1. 1. Cost Effective Influenza Sampling Strategies for Pigs Jorge Garrido Mantilla, Julio Alvarez, Marie Culhane, Montserrat Torremorell
2. 2. Introduction Materials and methods Results Conclusions This image cannot currently be displayed. OVERVIEW
3. 3. Manage the disease is not easy Surveillance is fundamental to the control, elimination and prevention of influenza Surveillance should be cost effective USDA Surveillance program reduced funding There is a need for cost effective surveillance since just detecting the virus is not enough: Need to conduct sequencing and isolate virus APHIS USDA. Influenza Virus Surveillance in Swine. Program Overview for Veterinarians
4. 4. Influenza surveillance Surveillance is a balance of cost, easiness to obtain sample, sensitivity, others. Sample size Easiness Sensitivity Sequence Isolation Cost Individual sampling Nasal swabs Group sampling Oral fluids
5. 5. What is the best and most cost effective sampling strategy to detect and to isolate influenza in pig farms?
6. 6. Objectives To determine the most sensitive sampling method to detect and isolate influenza virus in pigs To assess which sampling strategy is most cost effective. Hypothesis Group and environmental sampling strategies have similar sensitivity to individual sampling in pig farms for detecting influenza and isolating viruses.
7. 7. METHODS 6 breeding herds and 6 wean to finish facilities (+) Sample size calculation per farm - Individual samples: 30 samples tested in pools of 3a - Assuming 20% prevalence, 80% test sensitivity, 100% of specificity - Pen / litter samples: 8 10 samples - Assuming 40% prevalence, 80% test sensitivity, 100% specificity. - Environmental samples:8 10 samples - 40%b prevalence, 80% test sensitivity, 100% specificity. Tests: - FluA Matrix rRT-PCR and cell culture in Madin-Darby Canine Kidney (MDCK) cell line Statistical analysis and cost - Kappa, McNemar, z-test, GLMM a. Lee C, et al. The impact of pooling nasal swab samples on diagnostic sensitivity of IAV RRT-PCR. b. Neira V, et al. Characterization of Viral Load, Viability and Persistence of Influenza A Virus in Air and on Surfaces of Swine Production Facilities
8. 8. POS = ct < 35 SUS = ct 35.1 39.9 NEG = ct > 40 POS = ct < 35
9. 9. PCR results by sample type and farm 1 POS 8/10 (80) 7/10 (70) 10/10 (100) 3/3 (100) 9/10 (90) 10/10 (100) 10/10 (100) 10/10 2 POS 7/10 (70) 6/10 (60) 9/10 (90) 1/1 (100) 7/10 (70) 9/10 (90) 10/10 (100) 10/10 3 NEG 0/10 (0) 0/10 (0) 0/10 (0) 0/3 (0) 0/10 (0) 0/10 (0) 0/10 (0) 0/10 4 POS 2/10 (20) 3/10 (30) 4/10 (40) 1/2 (50) 3/10 (30) 5/10 (50) 5/10 10/10 5 POS 5/10 (50) 5/10 (50) 8/10 (80) 1/1 (100) 5/10 (50) 7/10 (70) 10/10 10/10 6 NEG 0/10 (0) 0/10 (0) 0/10 (0) 0/10 (0) 0/10 (0) 0/10 (0) 0/10 0/10 Total - 55.0% 53.0% 78.0% 86.0% 60.0% 78.0% 88.0% 100.0% 1 NEG 0/10 0/10 - 0/10 0/10 - 0/10 0/10 2 POS 6/10 6/10 - 4/10 3/10 - 0/10 1/10 3 POS 2/10 2/10 - 10/10 5/10 - 9/10 10/10 4 POS 4/10 4/10 - 5/10 5/10 - 7/10 6/8 5 POS 2/10 3/10 - 7/8 10/10 - 9/10 10/10 6 POS 1/10 1/10 - 4/10 2/10 - 4/10 4/10 Total - 30.0% 32.0% - 62.5% 50.0% - 58.0% 65.9% WEAN TO FINISH BREEDING HERDS
10. 10. Kappa showed moderate to substantial agreement among all sampling strategies Sampling technique kappa coefficient Kappa CI Nasal swabs Vs. Nasal wipes 0.760 (0.554, 0.965) Nasal swabs Vs. Oropharyngeal swabs 0.597 (0.375, 0.819) Udder wipes Vs. Oral fluids 0.775 (0.389, 1.161) Oral fluids Vs. Surfaces wipes 0.790 (0.423, 1.157) Surfaces wipes Vs. Udder wipes 0.552 (0.356, 0.749) Airborne particle deposition Vs. Air 0.794 (0.575, 1.014) Nasal swabs Vs. Nasal wipes 0.636 (0.452, 0.820) Oral fluids Vs. Surfaces wipes 0.440 (0.257, 0.623) Airborne particle deposition Vs. Air 0.492 (0.304, 0.679) BREEDING HERDS WEAN TO FINISH
11. 11. Generalized linear mixed model Two random effects (farm and litter/pen) Nasal swab as the baseline 1 2 5 10 20 50 100 15.97*** 6.63** 22.11*** 5.59* 1.99
12. 12. Conclusions In this study, group and environmental sampling strategies have similar sensitivity to individual sampling For individual sampling strategies, oropharyngeal swabs were the best Group and environmental sampling strategies based on PCR testing were more cost effective given that they detected more positives. Airborne influenza was readily detected in the air of farrowing rooms
13. 13. Acknowledgements Dr. Montserrat Torremorell Dr. Marie Culhane Dr. Julio Alvarez Swine group students My Yang Jayaveeramuthu Nirmala
14. 14. Thanks garri098@umn.edu