Early Phylogenetic Estimate Of The Effective Reproduction Number Of 2019-nCoV

To reconstruct the evolutionary dynamics of the 2019 novel coronavirus, 52 2019-nCOV genomes available on 04 February 2020 at GISAID were analysed.

The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10 ⁻⁴ subs/site/year (range 1.1×10 ⁻⁴ –15×10 ⁻⁴ ).

The estimated R value was 2.6 (range 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days.

This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.