1. SARS: A Multidisciplinary Exploration Nitya Jacob Doug Graham Eloise Carter Manish Chakrabarti

2. Teaching with an Epidemic  SARS as a topic to introduce problem solving in biology, medical epidemiology and bioinformatics  Diverse sources of information on SARS used to introduce the topic  Platform for developing questions that engage students  Use of existing data/information to develop analysis skills for future projects

3. SARS – Severe Acute Respiratory Syndrome  Coronovirus – SARS CoV  Global epidemic 2003  8,000 cases, 24 countries  Spread by respiratory droplets

4. SARS - Symptoms  High fever > 100oC  Headaches  Body aches and pains  All pneumonia

5. SARS – Integrating Topics  Biogeography  Epidemiology/Biology  Detection and Diagnosis  Time Line  Genome  Phylogeny  Bioinformatic Tools  Public Health – Quarantine, Education, etc.  Vaccine Development

6. Questions to Explore  Evolution/variation of sequences encoding specific proteins (Orf 1ab vs. spike)  Differences between Coronaviruses  Differences between strains from China and Taiwan vs. strains transmitted to North America

7. SARS Sequences Available FULL GENOME SEQUENCES  TOR2  SIN2500, SIN2748, SIN2774, SIN2677, SIN2679  URBANI  HKU39849  BJO1  HKU39849  CUHKUW1, CUHK-Su10  LLJ-2004  HSR1 – Italy  Frankfurt 1  Sino1-11  GD01 www.ncbi.nlm.nih.gov Salemi et al, 2004

8. SARS Protein Sequences  Spike glycoprotein (S)  Replicase polyprotein (Orf1ab)  Nucleocapsid (N)  Membrane protein (M) www.ncbi.nlm.nih.gov

9. Epidemiology  Origin of SARS coronavirus?  Case definition  Factors (biological/cultural) contributing to global spread

10. Bioinformatics Target Audience: Computer Science, Math and Statistics students. Exploration Ideas:  Search NCBI for the complete SARS Co-v genome (Accession number: NC_004718) NC_004718  Download the entire sequence in FASTA format (goal: learn about FASTA)  Now download the sequence in XML format (learn about the different XML formats such as GBSeqXML, TinySeqXM, etc.)

12. SARS Resources  Epidemic! The Natural History of Disease at the San Diego Natural History Museum www.sdnhm.org/exhibits/epidemic/resources.html www.sdnhm.org/exhibits/epidemic/resources.html  Useful site for additional web links and info http://microvet.arizona.edu/Courses/MIC438/collectjc04. html (images above) http://microvet.arizona.edu/Courses/MIC438/collectjc04. html http://microvet.arizona.edu/Courses/MIC438/collectjc04. html  CDC information http://www.cdc.gov/ncidod/EID/vol5no2/snacken.htm http://www.cdc.gov/ncidod/EID/vol5no2/snacken.htm  Maps and photos http://www.geo.arizona.edu/Antevs/nats104/00lect24sars.html (images above) http://www.geo.arizona.edu/Antevs/nats104/00lect24sars.html http://www.geo.arizona.edu/Antevs/nats104/00lect24sars.html

13. Resources for Evolution and Phylogeny  Salemi et al. 2004. “Severe Acute Respiratory Syndrome Coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis”. J of Virology 78:1602-1603.  Chinese SARS Molecular Epidemiology Consortium. 2004. “Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China.” Science 303:1666-1669.  Lan et al. 2005. “Phylogenetic analysis and sequence comparison of structural and non-structural SARS coronavirus proteins in Taiwan.” Infect. Genet. Evol. 5:261-9

14. Resources for Bioinformatics Complete SARS Genome  Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage - Snijder,E.J at al, J. Mol. Biol. 331 (5), 991-1004 (2003) PUBMED 12927536 12927536

15. Conclusions  This approach could be used in other areas of study  Epidemic diseases capture interest and integrate diverse skills and concepts  Meaningful connection of bioinformatics to timely and engaging problems  Find your favorite disease!