Science Page: Incidence risk and incidence rate

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’s Science page is a follow-up from the one presented last week and focuses on the difference between incidence rate and incidence risk. Those two epidemiological measurements are often mistaken for one another.

Key points from this week edition:

  • Incidence risk is a measure of disease occurrence over a defined period of time. It is a proportion, therefore takes values from 0 to 1 (0% to 100%).
  • Incidence rate takes into account the time an individual is at risk of disease. It is not a proportion since it defines the number of cases per animal or farm time at risk.
  • Incidence risk and Incidence rate are often confused. Incidence risk and rate are numerically the same when the period at risk does not vary across individuals being studied.

Take a look at the complete report to see an example of the difference between incidence risk and incidence rate on farms.


Science Page: PRRS cumulative incidence by status

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.

How does PRRS incidence vary based on farm status? This is the question answered in this week’s edition of the Science Page. Three different formulas were used to calculate the incidence in each of the group over type. First, the initial number of farms of each status at the beginning of the year was used as the denominator. Then, the denominator was changed to the total number of farms that entered each status since the beginning of the year. Lastly, weekly incidences calculated for each of the group since the beginning of the year were added. Calculations went back for the last 3 years.

Key points from this week edition:

  • Cumulative incidence is higher in those farms that are under status 2, 2vx and 2fvi.
  • The incidence is lower in farms that had recently an outbreak or those that are completely negative.
  • Different ways of calculating incidence by herd status lead to the same overall conclusion.

Take a look at PRRS incidences in farms of group 2 status, vaccinated or inoculated with live virus over the past years.

PhD seminar: Epidemiological investigation of a non-reportable endemic disease: PRRS in the US

Title: Epidemiological investigation of a non-reportable endemic disease: Porcine reproductive and respiratory syndrome (PRRS) in the US

Presented by:   Pablo Valdes-Donoso

Date:    Friday, June 9, 2017
Time:    3:00 – 4:00 pm
Place:    385-J, AS/VM Building

Abstract: Porcine reproductive and respiratory syndrome (PRRS), caused by a highly mutagenic and resistant RNA-virus, is an endemic disease that has been noted as one of the most important animal production diseases in the US because of its large economic damage on the swine industry. Nonetheless, there is no official control framework for this disease, so producers rely on voluntary regional control programs (RCPs) for its mitigation. Despite efforts to control PRRS, it persists in the environment, affecting a large number of farms every year. Using information shared by a specific RCP (RCP-N212), this dissertation focused on important aspects of PRRS dynamics within an RCP. Specifically, this dissertation encompassed five chapters. An introductory chapter is followed by the second chapter, which quantifies the extent to which RCPs contribute to PRRS control. After that, a prediction of network structure was made to forecast animal movements among farms within the RCP-N212. Then, longitudinal data collected from sow farms were used to measure the impacts of PRRS on production. Finally, a disaggregated disease diffusion model was used to depict PRRS dynamics within the RCP-N212, as well as to evaluate individual and collective strategies adopted by producers. This dissertation provides insight to the evaluation of regional control strategies that may be used as a framework for a formal PRRS control program.

Mycoplasma hyorhinis prevalence varies based on pigs’ age


  • Mycoplasma hyorhinis can cause polyserositis and arthritis in post-weaning pigs.
  • To study M.hyorhinis‘ prevalence based on age, nasal swabs were taken from pigs at 1, 7, 14, 21, 28, 35, 42, 49, 56, 63, 70 and 77 days as well as from sows, in 3 different Minnesotan herds (A, B, and C).
  • 8.8% of the sows were positive for M.hyorhinis in herds A and B whereas 3.3% of the sows were positive in herd C.
  • The percentage of positive piglets (<21 days of age) was low: between 0 and 10% depending on the herds.
  • At 28 days of age, the prevalence of M.hyorhinis in pigs increased dramatically to around 50% in herd A and 100% in herd B. After 42 days of age, the prevalence in those herds stayed above 95%.
  • The prevalence in herd C stayed close to 0% until the pigs reached the age of 77 days, time at which the prevalence increased to 100%.

Did you see our Science page on Mycoplasma hyorhinis and swine conjunctivitis?

Mhyorhinis prevalence baed on age Rovira 2017


Mycoplasma hyorhinis is one of the causative agents of polyserositis and arthritis in postweaning pigs. Knowledge regarding colonization frequency and age distribution in modern pig production is lacking. The objective of this study was to estimate the prevalence of M hyorhinis colonization in different age groups across three commercial pig populations. Nasal swabs were collected from sows, piglets and nursery pigs of different ages. Oral fluids were collected from nursery pigs. Necropsies were performed to assess the presence of M hyorhinis-associated disease. M hyorhinis was detected in 5/60 sows in herd A, 3/60 in herd B and none in herd C. In herd A and B, the prevalence was low in preweaning piglets (∼8 per cent) and high in postweaning pigs (∼98 per cent). A total of 7/8 oral fluids tested PCR positive in herds A and B, while 1/8 tested positive in herd C. In herd C, the preweaning and postweaning prevalence was low. In herds A and B, necropsied pigs had polyserositis lesions where M hyorhinis was detected by PCR. This study showed that prevalence of M hyorhinis colonization varies with pig age and across farms. Information generated will aid in the design and implementation of control and prevention strategies.

Link to the full paper

Can biosecurity measures prevent PEDV transmission?


Porcine Epidemic Diarrhea virus is highly contagious.

The 2013 Porcine Epidemic Diarrhea virus’ (PEDV) outbreak in the USA taught the swine industry that the virus is highly contagious. This event forced producers and veterinarians to review and upgrade their biosecurity procedures.

Drs. Torremorell, Cheeran, and Goyal from the University of Minnesota evaluated some of these measures and how they can prevent PEDV transmission.

Changing Personal Protective Equipment (PPE) and showering before entering a new room prevented contamination.

Among the measures included in this study were the use and change of PPE as well as showering in and out of a facility. In the low biosecurity setting, personnel went from a room with PEDV positive pig straight to a room with naive pigs, contaminating them after the very first movement. In the medium biosecurity setting, personnel washed their hands and face and change their PPE before being in contact with the naive pigs. In this situation, pigs stayed negative for PEDV but  two personnel hair/face swabs came back positive for viral genetic material. On the contrary, personnel showered before getting in contact with the high biosecurity group. Those pigs as well as all personnel tests remained negative for PEDV during the study.


Torremorell PEDV biosecurity 2017



The effectiveness of biosecurity methods to mitigate the transmission of porcine epidemic diarrhea virus (PEDV) via farm personnel or contaminated fomites is poorly understood. This study was undertaken to evaluate the effectiveness of biosecurity procedures directed at minimizing transmission via personnel following different biosecurity protocols using a controlled experimental setting.

PEDV RNA was detected from rectal swabs of experimentally infected (INF) and sentinel pigs by real-time reverse transcription polymerase chain reactio n (rRT-PCR). Virus shedding in INF pigs peaked at 1 day post infection (dpi) and viral RNA levels remained elevated through 19 dpi. Sentinel pigs in the low biosecurity group (LB) became PEDV positive after the first movement of study personnel from the INF group. However, rectal swabs from pigs in the medium biosecurity (MB) and high biosecurity (HB) groups were negative during the 10 consecutive days of movements and remained negative through 24 days post movement (dpm) when the first trial was terminated. Viral RNA was detected at 1 dpm through 3 dpm from the personal protective equipment (PPE) of LB personnel. In addition, at 1 dpm, 2 hair/face swabs from MB personnel were positive; however, transmission of virus was not detected. All swabs of fomite from the HB study personnel were negative.
These results indicate that indirect PEDV transmission through contaminated PPE occurs rapidly (within 24 h) under modeled conditions. Biosecurity procedures such as changing PPE, washing expose d skin areas, or taking a shower are recommended for pig production systems and appear to be an effective option for lowering the risk of PEDV transmission between groups of pigs.

Link to the full text

Characterizing Canadian rotavirus A strains and their similarity to a commercial vaccine


Rotaviruses A are genetically diverse.

Rotaviruses are responsible for increased mortality in neonatal swine populations. They are different genetically and more studies are needed to characterize their diversity. This is the objective of this study coordinated by Dr. Marthaler’s lab focusing on rotaviruses strains found in Canada.

Viral proteins 7 and 4 are used for rotavirus A classification.

Rotaviruses are classified based on two viral proteins (VP) found on their outer capsid called respectively VP7 and VP4. Those two proteins are also essential to induce an efficient immune response against the virus. This project characterized VP7 and VP4 sequences in 136 Canadian samples and compared them with the strains used in a rotavirus commercial vaccine.

The VP7 (n=32) and partial VP4 (n=25) were analyzed, identifying the G3P[13], G5P[7], G5P[x], G9P[7], G9P[13], G9P[19], and G9P[x] genotypes.
Minimal differences in the antigenic epitopes for the G5, G9, and P[7] strains were identified.
Major differences in the antigenic epitopes of the G3, P[13], and P[19] may question the effectiveness of the ProSystems RCE RVA.

Marthaler rotavirus A Canada 2017


Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA’s evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population.

Link to the full article

Air samples successful in detecting on-farm PRRSV, PEDV, and high-path avian influenza virus