This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.
This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.
We launched a new series on the blog last year. Once a month, we are sharing with you a presentation given at the Allen D. Leman swine conference, on topics that the swine group found interesting, innovative or that lead to great discussions.
We can find all of the presentations selected from last year’s conference on the blog here.
Our seventh presentation is by Dr. Andreia Arruda from the Ohio State University regarding the impact people can have on PRRS elimination success.
This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.
This week, Dr. Mariana Kikuti and the MSHMP team share the evolution of PRRS ORF 5 from the original strain discovered in the 90s.
Key Points
ORF5 sequencing for PRRSv monitoring have been increasing over time
ORF5 nucleotide divergence from the reference VR2332 averaged at around 10-15% throughout 2000-2018.
This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.
Across states, different EWMA patterns continue to be observed.
The expected high PRRS incidence during fall/winter was not as marked both in duration and magnitude in some states during the 2018-2019 season.
Reminder: What is the EWMA?
The Exponential Weighted Moving Average (EMWA) is a statistical method that averages data over time, continually decreasing the weight of data as it moves further back in time. An EWMA chart is particularly good at monitoring processes that drift over time and is used to detect small shifts in a trend.
In our project, EWMA is used to follow the evolution of the % of farms at risk that broke with PRRSV every week. EWMA incorporates all the weekly percentages recorded since the beginning of the project and gives less and less weight to the results as they are more removed in time. Therefore, the % of farms at risk that broke with PRRSV last week will have much more influence on the EMWA than the % of farms at risk that broke with PRRSV during the same week last year.
The charts depict: 1)the number of new cases (green dots – secondary Y axis) during a specific week and 2)the percentage of farms that broke during that week of the total in the MSHMP project in a smoothed way (blue line/Y axis). The red horizontal line indicates the threshold (upper confidence limit – UCL). This UCL is calculated based on the average of cases during the lowest PRRS months in the year, June, July and August and is recalculated every two years. When there are more cases than expected, the blue line crosses the threshold (red line) indicating there is an epidemic.
The formula used in the EWMA chart is the following:
where E is the smoothed % of infected herds, lambda the constant smoothing the curve, I the % of infected herds during that week and Et-1 is the smoothed % of infected herds during the previous week.
EWMAs by state
Minnesota: As expected, this season EWMA crossed the epidemic threshold by the end of October/beginning of November 2018. However, the magnitude and duration of the epidemic was lower and shorter than in the 2017-2018 season. Incidence dropped during December 2018-January 2019 but lingered above the epidemic threshold until Mid-February, 2019.
Iowa: The 2018/2019 PRRS season started slightly earlier than in Minnesota and it was higher in magnitude than in any other of the assessed states. Although it reached a similar peak than in the 2017-2018 PRRS season in Iowa, its duration appeared to have been shorter since the EWMA went below the epidemic threshold during Mid-February 2019, which was about three months earlier than in the previous season.
North Carolina: As the 2017-2018 PRRS season, the epidemic begun on Nov of 2018. However, the 2018-2019 PRRS season was about three months shorter than the 2017-2018 PRRS season. The EWMA crossed the epidemic threshold momentarily in September/October 2018 but dropped below it until Mid-November when it crossed the epidemic threshold again to remain above it for about four months.
Oklahoma: Had a drastically different PRRS pattern than the 2017Ͳ2018 MSHMP season. The 2017-2018 PRRS season continued well into the summer, and only stayed below the epidemic threshold for about two months. PRRS incidence during the 2018-2019 season has been drastically lower than the one during the 2017-2018 season, staying at around 0.5%, and moving below the epidemic threshold several times.
Nebraska: The 2018-2019 fall/winter were characterized by a pattern of fewer, and more intermittent cases than the 2017-2018 fall/winter. No obvious PRRS season can be observed since PRRS outbreaks occurred sporadically throughout the year.
Illinois: Had a long PRRS season in 2017-2018 with the EWMA remaining mostly above the epidemic threshold for almost a year. In comparison, the 2018-2019 PRRS season started almost three months later in the year and its incidence has been lower than in 2017-2018, with the EWMA sporadically crossing above the epidemic threshold during the 2018Ͳ2019 fall and winter.
