Thomas Leitner: The connection between transmission history and virus trees; definitions, inference, and meta-analysis of documented donor-recipient cases

Abstract:

Because many viruses evolve during their spread from host to host, there is a connection between who infected whom and the resulting virus phylogeny sampled from the infected hosts. Who infected whom can be described as a bifurcating tree, and since that is also the standard form of the inferred pathogen phylogeny, it is attractive to assume that these two trees are identical. While the evolution within each host facilitates this connection, it is not a trivial one-to-one correspondence. The connection between transmission tree and the resulting virus phylogeny can be understood via the so called pretransmission interval, which explains why phylogeny-based transmission times become backwards biased in time and who-infected-whom may become jumbled. However, adequately including within-host virus evolution makes it possible to probabilistically infer meaningful between-host epidemiological patterns. In this talk I will discuss the host-pathogen tree connection and describe new results from a large meta-study of known HIV-1 transmission cases. Paraphyly often reveals the donor, but transmission of multiple lineages, causing recipient polyphyly, causes complicated situations and difficult interpretation.