Date of Award
Doctor of Philosophy
Veterinary Diagnostic and Production Animal Medicine
Population Sciences in Animal Health
Daniel CL Linhares
Determining whether porcine reproductive and respiratory syndrome virus (PRRSV) is circulating within a breeding herd is a longstanding surveillance challenge. Most commonly, piglets in farrowing rooms are sampled to infer the PRRSV shedding status of the sow herd, with sample size based on the expectation of hypergeometric distribution and piglet selection based on simple random sampling (SRS), i.e., randomly selecting individuals from a population in a manner that all individuals have equal chance of being selected. The current PRRSV monitoring scheme guidelines from the American Association of Swine Veterinarians assumes that sampling 30 piglets will detect ≥ 1 viremic piglets with 95% confidence if prevalence is ≥ 10% (Cannon and Roe, 1982). However, some herds that met these criteria have tested again positive for PRRSV, with what appears to be the original outbreak virus, as determined by open reading frame (ORF)-5 sequencing (Linhares et al., 2014a). This implies that the virus was present at low prevalence, but undetected in the breeding herd. This demonstrates the need for more clear and reliable indicators regarding progress towards measuring PRRSV circulation in breeding herds, particularly at the final stages of virus elimination when prevalence is low.Processing fluid (PF) is defined as the serosanguineous fluid recovered from castration and tail docking tissues at the time of piglet processing (Lopez et al., 2018). The approach was first reported for antibody-based surveillance of sow farms using fluid recovered from castrated piglet tissues (Boettcher et al., 2010). At the room level, Lopez et al. (2018) showed that the probability of detecting PRRSV RNA was higher for one whole-room PF as opposed to 30 serum samples. Oral fluids samples offer advantages over serum from individual pigs for surveillance of swine populations: (1) they are easily collected by a single person; (2) they can be obtained without stress or risk to pigs or people; (3) at the population level, they provide a higher probability of detection than an equal number of serum samples, and (4) they can be used to screen populations for a variety of pathogens using nucleic acid-based or antibody-based testing (Prickett et al., 2008a; Prickett et al., 2008b; Kittawornrat et al., 2010b; Detmer et al., 2011; Prickett et al., 2011; Kittawornrat et al., 2012; Romagosa et al., 2012; Giménez-Lirola et al., 2013; Goodell et al., 2013; Mur et al., 2013; Panyasing et al., 2013; Vosloo et al., 2015; Bjustrom-Kraft et al., 2016; Gimenez-Lirola et al., 2016; Panyasing et al., 2016b). For these reasons, testing of oral fluids has been used extensively in group-housed growing pigs and adult animals (boars and gilts/sows). Although the collection of oral fluids from due-to-wean litters, i.e., litters within two days of weaning, would allow producers to improve surveillance in this age group and anticipate postweaning infectious disease challenges; a practical technique for collecting oral fluids from suckling piglets has not been described (Kittawornrat et al., 2014; Panyasing et al., 2016a). Family oral fluid (FOF) collection is an adaptation that takes advantage of the piglets' natural tendency to mimic their mother: if the dam interacts with the rope, her piglets will likely do the same (Yeske-Livermore et al., 2014b; Almeida et al., 2020) and is a sample type that can be used to monitor and surveil the due-to-wean litters. This dissertation compiles the current knowledge on PRRSV surveillance on swine breeding herds, with emphasis in family oral fluids, and provides guidelines for incorporating population-based specimens in monitoring and surveillance systems. Specifically, Chapter 2 characterized the pattern of distribution of PRRSV-viremic piglets in farrowing rooms and compared the efficiency of simple random sampling (SRS), two-stage stratified sampling (2SS), and risk-based sampling (RBS) for the detection of PRRSV-viremic piglets. Further, Chapter 2 demonstrated that the distribution of PRRSV-viremic piglets in modern US farrowing room facilities is rarely homogeneous and often clustered, with clustering of viremic piglets observed in a majority of cases. Additionally, SRS was less efficient than either 2SS or RBS in detecting PRRSV-viremic piglets in farrowing rooms, and based on simulation modeling, sample size estimates for the detection of ≥ 1 viremic piglet by PRRSV prevalence, population size, and power of detection (90%, 95%, 99%) were provided. Chapter 3 evaluated the optimum procedure for collecting oral fluid samples from due-to-wean litters. A comparison of litter oral fluids (LOF), i.e., a cotton rope hung where only the piglets could access it, and family oral fluids, i.e., a cotton rope hung where both the sow and her respective piglets could access it was performed in addition to trying different attractants, previous exposure to a rope and different exposure times. FOF-based procedures provided a significantly higher probability of collecting oral fluids from due-to-wean litters when compared to LOF-based methods. Chapter 4 compared PRRSV detection in FOF samples (n = 199) and serum from all individual piglets (n = 2,177) within litters collected. In total, 23 of 24 litters with ≥ 3 viremic piglets were PRRSV RNA positive in FOF; in 10 litters with ≤ 2 viremic piglets, 5 were FOF-positive. A logistic regression analysis estimated the probability of a positive FOF sample from litters with 1, 2, 3, 4, and ≥ 5 viremic piglets as 12.2%, 48.2%, 86.2%, 97.2%, and >99%, respectively. The odds of a positive FOF results of a first parity litter were 3.36 times (95% CI: 2.10 – 5.38) that of a parity > 2 litter. The odds of a positive FOF result for litters with ≤ 11 piglets were 9.90 times (95% CI: 4.62 – 21.22) that of a litter with > 11 piglets. Bayesian prevalence estimation under misclassification analysis for the condition in which all samples (serum and FOF) test PRRSV RNA negative showed that PRRSV may still be present in breeding herds when those conditions are satisfied. Family oral fluids was shown to be an efficacious sample type for PRRSV detection in farrowing rooms. Chapter 5 described PRRSV RNA detection over time in PF, FOF and piglet serum collected from farrowing groups in commercial breeding farms with the objective of moving toward the design of robust, efficient, practical and effective PRRSV surveillance protocols. A total of 561 PF room samples, 2,400 individual litter FOF samples, and 600 serum samples (120 pools of 5 samples) were collected during the study period and tested for PRRSV RNA. The detection of PRRSV was commonly sporadic over time within farms; was often non-uniform (negative and positive farrowing rooms at a given point in time); and PF and FOF testing results were sometimes discordant, i.e., PRRSV RNA detection in one was not always matched by detection in the other. Non-uniformity in PRRSV detection in rooms sampled within the same week and virus detection after ≥ 11 consecutive weeks of PRRSV-negative results in PF and FOF samples underline the challenge of consistent PRRSV detection, but likewise suggest that monitoring protocols for breeding herds attempting PRRSV stabilization or elimination will use both PF and FOF to improve PRRSV detection in suckling pig populations.
Marcelo Nunes de Almeida
Nunes de Almeida, Marcelo, "Improved porcine reproductive and respiratory syndrome virus surveillance in swine breeding herds" (2020). Graduate Theses and Dissertations. 18369.