Phylodynamic Analyses of outbreaks in China, Italy, Washington State (USA), and the Diamond Princess

13th march 2020

Timothy G. Vaughan et al

Virological.org

In this report, we outline phylodynamic analyses of four COVID-19 outbreaks, namely in China, Italy, Washington State (USA), and on the cruise ship Diamond Princess based on full-length SARS-CoV-2 genomes downloaded from GISAID 54. Acknowledgements for and details of the genome sequences are given in the table at the end of this post.
In particular, we performed Bayesian phylodynamic analyses in BEAST2 [1] in order to estimate the R0, the total number of cases through time, and the time of epidemic origin for each of the four epidemic outbreaks.

Method

The Chinese outbreak is the initial outbreak giving rise to the COVID-19 pandemic. From this outbreak, there were 13 sequences collected outside of China prior to or on January 23 (the onset of quarantine in Wuhan). 5 sequences were collected in the USA, 2 in Thailand, and 1 each in Australia, Singapore, Nepal, Japan, France, and Canada. Thus the sampling procedure is “migration from China to abroad followed by sequencing”.

The Italian COVID-19 epidemic was seeded at least twice (NextStrain Situation Report 2020-03-04 36). One introduction of COVID-19 into Italy led to an outbreak with 35 sampled sequences as of March 11 (NextStrain 20). For this analysis we considered 30 of these 35 sequences: 2 sequences were collected in Italy, 20 were collected abroad but had known or suspected travel history to Italy, and 8 were Dutch sequences that also cluster in this group. Although we do not have travel history for the Dutch cases, we note that until March 3 (the date of the last Dutch sequence considered) the majority of cases in the Netherlands were people returning from Northern Italy or their close contacts (source: RIVM 3). For these Dutch samples, we retained only one individual from each group of identical sequences. Again, our main sampling procedure is “migration from Italy to abroad followed by sequencing”.

Read the full report at Virological.org

shares