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Comprehensive Molecular Surveillance of Norovirus and Adenovirus in Australasia

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Comprehensive Molecular Surveillance of Norovirus and Adenovirus in Australasia Comprehensive Molecular Surveillance of Norovirus and Adenovirus in Australasia Jennifer Hoi Yin Lun A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy (Virology) School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales August 2018 Thesis/Dissertation Sheet Abstract: Viruses are responsible for more than 50% of all health-care associated gastroenteritis. Of those, norovirus is the leading cause of viral gastroenteritis and adenovirus can cause a wide range of clinical diseases, including gastroenteritis, respiratory illnesses and conjunctivitis. Therefore, molecular surveillance of these viruses is essential to identify prevalent strains that are linked to epidemics. In this thesis, two molecular epidemiological studies of norovirus were performed to characterise strains within Australia and New Zealand, between 2014 and 2017, by using both clinical and wastewater samples (Chapters 3 and 4). In chapter three, we identified a decline in the prevalence of the recent pandemic variant Sydney 2012 which was concomitant with the emergence of several novel recombinant viruses in both nations. Interestingly, two of these recombinants contained the GII.4 Sydney capsid which we hypothesised may have provided a higher epidemiological fitness to these noroviruses. In chapter 4, we sought to explore the potential mechanisms that could facilitate such a change. Analysis of full-length GII.4 Sydney 2012 capsid sequences revealed positive selection in residue 373 of epitope A in all three recombinant GII.4 Sydney 2012 strains. In addition, amino acid reversion to the predecessor New Orleans 2009 variant was observed in GII.P16/GII.4 Sydney 2012 capsid, an event likely to have facilitated the GII.4 Sydney capsid persistence observed. In chapter 5, we investigated the diversity of adenovirus within the Australian population also using wastewater and clinical samples. We successfully sequenced a total of 20 serotypes and identified F-41 as the most prevalent serotype (average of 68.5%) in the Australian population during 2016-2017. Collectively in chapters 3-5 we showed that NGS of wastewater samples provides a more informative summary of viruses that cause asymptomatic and symptomatic infections and not just the latter which is commonly reported from clinical samples. In summary, this is the first Australian study to assess population-level epidemiology of norovirus and adenovirus, highlighting the benefits of using both clinical and environmental samples for surveillance of viruses circulating within the population. A better understanding of the viral strains’ distribution will enhance the development of a successful vaccine. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all property rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only). ……………………………………………………………. ……………………………………..……………… ……….……………………...…….… Signature Witness Signature Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years must be made in writing. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. FOR OFFICE USE ONLY Date of completion of requirements for Award: i Originality Statement ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed………………………………………………….... Date……………………………..……….. ii Copyright statement ‘ I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International. I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation.' Signed………………………………………………….... Date……………………………..……….. Authenticity statement ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format.’ Signed………………………………………………….... Date……………………………..……….. iii INCLUSION OF PUBLICATIONS STATEMENT UNSW is supportive of candidates publishing their research results during their candidature as detailed in the UNSW Thesis Examination Procedure. Publications can be used in their thesis in lieu of a Chapter if: • The student contributed greater than 50% of the content in the publication and is the “primary author”, ie. the student was responsible primarily for the planning, execution and preparation of the work for publication • The student has approval to include the publication in their thesis in lieu of a Chapter from their supervisor and Postgraduate Coordinator. • The publication is not subject to any obligations or contractual agreements with a third party that would constrain its inclusion in the thesis Please indicate whether this thesis contains published material or not. This thesis contains no publications, either published or submitted for publication (if this box is checked, you may delete all the material on page 2) ☐ Some of the work described in this thesis has been published and it has been documented in the relevant Chapters with acknowledgement (if this box is checked, you may delete all ☐ the material on page 2) This thesis has publications (either published or submitted for publication) incorporated ☒ into it in lieu of a chapter and the details are presented below CANDIDATE’S DECLARATION I declare that: • I have complied with the Thesis Examination Procedure • where I have used a publication in lieu of a Chapter, the listed publication(s) below meet(s) the requirements to be included in the thesis. Name Signature Date (dd/mm/yy) Postgraduate Coordinator’s Declaration (to be filled in where publications are used in lieu of Chapters) I declare that: • the information below is accurate • where listed publication(s) have been used in lieu of Chapter(s), their use complies with the Thesis Examination Procedure • the minimum requirements for the format of the thesis have been met. PGC’s Name PGC’s Signature Date (dd/mm/yy) iv For each publication incorporated into the thesis in lieu of a Chapter, provide all of the requested details and signatures required Details of publication #1: Full title: Emerging recombinant noroviruses identified by clinical and waste water screening Authors: Lun JH, Hewitt J, Sitabkhan A, Eden JS, Enosi Tuipulotu D, Netzler NE, Morrell L, Merif J, Jones R, Huang B, Warrilow D, Ressler KA, Ferson MJ, Dwyer DE, Kok J, Rawlinson WD, Deere W, Crosbie ND and White PA Journal or book name: Emerging microbes & infections Volume/page numbers: 7(1): 50 Date accepted/ published: 29/03/2018 Status Published x Accepted and In In progress press (submitted) The Candidate’s Contribution to the Work First author. >50% contribution. Conceived and designed experiments, performed the experiments, contributed reagents/materials/analysis tools, analysed the data and wrote the paper. Location of the work in the thesis and/or how the work is incorporated in the thesis: Chapter 4 (pages 49-71) Primary Supervisor’s Declaration I declare that: • the information above is accurate • this has been discussed with the PGC and it is agreed that this publication can be included in this thesis in lieu of a Chapter • All of the co-authors of the publication have reviewed the above information and have agreed to its veracity by signing a ‘Co-Author Authorisation’ form. Supervisor’s name Supervisor’s signature Date (dd/mm/yy) v Details of publication #2: Full title: Recombinant GII.P16/GII.4 Sydney 2012 was the dominant
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