Recent outbreak of a novel coronavirus

In December 2019, a new illness was first detected in Wuhan, China. We now know this to be another outbreak of coronavirus in humans (the 7th). The virus has been named SARS-CoV-2 and the disease it causes is COVID-19.

As of March 6, 2020 over 100,685 cases and 3,411 deaths have been reported. The WHO currently estimates the case fatality rate at 3.4%, which is significantly less than the case fatality rate of SARS. The case counts are dramatically rising in part due to increased surveillance and testing.

While the outbreak seems to be centered in Wuhan, which is now under quarantine, the virus has spread throughout China and abroad, including Hong Kong, Singapore, Japan, and Thailand, as well as Europe, North America, South Asia, the Middle East, Africa, and Australia. Local transmission outside of China has been reported.

The origin of the virus is still unclear, however genomic analyis suggests SARS-CoV-2 is most closely related to viruses previously identified in bats. It is plausible that there were other intermediate animal transmissions before the introduction into humans. There is no evidence of snakes as an intermediary.

Further Reading:

  • New China virus: Five questions scientists are asking Nature news 2020-01-22
  • China virus latest: first US case confirmed Nature news 2020-01-21
  • New virus surging in Asia rattles scientists Nature news 2020-01-20
  • New virus identified as likely cause of mystery illness in China Nature news 2020-01-08
  • Interactive risk analysis by MOBS-lab 2010-01-29
  • Interactive risk analysis by ROCS-lab 2010-01-29

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to must be provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.


© 2015-2020 Trevor Bedford and Richard Neher