Dr Spouge has developed some general strategies for calculating probabilities relevant to evolutionary models. The results help infer events at the start of viral infection in a single host, with potential applications to, e.g., trials of HIV vaccines and preventative therapies. In particular, the results help estimate the basic reproduction number R0 (the average number of infected cells that derive from a single infected cell) of a virus at the beginning of an infection. In analogy to methods in human genetics, therefore, the mutational patterns in viral sequences sampled well after latent infection can remain informative about the initial R0. The analysis of the patterns in sequences derived from patient and animal trials of viral therapies may therefore be able to indicate subtle therapeutic progress, even in the absence of statistically significant differences in the infection of treatment and control groups.