key: cord-0748243-t1iagum7
authors: Zhang, Chi; Wang, Mei
title: Origin time and epidemic dynamics of the 2019 novel coronavirus
date: 2020-01-27
journal: bioRxiv
DOI: 10.1101/2020.01.25.919688
sha: b298f23d2779e73d087dfeb56a5da88374143617
doc_id: 748243
cord_uid: t1iagum7

The 2019 novel coronavirus (2019-nCoV) have emerged from Wuhan, China. Studying the epidemic dynamics is crucial for further surveillance and control of the outbreak. We employed a Bayesian framework to infer the time-calibrated phylogeny and the epidemic dynamics represented by the effective reproductive number (Re) changing over time from the genomic sequences available from GISAID. The origin time is estimated to be December 17, 2019 (95% CI: December 5, 2019 – December 23, 2019). The median estimate of Re ranges from 0.2 to 2.2 and changes drastically over time. This study provides an early insight of the 2019-nCoV epidemic.

Human to human transmission has been confirmed for this new type of coronavirus (Wang et 28 al. 2020) and more than 1,000 cases have been reported as of January 25, 2020 29 (https://bnonews.com/index.php/2020/01/the-latest-coronavirus-cases). They are also lacking a stochastic process to model the epidemic dynamics over time. However, 36 both the timing and dynamics are critical to understand the early outbreak of 2019-nCoV.

Furthermore, various sources of information and uncertainties are hard to be integrated in the 38 analyses without employing a Bayesian approach.

In this study, we used the birth-death skyline serial (BDSS) model (Stadler et al. 2013 ) to 40 infer the phylogeny, divergence times and epidemic dynamics of 2019-nCoV. This approach 41 takes the genomic sequences and sampling times of the viruses as input, and co-estimates the 42 phylogeny and key epidemic parameters in a Bayesian framework. To our knowledge, this is 43 the first study to perform such estimation on 2019-nCoV.

The phylogeny in Figure 1 shows the divergence times and relationships of the 24 The substitution model used was HKY+Γ4 (Hasegawa et al. 1985; Yang 1994 ) in which the 106 transition-transversion rate ratio κ was set a lognormal(1, 1.25) prior and the gamma shape 107 parameter α was an exponential(1) prior. Re Jan-Jan-0 Jan---2 -20

BEAST 2.5: An 124 advanced software platform for Bayesian evolutionary analysis

A familial 129 cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-130 person transmission: a study of a family cluster

Relaxed phylogenetics and 132 dating with confidence

MUSCLE: multiple sequence alignment with high accuracy and high 134 throughput

Coronavirus

Dating of the human-ape splitting by a molecular 137 clock of mitochondrial DNA

Posterior 139 summarization in Bayesian phylogenetics using Tracer 1.7

Inferring speciation times under an episodic molecular clock

Birth-death skyline plot reveals 143 temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

A novel coronavirus outbreak of global 146 health concern. The Lancet

World Health Organization (WHO)

World Health Organization (WHO)

Maximum likelihood phylogenetic estimation from DNA sequences with 153 variable rates over sites: approximate methods

Discovery of a novel coronavirus 158 associated with the recent pneumonia outbreak in humans and its potential bat origin