTBREAKS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1028506
Grant No.
2022-68014-37266
Cumulative Award Amt.
$1,000,000.00
Proposal No.
2021-10914
Multistate No.
(N/A)
Project Start Date
Jul 1, 2022
Project End Date
Jun 30, 2026
Grant Year
2022
Program Code
[A1261]- Inter-Disciplinary Engagement in Animal Systems
Project Director
Crisci, E.
Recipient Organization
NORTH CAROLINA STATE UNIV
COLLEGE OF VETERINARY MEDICINE
RALEIGH,NC 27606
Performing Department
Population Health Pathobiology
Non Technical Summary
The Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most detrimental pathogen for theswine industry. The high mutation rate of PRRSV represents a big challenge for controlling this virus and it raisestwo important questions for swine producers: Which PRRSV strain will hit my farm next? And which vaccine canbest protect my herd against it? Currently no technology can adequately answer those questions. To overcomethis issue, this project will combine two state-of-the-art technologies - PRRSV forecasting and heterologousvaccine efficacy prediction. These technologies will create the first proactive PRRSV mitigation system: Predictand Protect against PRRSV (PreProPRRSV). Thereby, for the first time, PRRSV outbreak mitigation will becomeproactive!We will establish the PreProPRRSV system in two integrated objectives:Objective 1 will establish a PRRSV strain specific forecasting technology. This forecasting methodology usescomputer-based prediction algorithms based on surveillance data relevant to predict PRRSV propagation viaseveral mode of between-farm transmission. This technology is expected to predict the spread of PRRSV strains.Objective 2 will establish a vaccine efficacy prediction system. This system consists of an immune biobank (cells+ serum) from pigs, which received different PRRSV vaccinations. This biobank will enable us to determinewithin around two weeks which vaccine induces the strongest immune response to the approaching PRRSVstrain.This interdisciplinary project combines computer-algorithm-based forecasting with translational immunology toenable precision animal management for PRRSV: It will determine the most effective vaccine BEFORE theemerging PRRSV strain arrives at a production site.The proactive PreProPRRSV outbreak mitigation system will drastically enhance animal health and production bydecreasing the impact of PRRS.
Animal Health Component
40%
Research Effort Categories
Basic
20%
Applied
40%
Developmental
40%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3113510109030%
3113510110130%
3113510117040%
Knowledge Area
311 - Animal Diseases;

Subject Of Investigation
3510 - Swine, live animal;

Field Of Science
1090 - Immunology; 1101 - Virology; 1170 - Epidemiology;
Goals / Objectives
Overview: The successful completion of the first two goals of this project will unlock the following two excitingtools. Goal 1 will create easy to understand geographical maps of the infection risk levels for specific PRRSVstrains (i.e., heat maps). These maps account for current PRRSV spatial distribution, available control measures,spatial risk factors, and extrinsic (e.g. landscape) and intrinsic factors, toestimate weekly PRRSV number ofinfected farms by individual strain. Goal 2 will first create an immune biobank of immunological samples(immune cells + serum for antibody analysis) from pigs vaccinated with commercially available PRRSV vaccines.After isolation of emerging PRRSV strains within the NC swine industry, this biobank can then be used todetermine the most immunogenic PRRSV vaccine against specific PRRSV strains. Together, these two tools willgenerate our Goal 3 "PreProPRRSV" - an optimized PRRSV intervention strategy. The established PreProPRRSVsystem will allow swine veterinarians to select the most effective vaccine against emerging PRRSV strainsBEFORE these strains arrive at a specific region (e.g. farm).
Project Methods
1. Development and implementation of PRRSV strain specific forecasting in NC: We will build upon thedeveloped discrete-time stochastic model described in the preliminary studies to simulate between-farm PRRSV transmission for specific strains. The model will include 6 main transmission routes,between-farm pig and transportation vehicle movements and local transmission (area transmission)which will account for the landscape and distance between susceptible and infected farms, namedhereafter simply as local transmission. Additionally, we will include the probability of the virus to persistwithin farms, causing re-break at sow farms. Among the main model outputs includes: i) the weeklyPRRSV number of infected farms by strain, both undetected and detected, ii) the estimated force ofinfection for each transmission route, farm production type and strain, and iii) forecasting risk areas forPRRSV and for each strain, and the comparison of simulated and observed infected locations to measuremodel accuracy and precision.2. Establishment of immune biobank, isolation of PRRSV strains from NC swine farms, and determinationof immunogenicity of PRRSV vaccines: The immune biobanks will be established four times throughoutthat project: In year 1, using a single vaccination with all currently available MLVs; and in years 2-4either using newly developed MLVs or using a prime/boost vaccination regimens including MLVs asprime and a multivalent AIV tailored to best fit the NC swine production as boost vaccination. In vivovaccination experiments: These vaccination regimens will be used to vaccinate nine pigs per group. Fourweeks post vaccination, pigs will be bled to isolate immune cells and serum. About 100 aliquots of eachserum (10 ml) and immune cell (107 PBMC) sample from each pig will be stored in the immune biobank.After blood isolation, pigs will be challenged with the most prevalent field strain in NC at the time theexperiment will be conducted. This PRRSV challenge will allow us to perform correlation analyses todetermine the best immune correlates of protection. Isolation of field PRRSV strains: PRRSV will beisolated from various field samples and grown on porcine alveolar macrophages (PAMs) for ten days. Invitro restimulation assays + pFCM: Immune cells from the biobank will be co-cultured with the isolatedPRRSV strain for four days. The isolated PRRSV strain will be incubated with serum from the biobank forone hour to allow for virus neutralization. Afterwards, remaining infectivity will be tested on PAMs by a24-hour incubation. The heterologous T-cell response and cross-neutralizing antibodies (nAbs) will bedetermined using polychromatic flow cytometry (pFCM). Thereby, this system allows the comparison ofa PRRSV-strain specific immunogenicity of different vaccination regimens. In combination with theestablished immune correlates of protection (e.g. nAbs, IFN-γ production, or effector memory T-helpercells) during the in vivo experiments, this system can educate the NC swine industry on the bestavailable vaccine regimen. In return, the swine industry will provide feedback of pig performance andprovide blood samples to further optimize the immune correlates of protection determination.3. Extension: Quarterly stakeholder meetings will be conducted with project participants - primarily swineveterinarians and other swine health personnel working for participating farms. The purpose of thesemeetings is to provide a forum for information exchange to identify knowledge gaps. To achieve this,meetings will aim to: i) provide participants regular updates on the project, clarify purpose andobjectives of research, and discuss findings; ii) create opportunities for exchange of information andideas on mechanisms of transmission and mitigation strategies; iii) identify additional ways toincorporate knowledge from local experience into the created tool; iv) document how the producers areusing the tool to make decisions about applying this project recommendations.

Progress 07/01/23 to 06/30/24

Outputs
Target Audience: North Carolina swine veterinarians and pig producers Elanco Swine Business Unit (USA) (Distinguished Research Scientist, Mark Hammer) Smithfield Foods Prestage Food Farms US pig producers Changes/Problems:Crisci lab has been looking for a new postdoctoral researcher since May 22nd 2024. Dr Crisci offered a position to an international candidate during July 2024. The candidate will need to process a VISA and there will be some delay in the starting date and participation in the project. The postdoc is the key personnel for Objective 2 (Crisci lab). Machado lab's graduate student will end the program during 2024. Machado lab will have a postdoc continuing the Objective 1. We will change salaries distributions in the budget. What opportunities for training and professional development has the project provided? Crisci lab: training activities on immunological/virological assay and animal handling were performed for undergraduate students (Christina Bourne and Katie Cortese), postdoc (Dr. Lanre Sulaiman) and research assistant (Jake Byrne). Machado lab: training activities on modelling, phylogenetics etc were performed for the graduate student (Faith Kennedy) How have the results been disseminated to communities of interest? The NC pig industry was informed about the progression of the project at the North Carolina Veterinary Conference (NCVC) Swine Meeting on 11/3/23 Raleigh NC and in the NC Swine veterinary meeting on 7/31/24 Kenansville, NC. The US pig industry was informed about the progression of the project at the NAPRRSV conference (12/2023) and with the swine black belt podcast episode. The project was communicated to the international pig community during the IVIS 2023 (South Africa). Outreach activities with Elanco, Smithfield Food industry, Country View Family Farms throughout the year were done by Drs Crisci, Machado, Ferreira and Almond. What do you plan to do during the next reporting period to accomplish the goals? 1 paper is in preparation for objective 2 of the project and will be submitted during year 3. The NC pig industry will be informed about the progress of the project duringthe 2024 NC veterinary conference swine meeting (November 2024). The US pig industry will be informed about the progress of the project during the following conferences: NAPRRSV 2024 and CRWAD 2025. Dr Crisci will provide additional information and updates on the PreProPRRSV project future Swine Health Blackbelt Podcast episodes with Dr. Clayton Johnson. Crisci lab will run another pig trial to create a new immune biobank to improve the vaccine efficacy prediction.

Impacts
What was accomplished under these goals? Objective 1 (Establish a PRRSV forecasting technology) year 2:1,822 PRRSV sequences have been collected and analyzed via IQ-Tree and Bayesian Evolutionary Analysis Sampling Trees (BEAST) and have been prepared to be used in our transmission model PigSpread. Thus, using real-world data, we determined the most common PRRSV lineages circulating in recent years. We incorporated actual swine movements into our model, promoting the accuracy and applicability of our results. In addition to this information, our new model incorporates multiple strains and multiple vaccines with varying levels of efficacy. To that end, we have reconstructed the pig population dynamics at the barn level to model the dissemination of single and multi-PRRSV staging dissemination. Our results demonstrated that the model confirmed the delay of PRRSV peaks when the vaccine matched the single strain circulation and the lack of significant effects over the dissemination when more than one strain is present. Data summarized in the preprint submitted (see product, preprint). Objective 2 (Establish a vaccine efficacy prediction system) year 2: The vaccine immune biobank has been tested in ELISPOT IFN-γ assay towards 7 PRRSV-2 strains: NC134 (RFLP 1-3-4), NC18-9-7 (RFLP 1-7-4), NC20-1 (RFLP 1-4-4), NC23-11 (RFLP 1-7-4), VR2332 (RFLP 2-5-2), NADC-20 (RFLP 1-4-2), NADC-30 (RFLP 1-4-4) and 5 vaccine strains: Ingelvac MLV strain, Fostera MLV strain, Prevacent MLV strain, PrimePac MLV strain, PRRSGard MLV strain. Preliminary Results: Difference in vaccine responses were observed based on the PRRSV-2 strains used. Using NC18-9-7 restimulation, Fostera vaccinated animals showed the highest IFN-γ production compared to other groups. Using VR2332 and NC23-11 restimulation, Fostera and Ingelvac showed the highest responses compared with other vaccine groups. Using NC20-1 restimulation, Ingelvac group showed the highest responses. All vaccines showed similar responses against NC134 and NADC-20. A Fluorescent Focus Neutralization (FFN) assay was performed as reference assay by South Dakota State University Diagnostic Laboratory to detect PRRSV neutralizing antibodies. In the FFN assay the immune biobank samples were used against 4 different PRRSV-2 strains: NC134, NC18-9-7, VR2232 and NADC-20.SDSU Results: Ingelvac and Primepac vaccinated animal showed highest PRRSV neutralizing antibody (nAb) titers against NADC-20. Ingelvac and Prevacent vaccinated animals had the highest nAb titers against VR2332. All vaccines did not show nAb titers against NC134 and NC18-9-7. Crisci lab has standardized an immunofluorescence-based sero-neutralization (SN) assay like FFN using SR30-A antibody (RTI). The comparison with the SDSU reference FFN results is ongoing. The lab will be using the in-house SN assay to evaluate PRRSV-neutralizing antibodies and their cross-reaction with all the different PRRSV-2 strains available in the lab. The lab is standardizing an avidity assay: the assay will measure the functional affinity (avidity) of antibodies toward a specific antigen (PRRSV). The assay will complement the SN assay in case low or null levels of neutralizing antibodies are detected with the in-house SN tests. Proliferation assay and Intracellular Cytokine Staining (ICS) assay using the immune biobank towards different PRRSV2- strains are ongoing. In the proliferation assay we evaluate CD4, CD8 and T- γδ cell subpopulations from each vaccinated animal (biobank) and their proliferation rate after restimulation with different PRRSV-2 strains. The ICS assay evaluates the levels of IFN-γ- producing T cell subpopulations (CD4, CD8, T- γδ) after restimulation with different PRRSV-2 strains. These assays will complement the ELISPOT IFN-γ assay in case low levels of IFN-γ producing cells are detected with ELISPOT. Preliminary results with ICS: Fostera showed consistently higher percentage of IFN-γ producing T-γδ against NC20-1, NC134 and VR2332 strains compared with other vaccine group. PRRSGard and Primepac groups showed the lower levels of IFN-γ producing CD4 cells after VR2332 restimulation, the other groups had similar responses. Ingelvac and Prevacent showed the lower levels of IFN-γ producing CD4 cells after NC134 and NC20-1 restimulations, the other groups showed similar responses. The Crisci lab has isolated a new NC PRRSV-2 strain from samples collected in a NC farm with a PRRSV-2 outbreak during Fall 2023. The PRRSV-2 strain was identified as lineage 1A, RFLP 1-7-4 at ISU-VDL. After reception of the sample from ISU-VDL the lab was able to successfully propagate the strain in porcine alveolar macrophages. The strain did not replicate in MA104 cells. The NC PRRSV-2 strain was submitted to Cambridge technologies for whole genome sequencing and was annotated as NC23-11 (see "other products" list). Crisci lab has received samples from NC outbreaks during Summer 2024 and is currently isolating the virus from those farms. Crisci lab in collaboration with Dr Hause (Cambridge technologies) has evaluated the sequence homology between the PRRSV-2 wild type strains used in the biobank (NC134, NC18-9-7, NC20-1, VR2332, NADC-20, NC23-11) and the vaccine strains (Ingelvac MLV strain, Fostera MLV strain, Prevacent MLV strain, PrimePac MLV strain, PRRSGard MLV strain) based on both ORF5 and whole genome sequencing (WGS). After the completion of ongoing in vitro assays, the homology between PRRSV WGS sequences will be used to predict vaccine efficacy with future strains isolated from the field.

Publications

  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: POSTER: PREDICT AND PROTECT AGAINST PRRSV (PREPROPRRSV): COMBINING PRRSV FORECASTING TECHNOLOGY WITH VACCINE EFFICACY PREDICTION TO PREVENT PRRSV OUTBREAK. Gustavo Machado, John Byrne, Lanre Sulaiman, Jason Ardila Galvis, Faith Kennedy, Juliana Ferreira, Glen Almond, Tobias K�ser, Elisa Crisci. NAPRRS/NC229: International Conference of swine viral diseases 2023, Chicago, USA, November 30-December 2, 2023.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: POSTER: PREDICT AND PROTECT AGAINST PRRSV (PREPROPRRSV): COMBINING PRRSV FORECASTING TECHNOLOGY WITH VACCINE EFFICACY PREDICTION TO PREVENT PRRSV OUTBREAK. Gustavo Machado, John Byrne, Lanre Sulaiman, Jason Ardila Galvis, Faith Kennedy, Juliana Ferreira, Glen Almond, Tobias K�ser, Elisa Crisci. 13th International Veterinary immunology Symposium (IVIS) 2023 Kruger Park South Africa, November 17-21, 2023.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: INVITED ORAL PRESENTATION: EVALUATING PRRSV IMMUNE RESPONSES WITH THE PRRS VACCINE CELL BANK. Elisa Crisci. North Carolina Veterinary Conference (NCVC) Swine meeting, November 3rd, 2023, Raleigh, NC.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2024 Citation: INVITED ORAL PRESENTATION: PreProPRRSV update. Gustavo Machado, John Byrne, Lanre Sulaiman, Jason Ardila Galvis, Faith Kennedy, Juliana Ferreira, Glen Almond, Tobias K�ser, Elisa Crisci. NC swine vet meeting in Kenansville on July 31st 2024. The NC pig industry was informed about the progression of the project.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2024 Citation: Abstract and ORAL PRESENTATION: PREDICT AND PROTECT AGAINST PRRSV (PREPROPRRSV): COMBINING PRRSV FORECASTING TECHNOLOGY WITH VACCINE EFFICACY PREDICTION TO PREVENT PRRSV OUTBREAK. Lanre Sulaiman, Gustavo Machado, John Byrne, Jason Ardila Galvis, Faith Kennedy, Juliana Ferreira, Glen Almond, Tobias K�ser, Elisa Crisci. Litwack day CVM Research Forum, August 11, 2024, Raleigh, NC
  • Type: Journal Articles Status: Other Year Published: 2024 Citation: Preprint: Kennedy, F., Cardenas, N., Galvis, J. A., Corzo, C. & Machado, G. Modeling the effects of vaccination against multiple strains of porcine reproductive and respiratory syndrome at the barn level. bioRxiv (2024) doi:10.1101/2024.08.06.606602. https://www.biorxiv.org/content/10.1101/2024.08.06.606602v1


Progress 07/01/22 to 06/30/23

Outputs
Target Audience: North Carolina swine veterinarians and pig producers Elanco Swine Business Unit (USA) (Distinguished Research Scientist ) Smithfield Foods Prestage Food Farms Changes/Problems: Resignation of Dr. Watanabe and removal from project, approved in USDA letter on 11/29/2022. Change in Leading PI from Dr. Kaeser to Dr. Crisci, approved in USDA letter on 11/29/2022. Change in leading PI of IACUC-approved protocol, updated on 9/27/2022, and accepted in USDA letter on 11/30/2022. Change in Co-I, accepted in USDA letter on 3/21/2023. Problem in availability of CVM animal facility area, pig space booked until June 2023. Problem in availability of PRRSV negative pigs. NCSU/CVM swine facility could not supply the pigs for our use/purchase as planned, which caused us to find an alternative source for PRRSV negative pigs. Smithfield has provided pigs for the immune biobank trial. What opportunities for training and professional development has the project provided? Dr. Crisci Lab: training activities on immunological/virological assay and animal handling were performed for an undergraduate student (W.Broderdorp), post doctorate (Dr. L.Sulaiman) and research assistant (J.Byrne). Dr. Machado Lab: training activities on modelling, phylogenetics etc were performed for the graduate student (F.Kennedy) How have the results been disseminated to communities of interest? North Carolina Veterinary Conference (NCVC) Swine Meeting on 11/4/22 Raleigh NC The NC pig industry was informed about the progression of the project and the availability of the immune biobank during the NC swine vet meeting in Kenansville on July 25th 2023. The update was presented by the post doc (Dr. Sulaiman) and the graduate student (F.Kennedy). Outreach activities with Elanco, Smithfield Food industry throughout the year done by Drs Crisci, Machado, Ferreira, Almond. What do you plan to do during the next reporting period to accomplish the goals? Prepare a paper for the project testing the immune biobank against different NC PRRSV-2 strains already present in Crisci lab (NC134, NC174, NC144), against prototype strains (e.g., VR2332, NADC20) and PRRSV-2 strains isolated from Winter 2023. Beginning of outbreaks is expected after October 2023. The NC pig industry will be informed about the progress of the project during the NCVC Swine meeting planned for November 3rd 2023.

Impacts
What was accomplished under these goals? Objective 1 (Establish a PRRSV forecasting technology) year 1: 1,822 PRRSV sequences have been collected and analyzed via IQ-Tree and Bayesian Evolutionary Analysis Sampling Trees (BEAST) and have been prepared to be used in our transmission model PigSpread. Objective 2 (Establish a vaccine efficacy prediction system) year 1: Creation of the immune biobank of immunological samples (immune cells + serum) from pig vaccinated with the commercially available PRRSV vaccines: Prevacent (Elanco), Fostera PRRS (Zoetis), Ingelvac PRRS MLV (Boehringer Ingelheim Vetmedica), Prime Pac PRRS RR (Merck Animal Health), PRRSGard (Pharmgate Animal Health), and controls. The immune biobank includes 9 pigs/group, 81 vials of plasma (1ml/tube) per pig, 81 vials of PBMCs per pig (range 10-100 million PBMCs/tube). The immune biobank has been established in Crisci lab at the NCSU CVM. Objective 2 (Establish a vaccine efficacy prediction system) year 1: Standardization of ELISpot assay using a NC PRRSV-2 isolates has been performed. Objective 2 (Establish a vaccine efficacy prediction system) year 1: PRRSV correlates of protection have been defined, and a review paper has been published on those (see products).

Publications

  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2023 Citation: Abstract: Predict and Protect against PRRSV (PreProPRRSV): Combining PRRSV forecasting technology with vaccine efficacy prediction to prevent PRRSV outbreak. Gustavo Machado, John Byrne, Lanre Sulaiman, Jason Ardila Galvis, Faith Kennedy, Juliana Ferreira, Glen Almond, Tobias K�ser, Elisa Crisci. Submitted to the NAPRRS/NC229 International Conference of Swine Viral Diseases, Chicago, USA, November 30-December 2, 2023.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Kick, A.R.; Grete, A.F.; Crisci, E.; Almond, G.W.; K�ser, T. Testable Candidate Immune Correlates of Protection for Porcine Reproductive and Respiratory Syndrome Virus Vaccination. Review. Vaccines 2023, 11, 594. https://doi.org/10.3390/vaccines11030594 https://www.mdpi.com/2076-393X/11/3/594
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Oral presentation: The (adaptive) immune response to PRRSV Dr. Kaeser at North Carolina Veterinary Conference, NCVC Swine Meeting held in Raleigh on 11/4/2022.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2023 Citation: Abstract: Predict and Protect against PRRSV (PreProPRRSV): Combining PRRSV forecasting technology with vaccine efficacy prediction to prevent PRRSV outbreak. Gustavo Machado, John Byrne, Lanre Sulaiman, Jason Ardila Galvis, Faith Kennedy, Juliana Ferreira, Glen Almond, Tobias K�ser, Elisa Crisci. Submitted to the 13th International Veterinary Immunology Symposium, Kruger National Park, South Africa, November 17-21 2023.