Characterization of the Fecal Virome and Fecal Virus Shedding Patterns of Commercial Mink (Neovison vison) by Xiao Ting (Wendy) Xie A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Pathobiology Guelph, Ontario, Canada © Xiao Ting Xie, September, 2017 ABSTRACT Characterization of the Fecal Virome and Fecal Virus Shedding Patterns of Commercial Mink (Neovison vison) Wendy Xie Advisor: University of Guelph, 2017 Dr. Patricia V. Turner This study characterized the mink fecal virome using next-generation sequencing and investigated fecal shedding of mink-specific astrovirus, rotavirus and hepatitis E virus (HEV) over 4-years, using pooled fecal samples from commercial adult females and kits. Sequencing of 30 female and 37 kit pooled fecal samples resulted in 112,144 viral sequences with similarity to existing genomes. Of 109,612 bacteriophage sequences, Escherichia and Enterococcus–associated phage (16% and 11%, respectively) were most prevalent. Of 1237 vertebrate sequences, viral families Parvoviridae and Circoviridae were most prevalent and 27% of viral sequences identified were of avian origin. Astrovirus, rotavirus, and HEV were detected in 14%, 3%, and 9% of samples, respectively. HEV was detected in significantly more kit than female samples (p<0.0001), and astrovirus in more summer samples than winter samples (p=0.001). This research permits improved understanding of potential causative agents of mink gastroenteritis, as well as virus shedding in healthy commercial mink. ii ACKNOWLEDGEMENTS Firstly, thank you to Dr. Patricia V. Turner for all the opportunities, experiences, and mentorship in the time that I have been a part of this wonderful lab. Thank you for allowing me to learn and grow as a researcher, and pushing me to achieve my goals in the field of microbiology. Perhaps most importantly, you have helped me to discover what I truly wish to accomplish in this field, and been unreserved in your commitment to my progress, both in this program and in my future. To my lab members and friends, Nicole Compo, Elein Hernández, Abbie Viscardi, and Jessica Walsh, thank you for the mountains of encouragement and advice over the past two years. I must also acknowledge my committee members Dr. Eva Nagy and Dr. J. Scott Weese, who have acted as the cornerstones of this project, and have provided their invaluable knowledge, time, and experience to ensure my success in this program. This work would not have been possible without the support of Brian Tapscott for the collection of samples, as well as Dr. Jutta Hammermeuller, Rachel Macdonald, and Deirdre Stuart for their tremendous technical contributions. It was an honour to work with you all. Additionally, thank you to Joyce Rousseau and Diego Gomez-Nieto, who must be acknowledged for dealing with my numerous emails filled with many questions during the beginning of my research. A thank you is also extended to Nicol Janecko of the Laboratory for Foodborne Zoonosis, Public Health Agency of Canada for her help in bacterial culture and susceptibility testing. Special thank you to the Ontario Veterinary College and the Canadian Mink Breeders Association for their financial support, with which all of my work, and the work of many others dedicated to the health and welfare of animals, have been made possible. Finally, I would like to acknowledge the two most important people in my life, my parents, who have provided me with unconditional love and support in all of my endeavors. - iii DECLARATION OF WORK PERFORMED All work presented in this thesis was completed by myself, with the following exceptions: • Collection of fecal samples was completed by Brian Tapscott (OMAFRA) • Initial receipt of fecal samples was conducted by Dr. Jutta Hammermeuller • Virus-specific PCRs were done in part by summer students Rachel MacDonald, Brianne Mercer, Sabrina Stevens, and Deidre Stuart • Culture and susceptibility testing was conducted by Nicol Janecko at the Laboratory for Foodborne Zoonosis in Guelph, ON, a branch of the Public Health Agency of Canada, Ottawa, ON • Fecal virome sequencing using Illumina NextSeq was conducted by the Donnelly Centre, University of Toronto • Sequence trimming and assembly was performed using iVirus (CyVerse, AZ USA) and SeqManNGen 12 (DNAStar, Lasergene, WI USA) • Sequence identification was performed using Geneious 10.1.3 software provided by Dr. Andrew Kropinski • Identification of antimicrobial resistance genes was performed using the CARD database provided by Dr. J Scott Weese iv TABLE OF CONTENTS ABSTRACT ........................................................................................................................... ii Acknowledgements ............................................................................................................... iii Declaration of Work Performed .......................................................................................... iv List of Tables ....................................................................................................................... viii List of Figures ........................................................................................................................ ix List of Appendices .................................................................................................................. x Abbreviations ........................................................................................................................ xi CHAPTER 1: VIRAL METAGENOMICS IN MINK: IMPORTANT EUKARYOTIC VIRUSES AND BACTERIOPHAGE AND THEIR ROLES IN MINK HEALTH 1.1 Introduction .......................................................................................................... 1 1.2 Commercial Mink Farming ................................................................................ 1 1.3 Viral Metagenomics in Domestic and Wild Mammal Species ......................... 2 1.3.1 Felids ....................................................................................................... 3 1.3.2 Ferrets ..................................................................................................... 7 1.3.3 Wild Carnivores and Rodents ................................................................. 9 1.4 Viral Diseases of Commercial Mink ................................................................. 12 1.4.1 Aleutian Disease ................................................................................... 12 1.4.2 Canine Distemper Virus ........................................................................ 14 1.4.3 Influenza A ............................................................................................ 15 1.4.4 Mink Viral Enteritis .............................................................................. 16 1.4.5 Shaking Mink Syndrome ...................................................................... 17 1.4.6 Catarrhal Gastroenteritis ....................................................................... 17 1.5 Other Enteric Viruses ........................................................................................ 18 1.5.1 Enteric Astrovirus Infections ................................................................ 18 1.5.2 Rotavirus Infections .............................................................................. 19 1.5.3 Hepatitis E Virus (HEV) Infections ...................................................... 19 1.6 Antimicrobial-resistance genes (ARG) in Phage Viruses and the Mink Microbiome ............................................................................................................... 20 1.6.1 Antimicrobial Resistance Genes in Phage ............................................ 21 1.6.2 Antimicrobial Resistance in Commercial Mink ................................... 22 1.7 Study Rationale .................................................................................................. 23 1.8 Study Objectives and Hypotheses .................................................................... 23 1.8.1 Study Objectives and Methods ............................................................. 23 v 1.8.2 Study Hypotheses.................................................................................. 24 CHAPTER 2: PREVALENCE OF ASTROVIRUS, ROTAVIRUS, AND HEPATITIS E VIRUS SHEDDING IN ONTARIO FARMED MINK (NEOVISON VISON) 2.1 Introduction ........................................................................................................ 26 2.2 Materials and Methods ...................................................................................... 28 2.2.1 Sample Collection ............................................................................................ 28 2.2.2 RNA Extraction and cDNA Synthesis ........................................................... 28 2.2.3 PCR Protocols and Gel Imaging .................................................................... 29 2.2.4 Data analysis ................................................................................................... 29 2.3 Results ................................................................................................................. 30 2.4 Discussion ........................................................................................................... 32 CHAPTER 3: PREVALENT EUKARYOTIC VIRUSES AND BACTERIOPHAGE IN ONTARIO FARMED MINK (NEOVISON VISON) 3.1 Introduction .......................................................................................................