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

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 (coalescen...

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Bibliographic Details
Published in:Journal of Medical Virology 2020-06, Vol.92 (6), p.675-679
Main Authors: Lai, Alessia, Bergna, Annalisa, Acciarri, Carla, Galli, Massimo, Zehender, Gianguglielmo
Format: Article
Language:English
Subjects:
Base Sequence
Bayes Theorem
Bayesian analysis
Betacoronavirus - classification
Betacoronavirus - genetics
Betacoronavirus - isolation & purification
Betacoronavirus - pathogenicity
Coronavirus Infections - diagnosis
Coronavirus Infections - epidemiology
Coronavirus Infections - transmission
Coronavirus Infections - virology
Coronaviruses
COVID-19
Epidemics
Epidemiological Monitoring
Evolution
Evolution, Molecular
evolutionary dynamics
Genome, Viral
Genomes
Humans
Infections
Influenza
Information Dissemination
Mathematical models
Models, Statistical
Open Reading Frames
Pandemics
Phylogeny
Pneumonia, Viral - diagnosis
Pneumonia, Viral - epidemiology
Pneumonia, Viral - transmission
Pneumonia, Viral - virology
Population dynamics
Reproduction
reproductive number
RNA, Viral - genetics
SARS-CoV-2
Sequence Alignment
Sequence Homology, Nucleic Acid
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Short Communication
Short Communications
Surveillance
Viral diseases
Virology
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Summary: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. Highlights The aim of this study was to investigate the temporal origin, rate of viral evolution and population dynamics of SARS‐CoV‐2. The Bayesian approach used indicated a most probable origin of the epidemic between October and November 2019. The estimated effective reproductive number increased from 0.8 to 2.4 in December 2019 when the mean doubling time was about 4 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections.
ISSN:0146-6615
1096-9071
DOI:10.1002/jmv.25723