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. 2020 Jun;92(6):675-679.
doi: 10.1002/jmv.25723. Epub 2020 Mar 3.

Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2

Alessia Lai  1   2 , Annalisa Bergna  1 , Carla Acciarri  1 , Massimo Galli  1   2 , Gianguglielmo Zehender  1   2   3
Affiliations

Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2

Alessia Lai et al. J Med Virol. 2020 Jun.

Abstract

To reconstruct the evolutionary dynamics of the 2019 novel-coronavirus recently causing an outbreak in Wuhan, China, 52 SARS-CoV-2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. 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 ) and a mean tMRCA of the tree root of 73 days. 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.

Keywords: SARS-CoV-2; evolutionary dynamics; reproductive number.

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Conflict of interest statement

The authors declare that there are no conflict of interests.

Figures

Figure 1
Figure 1
A, Bayesian skyline plot of the SARS‐CoV‐2 outbreak. The y‐axis indicates Ne and x‐axis shows the time in year units (0 = 30 January; 18.2 days; 36.5 days; 54.7 days; and 73 days before). The thick solid line represents the median value of the estimates, and the gray area the 95% HPD. B, Birth‐death skyline plot of the SARS‐CoV‐2 outbreak allowing two R e intervals. The curve and the orange area show the mean R e values and their 95% confidence intervals. The y and x‐axes, respectively, represent R values and time in days. HPD, highest posterior density
See this image and copyright information in PMC

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