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Occurrence of Human Norovirus GII and Human Enterovirus in Ontario Source Waters

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Occurrence of Human Norovirus GII and Human Enterovirus in Ontario Source Waters Occurrence of Human Norovirus GII and Human Enterovirus in Ontario Source Waters by Cassandra Diane LoFranco A Thesis Presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Environmental Biology Guelph, Ontario, Canada © Cassandra Diane LoFranco, October 23, 2017 ABSTRACT Occurrence of Human Norovirus and Human Enterovirus in Ontario Source Waters Cassandra Diane LoFranco Advisors: H. Lee University of Guelph, 2017 M. Habash S. Weir Norovirus and Enterovirus are common human viral pathogens found in water sources. Despite causing gastroenteritis outbreaks, most jurisdictions, including Ontario, do not monitor for enteric viruses in waters. The objective of this thesis was to monitor the presence of human Norovirus and Enterovirus in Ontario source waters intended for drinking. Two untreated source water types (river and ground water) were sampled routinely and following precipitation and snow melt events between January 2015 and April 2016. Physical, chemical, microbiological, and meteorological data were collected, coinciding with sampling events. A modified USEPA Method 1615 was applied to detect and quantify viruses and logistic regression was used to examine relationships between virus presence and environmental parameters. Norovirus was detected in 41% of river water and 33% of groundwater samples. Enterovirus was detected in 18% of river water and 29% of groundwater samples. No correlations between virus detection and environmental parameters were found. Acknowledgements With tremendous gratitude and appreciation, I’d like to thank the following people: Professors Hung Lee and Marc Habash who made the call inviting me to this project team and worked closely with me on the project and finer details of this paper and Dr's Susan Weir and Paul Sibley for their time and perspectives. Not only do I appreciate your knowledge and expertise, but your insightful comments and suggestions that most certainly improved the paper, but your enthusiasm and encouragement, which made it possible for me to forge ahead and complete my work. When faced with overwhelming personal and professional challenges throughout this journey, it was your support and confidence in me and my abilities that held me on course to attain this graduate degree, and for this I am forever grateful. Nicole, my being here today would not be possible without your initiative and interest in water safety and for your success in acquiring grant funding and establishing essential municipal connections necessary to carry out the investigation. Thank you to Tim and his professional staff at the Region of Waterloo, who were most kind and helpful with access to the sampling sites. My dear friends and seasoned experts: Sonya, Susan, Anne-Marie, Janis, Dae Young, and Rebecca, for always being there for me even when my inner voice and spirit were flailing. I couldn’t have done this without your broad shoulders, and supportive advice – thank you from the bottom of my heart for believing in me and keeping me grounded. For friends and colleagues at the Habash lab and MOECC, who supported my involvement on this project, thank you. And above all, my wonderful husband Doug and children, Domenic and Luca for their love and support, managing the day to day operations of our home so that I could focus on my research and writing, enabling me to spend long hours tapping away at my keyboard or at the lab running experiments until the early hours, I love you with all my heart. iii And to myself, I am proud to have been the oldest female graduate student (to date) within the SES department to compete the M. Sc., and I am so proud to have accomplished this long-standing personal goal – It was tough at times, but I never gave up! iv Dedication Dedication of this paper is to anyone of any age who keeps within their hearts a personal goal and is looking for hope, encouragement and support that they can make it happen. Never give up on your personal aspirations and never fear trying to attain your goals in the midst of the naysayers and personal and professional challenge. Be tenacious, be persistent; maintain that inner fire burning however tiny, as anything worth having, requires a lot of time, hard work and may require multiple attempts. To my dad, so dearly missed, - may he rest in peace and my mother for her early teachings on how to be independent and strong ... “Never stop learning” v Table of Contents ABSTRACT ................................................................................................................................................... 2 Acknowledgements ....................................................................................................................................... iii Dedication ..................................................................................................................................................... v Table of Contents ......................................................................................................................................... vi List of Tables ................................................................................................................................................. x List of Figures ............................................................................................................................................... xi List of Appendices ........................................................................................................................................ xii List of Abbreviations .................................................................................................................................... xiii Chapter 1: Introduction and Literature Review .............................................................................................. 1 1.1 Waterborne disease from human enteric viruses ............................................................................. 1 1.2 Norovirus ......................................................................................................................................... 4 1.2.1 Agent ....................................................................................................................................... 4 1.2.2 Taxonomy ................................................................................................................................ 5 1.2.3 Structure of the genome ........................................................................................................... 5 1.3 Enteroviruses .................................................................................................................................. 6 1.3.1 Agent ....................................................................................................................................... 6 1.3.2 Taxonomy ................................................................................................................................ 7 1.4 Seasonality of Norovirus and Enterovirus ........................................................................................ 8 1.5 Prevalence and persistence of human Norovirus and human Enterovirus in source waters .......... 11 1.5.1 Survival and Inactivation of Norovirus..................................................................................... 15 vi 1.5.2 Survival and Inactivation of Enteroviruses .............................................................................. 16 1.6 Methods for the Collection and Detection of Norovirus and Enterovirus from source waters ......... 17 1.6.1 Sampling for Norovirus and Enterovirus from source waters .................................................. 18 1.6.2 Concentration of Norovirus and Enterovirus from source waters ............................................ 19 1.7 Detection and Enumeration of Norovirus and Enterovirus from source waters .............................. 23 1.7.1 Cell culture ............................................................................................................................. 23 1.7.2 Polymerase Chain Reaction (PCR) ........................................................................................ 24 1.7.3 Immunoassay or enzyme linked immunosorbent assay (ELISA) ............................................ 26 1.7.4 Integrated Cell Culture (ICC) PCR .......................................................................................... 26 1.8 Qualitative Microbial Risk Assessment (QMRA) ............................................................................ 27 Chapter 2: Materials and Methods .............................................................................................................. 32 2.1 Norovirus and Enterovirus Nucleic Material ................................................................................... 32 2.2 Source Water Sampling................................................................................................................. 32 2.2.1 Water Sample Site Locations and Collection Technique ........................................................ 32 2.2.2 Ground Water (GW) Site Description ..................................................................................... 32 2.2.3 River Water Site Description .................................................................................................. 33 2.2.4 Wastewater (WW) .................................................................................................................
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