Genomic analysis of nCoV spread. Situation report 2020-01-23.

Abstract

Using 24 public shared novel coronavirus (nCoV) genomes, we examined genetic diversity to infer date of common ancestor and rate of spread. We find: 24 sampled genomes are nearly identical, differing by 0-3 mutations This lack of genetic diversity has a parsimonious explanation that the outbreak descends either from a single introduction into the human population or a small number of animal to human transmissions of very similar viruses. This event most likely occurred in November or early December 2019. There has been ongoing human-to-human spread since this point resulting in observed cases. Using estimates of total case count from Imperial College London of several thousand cases, we infer a reproductive number between 1.5 and 3.5 indicating rapid growth in the Nov-Jan period.