Fig. 5.—

Within-host microevolution and transmission of isolates within the Maela camp. (A) The tree represents the clade labeled “ML2” in figure 1, pruned to only include leaf nodes for which complete information on day and site of isolation was available. (B) The top inset shows the polymorphic sites identified in four isolates sampled successively from a single infant between January and April 2009, which form a small clade within the overall phylogeny. Positions refer to the reference sequence; shaded columns represent low confidence sites that likely represent false positive signals of variation. Bases are black, when they represent the “ancestral” form found in the first isolate sampled, and red when the bases represent “derived” alleles. Dashes indicate that no bases could be confidently identified at the displayed site. (C) The bottom inset shows a clade of ten isolates, eight of which were isolated from a single individual between July 2008 and March 2009, displayed in the same manner as inset (B). One isolate (H2) from a nearby household in the same month as this final isolate suggests that a transmission event has occurred between residences; a further isolate from the following month comes from the infant’s mother, indicating a within-household transmission.