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

该项目旨在制定一种战略方法，在菲律宾查明和防治猪繁殖与呼吸综合征病毒（PRRSV）疫情和其他猪病毒性疾病。菲律宾是世界第八大猪肉生产国，每年生产超过1700万吨猪肉。然而，猪肉生产仍主要依赖后院农场，据报道，2016年，该国约1250万头猪中有64%是后院农场饲养的。后院农场和商业农场在耕作方式上的差异需要强有力的战略方法来防止病原体在农场和系统之间传播。后院农场通常使用杂交的商业西方/本土品种猪，几乎没有适当的生物安全措施，很少依赖兽医咨询，缺乏诊断，并且允许相当自由和无监督地使用抗生素。相比之下，商业化养猪场依赖于商业化的优质西方猪品种，主要是从领先的育种公司（如PIC和Topigs Norsvim等）引进的长白猪/大白猪/杜洛克猪杂交品种。商业农场尽管很少使用诊断方法来支持临床诊断，但正在采用广泛的疫苗接种计划；然而，目前这在预防疾病方面并不总是有效。改进诊断、监测、监督和审查目前的生物安全和疫苗接种战略对于采取有针对性的方法进行疾病控制至关重要。因此，本项目旨在评估商业养殖场和后院养殖场目前的卫生状况，确定当前的疫苗接种策略，并确定PRRSV和PEDV的流行毒株和亚型。我们将利用传统的Sanger和下一代野外样本测序进行系统动力学和系统地理学分析，这将有助于了解PRRSV和PEDV暴发的传播和来源，并进一步为疾病预防策略提供帮助。这些结果将使我们对菲律宾养猪业目前的健康和生物安全状况有一个总体的了解，并将使我们能够开发具体的、易于使用的诊断工具，使农民能够明确地识别其库存中存在的疾病，并建议有针对性的疫苗接种和生物安全措施。我们的目标是开发基于逆转录环介导的等温扩增（RT-LAMP）或逆转录重组酶聚合酶扩增（RT-RPA）的鉴别诊断工具，用于系统性病毒性疾病，包括PRRSV、CSFV、PCV2和IAV-S，以及肠道病毒性疾病，包括PEDV、TGEV和轮状病毒。我们将采用易于使用的流条检测方法来开发允许区分病毒和/或亚型的多重测试。根据我们的研究结果，我们的目标是为商业和后院农场提供有针对性的建议，以预防和对抗猪的病毒性疾病。

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.