The global spread of 2019-nCoV: a molecular evolutionary analysis

Pathog Glob Health. 2020 Mar;114(2):64-67. doi: 10.1080/20477724.2020.1725339. Epub 2020 Feb 12.


The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019-2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the Rhinolophus bat family. In agreement with epidemiological observations, the most likely geographic origin of the new outbreak was the city of Wuhan, China, where 2019-nCoV time of the most recent common ancestor emerged, according to molecular clock analysis, around November 25th, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to Betacoronavirus. Moreover, our study describes the same population genetic dynamic underlying the SARS 2003 epidemic, and suggests the urgent need for the development of effective molecular surveillance strategies of Betacoronavirus among animals and Rhinolophus of the bat family.

Keywords: 2019-nCoV; SARS; molecular Epidemiology; phylogeny.

MeSH terms

  • Animals
  • Bayes Theorem
  • Betacoronavirus / genetics*
  • COVID-19
  • China / epidemiology
  • Chiroptera / virology*
  • Coronavirus / genetics*
  • Coronavirus / isolation & purification
  • Coronavirus Infections / epidemiology
  • Coronavirus Infections / genetics*
  • Coronavirus Infections / virology
  • DNA, Viral / genetics
  • Disease Outbreaks
  • Disease Reservoirs / virology
  • Evolution, Molecular*
  • Genome, Viral*
  • Global Health
  • Humans
  • Pandemics
  • Phylogeny*
  • Pneumonia, Viral / epidemiology
  • Pneumonia, Viral / genetics*
  • Pneumonia, Viral / virology
  • SARS-CoV-2
  • Sequence Analysis, Protein
  • Zoonoses / epidemiology
  • Zoonoses / genetics


  • DNA, Viral