Sampling guidelines for oral fluid-based surveys of group-housed animals.

Formulas and software for calculating sample size for surveys based on individual animal samples are readily available. However, sample size formulas are not available for oral fluids and other aggregate samples that are increasingly used in production settings. Therefore, the objective of this study was to develop sampling guidelines for oral fluid-based porcine reproductive and respiratory syndrome virus (PRRSV) surveys in commercial swine farms. Oral fluid samples were collected in 9 weekly samplings from all pens in 3 barns on one production site beginning shortly after placement of weaned pigs. Samples (n=972) were tested by real-time reverse-transcription PCR (RT-rtPCR) and the binary results analyzed using a piecewise exponential survival model for interval-censored, time-to-event data with misclassification. Thereafter, simulation studies were used to study the barn-level probability of PRRSV detection as a function of sample size, sample allocation (simple random sampling vs fixed spatial sampling), assay diagnostic sensitivity and specificity, and pen-level prevalence. These studies provided estimates of the probability of detection by sample size and within-barn prevalence. Detection using fixed spatial sampling was as good as, or better than, simple random sampling. Sampling multiple barns on a site increased the probability of detection with the number of barns sampled. These results are relevant to PRRSV control or elimination projects at the herd, regional, or national levels, but the results are also broadly applicable to contagious pathogens of swine for which oral fluid tests of equivalent performance are available.

Full-Length Genome Sequence of Porcine Deltacoronavirus Strain USA/IA/2014/8734.

Porcine deltacoronavirus (PDCoV) was detected in feces from diarrheic sows during an epidemic of acute and transmissible diarrhea. No transmissible gastroenteritis virus or porcine epidemic diarrhea virus was detected. The PDCoV USA/IA/2014/8734 from the herd was sequenced for full-length genomic RNA to further characterize PDCoV in U.S. swine.

Detection of Porcine reproductive and respiratory syndrome virus (PRRSV) antibodies in oral fluid specimens using a commercial PRRSV serum antibody enzyme-linked immunosorbent assay.

The purpose of the present study was to evaluate the diagnostic performance of a commercial serum antibody enzyme-linked immunosorbent assay (ELISA) modified to detect anti-Porcine reproductive and respiratory syndrome virus (PRRSV) antibodies in pen-based oral fluid specimens. Experimental and field oral fluid samples of defined status in reference to exposure of swine with PRRSV were used to derive the kinetics of detectable concentrations of antibody against PRRSV. Immunoglobulin (Ig)M and IgA were readily detected in oral fluid specimens from populations in which PRRSV infection was synchronized among all individuals but not in samples collected in commecial herds. In contrast, IgG was readily detected at diagnostically useful levels in both experimental and field samples for up to 126 days. Estimates of the IgG oral fluid ELISA performance were based on results from testing positive oral fluid samples (n = 492) from experimentally inoculated pigs (n = 251) and field samples (n = 241) and negative oral fluid samples (n = 367) from experimentally inoculated pigs (n = 84) and field samples (n = 283). Receiver operating characteristic analysis estimated the diagnostic sensitivity and specificity of the assay as 94.7% (95% confidence interval [CI]: 92.4, 96.5) and 100% (95% CI: 99.0, 100.0), respectively, at a sample-to-positive ratio cutoff of ≥0.40. The results of the study suggest that the IgG oral fluid ELISA can provide efficient, cost-effective PRRSV monitoring in commercial herds and PRRSV surveillance in elimination programs.

Efficient surveillance of pig populations using oral fluids.

Currently virus surveillance in swine herds is constrained by the cost-effectiveness and efficiency of sampling methods. The objective of this study was to assess the value of using oral fluids collected by barn personnel as a method of surveillance based on PCR testing. Approximately 12,150 pigs in 10 wean-to-finish barns on 10 farms were monitored for the presence of porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus (IAV), and Torque teno virus genogroups 1 (TTV1) and 2 (TTV2) by sampling oral fluid specimens. Oral fluid samples were collected from 6 pens at each site starting at the time of pig placement (∼3 weeks of age) and continuing thereafter at 2-week intervals for a period of 18 weeks. Data were analyzed both on a pen basis and barn basis. Overall, 508 (85%) samples were positive for PCV2, 73 (12%) for PRRSV, 46 (8%) for IAV, 483 (81%) for TTV2, and 155 (26%) for TTV1 during the study period. The estimated arithmetic means of the quantitative PCR-positive oral fluids for PCV2, PRRSV, and IAV were 1×10(4.62), 1×10(4.97), and 1×10(5.49)per ml. With a single exception, all barns were positive for PCV2 and TTV2 at every sampling point in the study. Virus detection varied among barns, particularly for IAV and PRRSV. The pen level, cumulative distribution of agent combinations between all 10 barns were statistically different. The most commonly observed patterns were PCV2+TTV2 (239 pen samples, 40%), PCV2+TTV1+TTV2 (88 pen samples, 15%), and PCV2 alone (66 pen samples, 11%). This "proof-of-concept" project showed that a variety of viruses could be detected either intermittently or continuously in pig populations and demonstrated that barn herd virus status is highly variable, even among barns in the same production system. Oral fluid sampling is a promising approach for increasing the efficiency and cost effectiveness of virus surveillance in swine herds.