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Bugs we get from the animals we live with, or eat.

Recently I was in Cambodia with a group of Googlers for "Gcamp" at the Royal University of Phnom Penh when the country's first H1N1 (swine flu) case was discovered - a 16-year old American girl on an exchange student visit. The pandemic had traveled the globe and reached South-East Asia. All visitors to the country are now greeted by quarantine unit officers, equipped with paper forms and a fishbowl-like isolation room for suspected carriers, trying to keep the bug out. For years the world feared a possible flu pandemic not traveling to, but coming from Cambodia or one of its neighbors - an H5N1 (bird flu) pandemic that has not happened yet. So far we have been lucky - bird flu is quite deadly but has not yet been very contagious. Swine flu has quickly become a pandemic but is not yet very virulent.

We get many new infectious diseases from the animals we eat or live with - poultry, livestock, wildlife, or insects such as mosquitoes. Some diseases have been around for a long time but we know surprisingly little about them. Rift Valley Fever, for example, periodically kills people and livestock in east Africa, most recently in early 2007 when 300 people died in Kenya, Tanzania and Somalia. But we don't know where the disease hides between outbreaks, how it gets transmitted, or whether people are getting sick because they get infected by mosquitoes or by handling, or eating, sick animals. Late last year made a $5 million grant to icipe (African Insect Science for Food and Health) and partners to improve the discovery and surveillance of insect-carried infectious diseases, particularly Rift Valley Fever in East Africa. The project will collect an estimated 25,000 insect, wildlife, livestock and human samples and hunt for bugs using state-of-the-art biotech methods. Roche, the health care company, has now donated a 454 Genome Sequencer FLX system to the project to strengthen the labs of one of the project's partners, ILRI-BecA, biotech center of excellence for East Africa. This is the first second generation sequencing platform to be installed in the region and will significantly increase the project capacity to discover new pathogens.

The project will screen the samples with multiplex PCR and/or sequence on the Roche 454 platform and will meet its goals if it finds, within 3 years:

* 5 novel Rift Valley Fever variants
* 5 new disease vectors (e.g. insects)
* 20 known viruses that are identified in Kenya for the first time, and
* 5 novel potential pathogen variants (i.e. 5 new diseases).

If those goals are met then we will be one step closer to predicting and preventing the next pandemic that may come out of East Africa.

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