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

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Presentation transcript:

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

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

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

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

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

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

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 Salemi et al, 2004

SARS Protein Sequences  Spike glycoprotein (S)  Replicase polyprotein (Orf1ab)  Nucleocapsid (N)  Membrane protein (M)

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

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_  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.)

SARS Resources  Epidemic! The Natural History of Disease at the San Diego Natural History Museum  Useful site for additional web links and info html (images above) html html  CDC information  Maps and photos (images above)

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

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), (2003) PUBMED

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!