Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
Fig 5
Graphics depicting proposal steps A-F for new transmission and phylogenetic trees. In panels A, B, D, and E, the initial situation is at the top, and the proposal below. In panels C and F, the initial situation is in the middle, and two alternative proposal above and below. Every panel shows an outbreak with four hosts, with red arrows indicating transmission: the purple host is the focal host, with the purple arrow indicating the proposal for the new infection time Ii’; filled hosts have a new phylogenetic mini-tree proposed; greyed-out hosts do not play a role in the proposal. (A) the focal host is the index case, and Ii’ is before the first transmission event; (B) the focal host is the index case, and Ii’ is after the first, but before the second secondary case; (C) the focal host is the index case and Ii’ is after his second secondary case; (D) the focal host is not the index case and Ii’ is before infection of the index case; (E) the focal host is not the index case and Ii’ is before his first secondary case; (F) the focal host is not the index case and Ii’ is after his first secondary case.