It is a hot and humid April in San Diego, California. The credit crisis has devastated the state and county. Due to record unemployment, people are not coming into the doctor unless they are very sick. An unknown illness appears to be affecting the San Diego County border region.
There have been two mysterious deaths on the USS Reagan, a naval ship that recently returned from a 6 month deployment in Southeast Asia. Two other deaths were reported in a Tijuana hospital.
There has been speculation that San Diego may be a target of bioterrorism. Others denounce this accusation and say this is a case of an emerging infectious disease.
A pandemic in San Diego poses several issues because of its proximity to the border, because of its role as a military base, and because it is a popular tourist destination.
A lead scientist at The San Diego County Health, Dr. Gooseneck, has decided to bring in a team of crack-shot scientists to help prevent a countywide epidemic or worse. She contacts a group of crack-shot scientists at High Tech High to help.
You will need to help Dr. Gooseneck by reviewing and analyzing pathology reports and DNA sequence data, which will be received in increments over a series of days. You will hypothesize which pathogens are responsible query genome databases with short (500-900 base pair) DNA sequences. From this information, you will be able to make decisions as to which pathogens are causing the outbreak. Each day you will need to:
- Patient symptoms
- PCR data and shotgun sequencing
- Recommended treatments
- Public health implications and preventative measures