Genomic analysis of nCoV spread. Situation report 2020-01-23.
Trevor Bedford, Richard A. Neher, James Hadfield, Emma B. Hodcroft, Misja Ilcisin, Nicola F. Müller
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: \n24 sampled genomes are nearly identical, differing by 0-3 mutations \nThis 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. \nThis event most likely occurred in November or early December 2019. \nThere has been ongoing human-to-human spread since this point resulting in observed cases. \nUsing 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.