Predicting PED Outbreaks, PRRS Transmission, and Adding Genetic Analysis to SHIC-Funded MSHMP
July 8, 2020 — Paul Sundberg
Building capacity for disease response means an outbreak has happened and a response is needed. How about stopping the outbreak from happening? One of the goals of the Morrison Swine Health Monitoring Program (MSHMP), partially funded by the Swine Health Information Center (SHIC), is to make real-time farm-level risk predictions for porcine epidemic diarrhea virus (PEDv) and porcine reproductive and respiratory virus (PRRSv). Making the predictions two weeks in advance allows production systems to take actions to prevent or mitigate the impact of a disease outbreak.
The forecasting process is intended to be achieved via a server-run machine learning model that will take into account the past weeks' status of farms, animal movements, and environmental characteristics (temperature, humidity, season, land cover, among others). To create the machine learning model, MSHMP collected retrospective movement and farm status data (2014-2017) from systems representing approximately 30% of the US sow herd. Based on retrospective data, the model was able to correctly detect ~20% of PEDV outbreaks, and 70% of outbreaks predicted by the model did subsequently occur. PRRSV prediction has shown to be more challenging, possibly related to its intense genetic variation that might reflect in immune interactions not present in PEDV.
In December 2019, MSHMP began sending partnering systems weekly real-time PEDV predictions. Veterinarians receiving these reports are sent a ranked list of their sow farms according to which ones are most at risk of outbreaks, and this information is being used in decisions about whether or not to implement interventions and to emphasize biosecurity compliance on high-risk farms.
Data gathered from MSHMP have also been used to understand animal movements and their role in PRRS transmission in the US swine industry. MSHMP has been able to demonstrate that more PRRS spread is associated with farm contacts through animal movements as opposed to local area spread. Furthermore, the length of potential outgoing infection chains disseminated from some farms can be extremely large, upwards of 650 farms in extreme cases (which was approximately 25% of the farms in the network) in a period of six months. This is indicative of the presence of "super-spreader" farms within the network which may contribute to rapid disease spread via animal movements.
Overall, the risk of 1-7-4 (Lineage L1A) occurrence in a given farm increased not only as a result of direct contact via animal movements with an L1A-positive farm, but also increased as a result of indirect connections (contact of a contact) with L1A-positive farms. Moreover, farms that engaged in more outgoing movements also experienced higher risk. This suggests the risk due to animal movements is not only associated with movements of infected animals to the destination, but also from potential movement-related breaches in biosecurity on the origin farm and underscores the importance of transport-related biosecurity.
MSHMP also is cataloging and analyzing PRRSV genetic sequences shared by participants in order to better understand the drivers of regional circulation and spread of PRRSV. With this genetic data, MSHMP documented the ongoing diversification and temporal dynamics of different PRRSV lineages, including the emergence of specific sub-lineages that appeared to be absent globally pre-2008. MSHMP also identified evidence of positive selection on immunologically important regions of the genome, which supports the hypothesis that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This work is published in a scientific journal (Frontiers in Microbiology, Impact Factor 4.076) and can be found here.
As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America's pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit http://www.swinehealth.org or contact Dr. Sundberg at firstname.lastname@example.org.
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