2 Short biographies and contact information of the workshop organizers

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1 1 Title of the workshop from sequence to surveillance 2 Short biographies and contact information of the workshop organizers Dr Peter Durr - peter.durr@csiro.au Veterinary epidemiologist, Australian Animal Health Laboratory (AAHL), which is Australia s exotic animal disease laboratory. Extensive experience in animal disease surveillance and epidemiology, with a recent focus on emergency animal diseases in southeast Asia. Is leading a project to develop an integrated molecular surveillance platform for the FAO in Indonesia ( IVM Online ), and has carried out bioinformatics analysis on Highly Pathogenic Avian Influenza virus (H5N1), Rift Valley Fever virus (RFFV), Murray Valley Encephalitis virus, Mycobacterium bovis and Mycoplasma suis. Dr Kim Halpin Kim.Halpin@csiro.au Veterinary molecular virologist, also at AAHL. Previously has worked with Life Technologies in Singapore developing molecular diagnostic tests for animal health and food safety. Has also worked at CDC, Atlanta. Has organized and run many workshops on emergency animal diseases in Australia. Has diverse experience with molecular diagnostics and specialist knowledge of a number of emergency animal diseases including Hendra virus and Nipah virus. 3 Workshop s learning outcomes The overall objective is to provide an introduction to discipline of bioinformatics for epidemiologist The specific learning objectives are: 1 To introduce the main concepts of molecular biology and bioinformatics 2 To show how to access the main sequence data repositories 3 To provide familiarity with a range of open-source and internet accessible bioinformatics tools 4 To demonstrate how bioinformatics has been used in the surveillance and diagnosis of some important diseases of livestock, fish as well as zoonotic human disease. Examples that will be covered include HPAI H5N1 virus, foot-and-mouth disease, viral hemorrhagic septicaemia, Hendra virus infection and zoonotic E. coli O To provide an understanding of Next Generation Sequencing (NGS) and how NGS sequence data is managed 6 ±To provide guidance for specific bioinformatics analyses attendees have undertaken or are intending to undertake.

2 4 Background skills and knowledge This is an entry level course and no prior knowledge of molecular biology or bioinformatics is assumed. To help us aim the course at the correct level, we will ask attendees to complete a short questionnaire detailing their current level of knowledge before the course. 5 History of the workshop The workshop was initiated in 2014, and has been given at the CAVEPM / Epi on the Island 2014 Joint conference over a 3-day period (June 11th- June 13 th 2014) at the Atlantic Veterinary College, University of Prince Edward Island. This was the post-conference course given in the University s main lecture theatre. The number of attendees was 22. The course was formally evaluated via an online questionnaire. Of the 18 responders, 17 said the course either met or exceeded their expectations and 17 said they would recommend this course to their colleagues. Appendix 1 provides some of the comments from the course participants. 6 Workshop specification Language: English Pre or post conference: Post conference Number of attendees: minimum 20 maximum 30 Duration of the workshop: 3 days Specific needs for the workshop: Package of accessories that includes one laptop projector, power strips, extension cords, and adapter 7 Workshop content and schedule 7.1 Motivation: Full genome sequencing of animal disease pathogens is rapidly becoming mainstream technology. We are entering an era when isolates from clinical lesions are routinely sequenced following their isolation. This applies particularly to viruses, as exemplified by the swine flu H1N1 pandemic, wherein a significant number of the isolates were sequenced. This impending sequencing revolution will have enormous impacts on disease surveillance and control programs, and will require animal disease managers and epidemiologists to have a working knowledge of pathogen genome sequencing and bioinformatics.

3 7.2 Course description This is a practical workshop, intending to expose attendees to both the diversity of techniques being developed within bioinformatics, as well as relating these techniques to real world epidemiological and disease control problems. The focus is on viral diseases, as reflects their current importance in terms of Emergency Animal Disease (EAD) problems. However, there will also be examples from selected bacterial pathogens. Bioinformatics approaches for pathogenic protozoa, nematodes and arthropods will not be specifically covered. 7.3 Teaching style The course is highly structured, with 4 sessions per day, each taking 1.5 hours (see Timetable). Each session will comprise of a minute presentation, which will then be followed by a computer practical. These practicals will follow a "follow-along" style, wherein an exercise using bioinformatics software will be completed. 7.4 Computer/software requirements Attendees need to have access to a PC to complete the practicals, and by preference use their own laptop with permission to add software. All the software that will be used is freely available, and will be provided on a USB stick, or else may be downloaded during or before the course. Although the preferred operating systems for professional bioinformaticians tends to be UNIX based (Linux or Mac), we have based our course on software which runs on both Windows and Macs, as reflects our knowledge of the veterinary epidemiology community. The course assumes that attendees will have good internet access. 7.5 Course material and handouts PDF copies of all the material lectures, exercises and software - will be provided on a USB stick handed round to participants at the start of each session. 8 Cost USD 750 / person (all inclusive)

4 9 Timetable (draft*) Day 1 The basics of bioinformatics Day 2 More advanced topics Day 3 Case studies of using bioinformatics in surveillance 08:30-09:00 Registration & Introduction (PD) 09:00-10:30 Session 1: Basic molecular biology ; Sequencing techniques (KH) Practical : Exercises in basic molecular biology; viewing raw sequence data using CLC sequence viewer Session 5 Molecular evolution of pathogens / quasi-species / co-evolution PD) Practical: Using MEGA to infer the evolution of H5N1 Session 9 Case studies (II) EHEC O104:H4 in Germany & France 2011 (KH) Practical: using snptree to construct a ML tree of the outbreak of EHEC 0404:H4 and derive epidemiological insight 10:30-11:00 Coffee break 11:00-12:30 Session 2 - Sequences and sequence databases (PD) Practical: Using Genbank, Uniprot to derive information about nucleotide sequences (M. suis) then BLAST to find similar sequences Session 6 - Whole genome sequencing (KH) Practical: Determining quality scores and SNPs using webprograms (e.g. PRINSEQ) Session 10 - Case studies (III): using sequence variation to determine paths of transmission during an outbreak of FMD (PD) Practical: the microevolutioin of FMDV during farm-to-farm transmission in England in :30-13:30 Lunch break 13:30-15:00 Session 3 - Sequence variation (and error) & sequence alignment (KH) Practical: Using CLC SV to import and align sequences (M. suis) and assess possible error Session 7 Protein & Structural bioinformatics (PD) Practical: Using CLC SV to visualise antigenic sites of viruses (H5N1) Session 11 Case studies (IV): Diagnostic test failures (KH) Practical: Using BLAST searches to determine the possible causes of molecular diagnostic test failures 15:00-15:30 Coffee break 15:30-17:00 Lesson 4 - Phylogenetic trees (PD) Practical: Using or CLC SV to construct a NJ tree (M. suis) Open discussion: data quality and phylogenetic inference Session 8 Case studies (I): the discovery of VHSV in olive founder China (PD) Practical: Is a novel virus isolated from olive flounder in China the same as VHSV? Session 12 Some advanced bioinformatics programming, Bayesian phylogenetics etc. (PD) ±Practical: Explore IVM Online interface and code Open discussion: how did the workshop match up to expectations *pending a short questionnaire of participants

5 10 Evaluation comments from the course run at CAVEPM in June 2014 (taken from the evaluation survey) You built the course from the "bases" up, literally. It was good to remember the basics before plunging into the more specific material. I have never worked with this kind of data before and this introduction to the field was really good. I think I can now at least ask questions and more critically read a paper from this field. I also appreciated to learn how this data are shared in open databases. The level of teaching was perfect for my knowledge of molecular biology and background as a veterinary epidemiologist. It was also a perfect balance between theory and practical. I also really appreciated the time that both instructors took to help the participants through the exercises and answering ALL of our questions, no matter if they were directly related to the practicals or not. The instructors were great as well as the "review" slides. It really helped with the background of what we were learning. Both the presentations and hands on exercises were very relevant. Thank you. Excellent, knowledgeable instructors! The assignments were easy to follow and gave us experience with the many different tools available and different ways to manipulate and present genomic data.