Novel approaches to investigation and control of important viral diseases in swine populations

传染病病原传播的调查和成功控制是猪群卫生管理的重要目标。猪繁殖与呼吸综合征病毒（PRRSV）等传染性病原体仍然是猪死亡和产量损失的最重要原因。尽管PRRSV和其他病原体地方性传播，但调查它们的传播并不简单，因为PRRSV存在许多变体，而且病毒不断进化。因此，即使人群以前接触过另一种变种，新出现的PRRSV也可能发生流行传播。先前的研究表明，各个站点之间的连通性很高；要么通过动物运动，要么通过专门的服务提供商。尽管如此，应用新方法，如基于核苷酸序列（NSeq）数据估计最可能的传播链，可用于协助疫情调查。NSeq数据应辅以流行病学数据，如动物运动或畜群之间的其他接触。畜群之间的相互联系也对生产系统一级和区域内控制策略的设计产生影响。这是因为在一个生产阶段实施的干预措施可能对其他生产阶段的感染产生影响。在具有多个地点的整个生产系统层面应用这种干预措施的有效性的直接证据很少。因此，需要考虑其他方法，以帮助了解野外条件下病原体的动态，调查成功干预应针对的关键点，基于相关生产系统和问题进行模拟，并根据观察到的数据评估模拟结果。该提案的总体目标是将现有的猪健康数据与观察和模拟研究相结合，以进行有效的疾病调查，实时监测疾病频率趋势，并设计猪群中重要病毒感染的控制策略。该项目的具体目标是：(i)利用分子和经典流行病学方法确定PRRSV在猪群中的传播机制，（ii）建立对来自多个来源的猪健康数据进行持续处理、分析、可视化和解释的机制，（iii）进一步开发猪群和地区层面的病毒感染控制模型，以及（iv）描述加拿大养猪业从业者关于疾病控制选择的信息流。本提案将讨论的感染因子包括PRRSV、甲型流感病毒和新出现的PEDV。数据来源将是现有的疾病控制规划；数据分析将使用统计和数学模型以及网络分析进行

Investigation of transmission of infectious agents and their successful control are important goals in the health management of swine populations. Infectious agents such as porcine reproductive and respiratory syndrome virus (PRRSV) continue to be the most important cause of mortality and production loss in swine. Although PRRSV and other pathogens circulate endemically, investigating their spread is not straightforward because many variants of the PRRSV exist and the virus continuous to evolve. Thus, epidemic spread of a newly emerging PRRSV could occur even if populations were previously exposed to another variant. Previous work indicates high level of connectivity among individual sites; either through animal movement or specialized service providers. Nonetheless, application of novel approaches such as estimation of the most likely transmission chain based on nucleotide sequence (NSeq) data could be used to assist in outbreak investigations. NSeq data should be augmented by epidemiological data such as animal movement, or other contacts among herds. The interconnectedness of herds also has consequences on the design of control strategies, both at the level of a production system and within a region. This is because interventions applied in one production phase could have implications on infection in other phases of production. Direct evidence for efficacy of such interventions applied at the level of entire production systems with multiple sites is scarce. Thus, additional approaches need to be considered to help understand dynamics of pathogens under field conditions, to investigate critical points that should be targeted for successful intervention, to conduct simulations based on relevant production systems and questions, and to evaluate results of simulations against the observed data. The overarching goal of this proposal is to integrate existing swine health data with observational and simulation studies for the purposes of efficient disease investigations, real-time surveillance of trends in disease frequency, and design of control strategies for important viral infections in swine populations. Specific objectives of this program are to: (i) determine mechanisms of spread of PRRSV among swine herds using molecular and classical epidemiological methods, (ii) establish mechanisms of ongoing processing, analysis, visualization, and interpretation of swine health data from multiple sources, (iii) further develop herd- and regional-level control models for viral infections, and (iv) characterize flow of information regarding disease control options among swine practitioners in Canada. Infectious agents that will be addressed in this proposal include PRRSV, influenza A virus, and newly emerged PEDV. Sources of data will be existing disease control programs; the data analysis will be conducted using statistical and mathematical models and network analysis.**