 The increased resolution of pathogen whole genome sequencing has improved our ability to infer transmission events, but the lack of genomic variation between source cases and infected contacts often limits this ability. We hypothesized that including within sample variation in a phylogenetic model would help identify who infected whom in instances where this was previously impossible. Using SARS-CoV-2 multi-institutional outbreaks as an example, we show how within sample diversity is partially maintained among repeated serial samples from the same host and can be transmitted between cases with known epidemiological links. Our technique has immediate clinical utility in infection prevention and control and is applicable to other infectious diseases. This article was authored by Arturo Torres Ortiz, Michelle Kendall, Nathaniel Story, and others.