Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Measurement of surveillance: the q2 coefficient. We propose a quantitative measure of pathogen surveillance that reflects both the evolutionary rate and the biodiversity of a given population. For each host and subtype, sequences were first temporally ordered from the oldest sequence to the newest. For each sequence, we identified the sequence from the past with the highest homology and recorded its genetic distance, such that for N sequences, we compiled a vector of N distances. We defined the surveillance measurement q2 coefficient, a measurement between 0 and 1, as the proportion of sequences within genetic distance R of the most closely related ancestor.