Researchers were also able to track the emergence of a new variant of an influenza virus–one of the advantages of using sequencing to monitor viruses and other pathogens. Very small changes in DNA, even just single base pairs, can make microbes more dangerous or drug-resistant, says George Church, a geneticist at Harvard Medical School who is working on a similar project. With the Pacific Biosciences testing, researchers identified two novel mutations in a particular influenza virus, and then tracked how the new variant became more common than the original one.
As part of the same project, collaborators at the University of California, San Francisco, collected samples from local sewage treatment facilities, with the aim of sampling the viruses in a community on a much broader level. While the researchers are still working on the technical details of isolating viral DNA from bacteria-laden sewage, they did find some interesting strains. “When you zoom in, you not only find pathogens that cause illnesses in people, such as enterovirus and other viruses of both the respiratory and intestinal tract, but we’re also finding lots of other viruses specific to different foods you eat,” says Schadt. For example, they detected a virus common in tomato and pepper plants. “We can start thinking about epidemiological studies to identify patterns of food consumed in different areas, which would be interesting to correlate with disease.”
Rob Knight, a biologist at the University of Colorado at Boulder, and his collaborators are working on a similar project, called BioWeatherMap. They are sequencing genetic material recovered from dollar bills collected from all over the country and beyond to determine how accurately money reflects the microbial communities on our hands, as well as to search for differences by source, comparing emergency rooms with college cafeterias, for example.
Schadt aims to use the pilot data to garner funding from Google or other sources to expand the effort. Obviously, predictive power will be crucial to the project’s success. It’s not clear how much sequencing they’ll have to do to have an impact on public health. “We’re not ready to analyze hundreds of samples at once,” says Schadt, adding that, by 2014, the company expects the PacBio machine to be able to sequence gigabytes of DNA in 15 minutes. At that rate, it could sequence viruses such as influenza A, which has only about 13,000 letters of DNA, at the rate of approximately 300,000 per hour.