A strategic approach to identifying and combating porcine reproductive and respiratory syndrome virus outbreaks and other porcine viral diseases

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

This project aims to develop a strategic approach to identify and combat porcine reproductive and respiratory syndrome virus (PRRSV) outbreaks and other porcine viral diseases in the Philippines. The Philippines are the world's 8th largest producer of pork producing over 1,700 mega tons of pork meat per year. However, the pork production still relies largely on backyard farms, which, in 2016, were reported to house 64% of the roughly 12.5 million animals in the country. This divergence in farming practises between backyard and commercial farms requires a robust strategic approach to prevent pathogen spread across farms and systems. The backyard farms often use crossbred commercial western/indigenous breed pigs, with few biosafety measures in place, rarely rely on veterinary consultation, lack diagnostics, and allow fairly liberal and unsupervised access to antibiotics. In contrast, the commercial farms rely on commercial highly bred western pig breeds, mostly Landrace/Large White/Duroc crosses brought in from leading breeding companies, such as PIC and Topigs Norsvim, amongst others. The commercial farms, despite little usage of diagnostics to support clinical diagnoses, are employing extensive vaccination schemes; however, currently this isn't always effective in preventing disease. Improved diagnostics, monitoring, surveillance and reviewing of current biosafety and vaccination strategies are essential to employ a targeted approach to disease control.

Therefore, this project aims to assess the current health situation in commercial and backyard farms, to identify current vaccination strategies, and to identify circulating strains and subtypes of PRRSV and PEDV. We will use traditional Sanger and next generation sequencing of field samples to conduct phylodynamic and phylogeographic analysis, which will help to inform the spread and source of PRRSV and PEDV outbreaks, and which will further aid disease prevention strategies. The outcomes will give us an overview of the current health and biosafety situation in the Filipino pig industry and will allow us to develop specific, easy-to-use diagnostic tools that will enable farmers to specifically identify diseases present in their stock and advise targeted vaccination and biosafety measures. We aim to develop differential diagnostic tools based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) or reverse transcription recombinase polymerase amplification (RT-RPA) for systemic viral diseases including PRRSV, CSFV, PCV2, and IAV-S, and for enteric viral diseases including PEDV, TGEV, and rotaviruses. We will employ easy-to-use flow strip detection methods to develop multiplex tests that allow differentiation between viruses and/or subtypes. From our results, we aim to generate targeted advice for both commercial and backyard farms in order to prevent and combat viral diseases in pigs.

Planned Impact

Who will benefit from this research?

The potential non-academic beneficiaries of this research include pig diagnostic labs, pig health companies, pig breeding companies, pig producers and ultimately the entire chain of users of pig products, including meat packers, processors, retailers and consumers. There are also potential benefits to the pig vaccine sector.

How will they benefit from this research?

Porcine viral disease is of major impact to pigs of all ages. Clinical manifest disease often leads to high mortality in suckling and weaned piglets and slower weight gain in animals of all ages. Therefore, this has an immediate effect on feed efficiency, productivity and the livelihood of farmers. Accurate and fast diagnostic will allow to take the correct biosafety and biosecurity measures to prevent disease spread, advise the use of appropriate vaccination where available, and in consequence improve the health of one farm and prevent spread to other farms. This benefits the pig producers, as well as the pig product chain immediately. Pig diagnostic labs and pig health companies can be involved in the commercialisation and distribution of such diagnostic tools and the pig breeding companies are benefiting from wealthier farmers that can afford high breed animals, but also their own elite and producer farms will be benefiting from these tools.

Publications

10 25 50
 
Description We have successfully developed robust protocols to sequence and assemble full-length genomes of porcine reproductive and respiratory syndrome virus (PRRSV) using Nanopore MinION sequencing from serum samples and tissue culture amplified virus by cDNA, PCR-product, and RNA sequencing. We are in the process of publishing these findings.

Samples from regions IV, III, X, and V have been collected and so far 40 samples were found to be PRRSV-positive. Due to the outbreak of ASFV in autumn 2019 sampling has been disrupted. Therefore, we opted for using samples linked to the ASFV depopulation, which will give us further PRRSV-positive samples from ASFV-negative farm pools.

Reagents and protocols for multiplex porcine virus diagnostics have been developed and are currently being assessed and protocols optimised. Whilst multiplexing works in the lab we are currently putting this on hold due to the difficulties of obtaining RPA reagents in the Philippines, which makes the application of the diagnostic test difficult. Therefore, we have focused on the development of RT-LAMP assays and we have robust protocols for CSFV, PRRSV-1 and -2, PEDV, as well as ASFV. Our Filipino collaborators have obtained follow-on funding to further optimise the ASFV RT-LAMP for application within the current outbreak.
Exploitation Route As most of the protocols are still being developed the findings are currently not ready for use by others. However, we have assisted and obtained further funding in association with this project to analyse PRRSV sequences from an experimental infection challenge performed within the SAPHIR EU project.
Sectors Agriculture, Food and Drink,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Development of rapid diagnostics for ASFV by RT-LAMP (grant obtained by our collaborator on this project, Dr Clarissa Domingo)
Amount Php11,000,000 (PHP)
Organisation Government of the Republic of the Philippines 
Sector Public
Country Philippines
Start 12/2019 
End 07/2021
 
Description Strengthening Animal Production and Health through the Immune Response (SAPHIR) - Sequencing of PRRSV samples
Amount € 10,549,121 (EUR)
Funding ID 633184 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 03/2015 
End 02/2019
 
Description [18-EEID US-UK DDCOVMP] Drivers of diversity and transmission of co-circulating viral lineages in host meta-populations
Amount £407,215 (GBP)
Funding ID BB/T004401/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2019 
End 08/2023
 
Description CLSU "Updates on Swine Diagnostics" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact A presentation on the benefits of new pen-side diagnostics and how they could help decision making by farmers and veterinary professionals. The audience were Veterinary students from Central Luzon State University (The Philippines).
Year(s) Of Engagement Activity 2018
 
Description Invited talk European Veterinary Vaccinology Workshop 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk on career opportunities in academia for young scientists
Year(s) Of Engagement Activity 2018
URL https://www.youtube.com/watch?v=hTujbImUCcI
 
Description Novel Control Strategies for Livestock and Poultry Diseases 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our collaboration partner Clarisssa Y. Domingo co-organised and participated in a workshop in Manila, bringing together British and Filipino Veterinary practitioners, policy makers and scientists to discuss " Novel Control Strategies for Livestock and Poultry Diseases" and how improved diagnostics and epidemiological analysis can help with this process.
Year(s) Of Engagement Activity 2019
 
Description Panel interview for Chinese media 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Under the framework of the Newton Swine and Poultry Workshop in Beijing, China, a panel interview with selected grant holders of the "UK-China-Philippines-Thailand Swine and Poultry Research Initiative" was held at China Agricultrual University. Chinese and China-based international press was in attendance (amongst others, Reuters) and reported on the initiative, developing new antiviral strategies, diagnostics and on other developments in the pig- and poultry industry in China and related research.
Year(s) Of Engagement Activity 2018
 
Description Seminar on genome editing for PRRSV resistance at CLSU, Munoz, The Philippines 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Genome editing for disease resistance in livestock in general and in pigs for PRRSV resistance was presented to all veterinary students and other department students at Central Luzon State University in the Philippines. Students could inquire the techniques and developments in this field and assess identify new approaches to disease treatments / prevention in animals.
Year(s) Of Engagement Activity 2019