Molecular Characterization of Economically Important Poultry Viruses in Western Canada
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University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2020-12-04 Molecular characterization of economically important poultry viruses in western Canada Palomino-Tapia, Victor A. Palomino-Tapia, V. A. (2020). Molecular characterization of economically important poultry viruses in western Canada (Unpublished doctoral thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/112814 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Molecular characterization of economically important poultry viruses in western Canada by Victor A. Palomino-Tapia A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN VETERINARY MEDICAL SCIENCES CALGARY, ALBERTA DECEMBER, 2020 © Victor A. Palomino-Tapia 2020 Abstract Avian Reovirus (ARV), Chicken Astrovirus (CAstV), and Hemorrhagic Enteritis Virus (HEV) are important enteric pathogens affecting poultry production around the world. These agents are the causative agents of Viral Arthritis (VA), White Chick Syndrome (WCS), and Hemorrhagic Enteritis (HE), respectively. In meat-type chickens, pathogenic strains of ARV can replicate in the joints leading to edema, inflammatory cell infiltrate, and fibrosis, which results in rupture of tendons. Similarly, pathogenic strains of CAstV can cause transient increase in mid to late embryo mortality, reducing hatchability between 4-68%, with some hatched birds exhibiting pale plumage; these “white chicks” (WCS) usually die within the first week of life. In turkeys, HEV infection has two presentations: 1) A clinical disease consisting on gastrointestinal hemorrhages, depression and immunosuppression (Clinical HE); and 2) subclinical infection, consisting in immunosuppression and causing economical losses due to secondary infections and plant condemnations. In recent years, these diseases have gained importance in western Canada as a result of the economic losses sustained from these infections in: a) feed conversion, b) high number of culls/first week mortality, c) secondary bacterial infections, c) processing plant condemnations; and d) costly disruptions to the Canadian Supply Management system. This thesis focuses on molecular characterization of ARV, CAstV, and HEV obtained either from clinical samples (ARV, CAstV), or from cases suspected to have subclinical infection (HEV) in poultry farms located in western Canada. The biological samples from chickens (ARV, CAStV) and turkeys (HEV) were collected from cases submitted for post-mortem examination and diagnosis to Poultry Health Services (PHS), a private poultry consulting firm, located in Airdrie, Alberta, western Canada. ii Further studies are required to assess the virulence of these isolates for understanding their impact in the western Canada Poultry Industry and for the implementation or enhancement of vaccination practices. Keywords: Molecular characterization; Avian Reovirus; Viral Arthritis; Chicken Astrovirus; White Chick Syndrome; Turkey Hemorrhagic Enteritis Virus; Hemorrhagic Enteritis; poultry enteric viruses, mutation, recombination. iii Preface The studies described in this dissertation, were performed at The Beef Microbiology Laboratory Alberta Agriculture and Forestry – Airdrie Centre (Airdrie AB, Canada); and at the Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada. The research described in the manuscripts contained in this document was carried out by myself, Victor A. Palomino-Tapia, from September 2016 to September 2020 under the supervision of Dr. Faizal Abdul-Careem. This dissertation contains the following manuscripts already published with the participation of all our co-authors which are mentioned below. Chapter 2. Palomino-Tapia, V.; Mitevski, D.; Inglis, T.; van der Meer, F.; Abdul-Careem, M. F., Molecular characterization of emerging avian reovirus variants isolated from viral arthritis cases in western Canada 2012-2017 based on partial sigma (sigma)C gene. Virology 2018, 522, 138-146 [1]. • The authors contributions were as follows: Conceptualization, F.v.d.M., M.F.A.-C., and V.P.-T.; methodology, M.F.A.-C., D.M., T.I., and V.P.-T.; software, F.v.d.M., and V.P.- T.; validation, F.v.d.M., M.F.A.-C., and V.P.-T.; formal analysis, F.v.d.M., and V.P.-T; investigation, D.M., T.I., and V.P.-T; resources, M.F.A.-C., D.M., T.I., and F.v.d.M.; data curation, F.v.d.M., and V.P.-T.; writing—original draft preparation, V.P.-T.; writing— review and editing, F.v.d.M, M.F.A.-C., and V.P.-T.; visualization, F.v.d.M., M.F.A.-C., and V.P.-T.; supervision, F.v.d.M., M.F.A.-C., T.I., and D.M.; project administration, M.F.A.-C., D.M., and T.I.; funding acquisition, M.F.A.-C., D.M., T.I., and V.P.-T. All authors have read and agreed to the published version of the manuscript iv Chapter 3. Palomino-Tapia, V.; Mitevski, D.; Inglis, T.; van der Meer, F.; Martin, E.; Brash, M.; Provost, Ch.; Gagnon C.; Abdul-Careem, M. F. Chicken Astrovirus (CAstV) molecular studies reveal evidence of multiple past-recombinations events in sequences originated from clinical samples of White Chick Syndrome (WCS) in western Canada –Viruses 2020, 12, (10), 1096 [2]. • The authors contributions were as follows: Conceptualization, F.v.d.M., M.F.A.-C., and V.P.-T.; methodology, M.F.A.-C., D.M., T.I., and V.P.-T.; histopathology, M.B. and E.M.; software, F.v.d.M., C.P., C.A.G., and V.P.-T.; validation, F.v.d.M., M.F.A.-C., C.P., C.A.G., and V.P.-T.; formal analysis, F.v.d.M., C.P., C.A.G., and V.P.-T; investigation, D.M., T.I., and V.P.-T; resources, M.F.A.-C., D.M., T.I., and F.v.d.M.; data curation, F.v.d.M., C.P., C.A.G., and V.P.-T.; writing—original draft preparation, V.P.-T.; writing— review and editing, F.v.d.M, M.F.A.-C., and V.P.-T.; visualization, F.v.d.M., M.F.A.-C., and V.P.-T.; supervision, F.v.d.M., M.F.A.-C., T.I., and D.M.; project administration, M.F.A.-C., D.M., and T.I.; funding acquisition, M.F.A.-C., D.M., T.I., and V.P.-T. All authors have read and agreed to the published version of the manuscript Chapter 4. Palomino-Tapia, V.; Mitevski, D.; Inglis, T.; van der Meer, F.; Abdul-Careem, M. F., Molecular characterization of Hemorrhagic Enteritis Virus (HEV) obtained from clinical samples in western Canada 2017-2018. Viruses 2020, 12, (9) [3]. • The authors contributions were as follows: Conceptualization, F.v.d.M., M.F.A.-C., and V.P.-T.; methodology, M.F.A.-C., D.M., T.I., and V.P.-T.; software, F.v.d.M., and V.P.- T.; validation, F.v.d.M., M.F.A.-C., and V.P.-T.; formal analysis, F.v.d.M., and V.P.-T.; investigation, D.M., T.I., and V.P.-T.; resources, M.F.A.-C., D.M., T.I., and F.v.d.M.; data curation, F.v.d.M., and V.P.-T.; writing—original draft preparation, V.P.-T.; writing— review and editing, F.v.d.M., M.F.A.-C., and V.P.-T.; visualization, F.v.d.M., M.F.A.-C., and V.P.-T.; supervision, F.v.d.M., M.F.A.-C., T.I. and D.M.; project administration, M.F.A.-C., D.M., and T.I.; funding acquisition, M.F.A.-C., D.M., T.I., and V.P.-T. All authors have read and agreed to the published version of the manuscript. v Acknowledgements Looking back, I must recognize that I have been extremely lucky and fortunate. Many friends and family members have told me or suggested, in private or in public, that I am talented and/or that I work a lot (perhaps too much, in detriment of my personal life and my poor wife). However, I feel neither of these perceived features can fully account for how an average Peruvian kid could have wound up studying abroad and having access to fully funded Master and Doctorate poultry programs in North America. Please, allow me to make my point by telling you a short story. Around ten years ago, while consulting for layer poultry farm in Peru, I found that a humble foreman had designed a novel drinking nipple system for caged layers by combining expensive commercial poultry nipples with cheap PVC pipes, toilet tanks, and concrete. This noble foreman, who did not finish elementary school, had saved his employer several thousand dollars in equipment as well as in maintenance by sheer force of mind and resourcefulness. For me, it was and still is inevitable to think that, under similar conditions, he would have fared much, much better than me. Sometimes, at the end of a difficult long day, I think of him and decide to push myself just a little bit more. I would also like to thank the following: - My major professor, Dr. Faizal Abdul-Careem, for his guidance and teaching. Your devotion to your students is an example to all of us. - My committee, Drs. Frank van der Meer, Darko Mitevski, and Holly Sellers. Thank you for your continuing mentoring and help.