2017-12-12

Inferring who infected whom

Transmission tree, transmission chain

  • transmission tree: directed acyclic graph representing transmission events of an outbreak
  • transmission chain: path from a case to a descending case

Why does it matter?

Different transmission contexts need different responses.

A difficult problem

The number of possible transmission trees grows very fast:

  • for 10 cases with unique onsets, \(\sim 3,500,000\) trees

  • for 60 cases with unique onsets, \(\sim 8^{81}\) trees (more or less the estimated number of atoms in the universe)

Some data can be informative

  • mutations accumulate in the pathogen genome along the transmission chains

  • can be used to reconstruct transmission trees

But even genomic data have limits


For most diseases, whole genome sequences alone are not sufficient for reconstructing transmission trees.

An evidence synthesis approach