Premium
Early phylogenetic estimate of the effective reproduction number of SARS‐CoV‐2
Author(s) -
Lai Alessia,
Bergna Annalisa,
Acciarri Carla,
Galli Massimo,
Zehender Gianguglielmo
Publication year - 2020
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.25723
Subject(s) - coalescent theory , phylogenetic tree , biology , basic reproduction number , outbreak , range (aeronautics) , phylogenetics , pandemic , covid-19 , reproduction , demography , statistics , evolutionary biology , virology , mathematics , genetics , medicine , infectious disease (medical specialty) , gene , population , materials science , disease , pathology , sociology , composite material
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.