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Breeder Demographic Survey and Molecular Period Prevalence of Equid Alphaherpesvirus 1 in Healthy Ontario Broodmares

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Breeder Demographic Survey and Molecular Period Prevalence of Equid Alphaherpesvirus 1 in Healthy Ontario Broodmares Breeder Demographic Survey and Molecular Period Prevalence of Equid Alphaherpesvirus 1 in Healthy Ontario Broodmares by Carina J. Cooper A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Pathobiology Guelph, Ontario, Canada © Carina Cooper, September 2020 ABSTRACT BREEDER DEMOGRAPHIC SURVEY AND MOLECULAR PERIOD PREVALENCE OF EQUID ALPHAHERPESVIRUS 1 IN HEALTHY ONTARIO BROODMARES Carina J. Cooper Advisors: University of Guelph, 2020 Brandon N. Lillie Luis G. Arroyo Equid alphaherpesvirus 1 (EHV-1) causes disease in all ages of horses, from abortion and neonatal death to encephalomyelopathy in adults. The main objective of this thesis was to investigate the current opinions of breeders in Ontario, provide prevalence estimates, and describe current vaccine use for EHV-1, which have not been studied. A survey of 88 breeders in Ontario indicated 72.7 % currently vaccinate their herds, and most consult veterinarians for assistance only when encountering abortions, not respiratory disease. Most herds were vaccinated either twice annually or using a “pre-foaling protocol”. In a follow up study, a period prevalence estimate was generated by sampling 381 broodmares from 42 farms across Ontario every two months from December 2016 through October 2017. Samples were collected from the nose, blood and vaginal mucosa and analysed using droplet digital PCR (ddPCR). A total of 85.0 % of broodmares were positive for EHV-1 at some point during the sampling period, and vagina was identified as a source of EHV-1, with viral DNA collected more often from the vagina than the nose. Using mixed logistic regression models, we found no association between virus presence and age or breed. Nasal shedding occurred more often in pregnant mares, and vaccination was only associated with reduced virus in blood samples. When describing the virus neutralization titer response in this population, 32.3 % of mares did not respond to vaccination, and 48.5 % of all mares had no biologically significant changes in titers over the sampling period. Using IgG subisotyping, differing immune responses were observed depending on vaccine product most recently administered. There was no association between IgG subisotype and neutralizing virus titers, nor was there an association with serological titers and ddPCR positivity. Titers did generally increase with age and were typically highest in Standardbred and Thoroughbreds. In conclusion, although most respondents were concerned about EHV-1 enough to vaccinate, many did not, leaving the population at risk for outbreaks. Although vaccines were widely used, they were not consistent in their immune stimulation, potentially creating a false sense of security among breeders. Furthermore, most broodmares harbour the virus and shed intermittently. Dedication This thesis is dedicated to 3 very important people who supported me and gave up so much of their time to see me succeed and complete this thesis. Without each of you, I would be lost and not nearly as proud of the final product. To Dr. Gisela Hussey: Your dedication, care, and commitment to a stranger from another country and another University is amazing. You were not only willing to work with me, share your lab, and help me with my research, you also gave up hours to guide me through writing my thesis, and taught me so much about EHV-1 immunology. You are a friend and dream mentor that I will never forget. I am so lucky to have met you! To my husband and to my mother: You have been more than patient with my whims, my travels, and my unrelenting quest for knowledge. You have been my rocks and my guiding lights. Thank you for always having my back and pushing me to my goals when I got tired. Thank you, Allen Cooper for being an amazing father, being dedicated to our son so I could focus on my schooling, and for being so dependable when life threw us curve balls. Thank you, Dr. Marion Joppe, Mom, for showing me how to persevere, and supporting my family and I so I could focus on my education. Thank you for everything you do for me! iv Acknowledgments This thesis could not have been possible without a small army of advisors and committee members, students, technicians, and friends. Thank you first and foremost to my Advisors, Drs. Brandon Lillie and Luis (Memo) Arroyo for putting up with my determination to make a DVSc into a PhD and supporting me through my internal medicine residency. In addition, none of my work would be possible without the steady guiding hand of Dr. David Pearl, who has taught me about epidemiological statistics and manuscript writing. Thank you as well to Drs. Joanne Hewson and Sarah Wootton who have made themselves available to edit and review all the verbose documents that I have sent their way, patiently moulding my writing and ideas into a cohesive story. Thank you, Dr. Jutta Hammermueller. Technician extraordinaire. Encyclopedia of laboratory knowledge. Dedicated, friendly, supportive, and a thousand other complimentary adjectives. You are what made this project possible, with your organization and enthusiasm, your attention for detail and knowledge of lab procedures. I still can’t believe we managed to work on over 7000 samples without losing our minds! I want to thank Dr. Michaela Botts and soon-to-be Dr. Bailey Fuller, both I got to work with as summer students. You are such hard workers and amazing personalities – making long drives and days in the lab so much fun! Best of luck to you both and whatever adventures you seek! I would also like to acknowledge and thank the Diagnostic Center for Population and Animal Health at Michigan State University led by Dr. Roger Maes, and his technicians Suzanne Mason and Keenan Mullaney, without whom none of the virus neutralization would be possible. I also really appreciate the warm welcome and help I received from Dr. Hussey’s graduate students, Drs. Lila Zarski, Yao Lee, and Kim Giessler. Congratulations on your research and thesis successes! Finally, thank you to my external examiner, Dr. D. Paul Lunn for your suggestions, revisions, edits and comments. It was an honour to work with you and to have your support for my thesis. v Declaration of Work Performed All of the work described in this thesis was performed by me, with the following exceptions: Chapter 3: Sampling was performed by the farm owners, Dr. Luis Arroyo, me with the assistance of visiting students Dr. Bruna Parapinski and Veridianna Cunha, and summer students, Drs. Michaela Botts, and Bailey Fuller. DNA isolation and preparation of PCR samples was done by Drs. Jutta Hammermueller, Michaela Botts, and Bailey Fuller, as well as me. The droplet digital PCR analysis was performed by the Animal Health Laboratory at the University of Guelph (Guelph, ON, Canada). Chapter 4: Virus neutralization of serum samples was performed by Keenan Mullaney under the supervision of Dr. Roger Maes at the Diagnostic Center for Public and Animal Health at Michigan State University (Lansing, MI, USA). The IgG subisotype ELISA was performed by Drs. Jutta Hammermueller, Bailey Fuller, and Solstice Pecile, a visiting student laboratory technician, and me. vi Table of Contents Abstract .......................................................................................................................................... ii Dedication ..................................................................................................................................... iv Acknowledgments ......................................................................................................................... v Declaration of Work Performed ................................................................................................. vi Table of Contents ........................................................................................................................ vii List of Tables ................................................................................................................................. x List of Figures ............................................................................................................................... xi List of Abbreviations .................................................................................................................. xii List of Appendices ...................................................................................................................... xiv Chapter 1 Literature Review ....................................................................................................... 1 1.1 Introduction ........................................................................................................................... 1 1.2 Herpesvirus ........................................................................................................................... 3 1.2.1. General characteristics and classification ..................................................................... 3 1.2.2. Virus genomic structure and proteins ........................................................................... 3 1.2.3. Replication .................................................................................................................... 4 1.2.4. Herpesvirus immune evasion ........................................................................................ 6 1.2.5. Reactivation and recrudescence .................................................................................... 8 1.3 Equid alphaherpesvirus
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