BBSRC Systems Biology Grantholder Workshop, University of Nottingham, 16 December 2008.
More fully, he's talking about the micro-evolutionary dynamics of RNA viruses. They want to get a full picture of what happens from the infection of a single cell to an entire outbreak, and all the intermediate scales. The levels of granularity he's looking at goes as follows: within cell, within host (not all viral particles in one host are genetically identical), within group (physical proximity of host to others), between groups (long-distance spreading). The data at each stage is different: from molecular data to epidemiological data. They looked at foot-and-mouth disease (FMD) and plum pox virus (PPV, transmitted by vectors), both RNA viruses. 10,000 farms were culled in the 2001 UK FMD outbreak. However, during this time, modellers were consulted. Samples were taken from every infected farm, and are stored at the IAH Purbright. This means that there's lots of data available. Then, he described a genetic tree that was built based on the FM viruses found in farms in Durham county during the outbreak. However, many transmission patterns are compatible with the tree. With some basic parameters, you can estimate how likely it is that one farm infected another. Among the total set of transmission trees (~2000), only 4 matched the values properly, and can therefore choose the most-likely tree (which accounted for about 50% of the likelihood), and therefore the most likely transmission pattern. Some of the movements show very large distances (of about 15 km). Is it a fault of the model, or a signature of some extrinsic event like transmission via car travel (human) or delivery of infected material. They still have more data (e.g. timing of transmissions) that they still have to use.
These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. 🙂