Coronaviruses (CoV) are members of a diverse species of positive-sense single-stranded RNA ((+)ssRNA) viruses which have a history of causing respiratory infections in humans. Some variants of coronaviruses are associated with outbreaks, others are continuously circulating and cause mostly mild respiratory infections (e.g. the common cold).
The most well known of these coronaviruses is SARS-CoV (“severe acute respiratory syndrome”), which in a November 2002 to July 2003 outbreak spread around the world and resulted in over 8000 cases and 774 deaths, with a case fatality rate of around 9–11%.
In 2012, a novel coronavirus, MERS-CoV (“Middle East respiratory syndrome”), causing severe respiratory symptoms was identified. MERS has resulted in fatalities comparable to SARS, however the transmission route of MERS is very different. Whereas SARS was efficiently spread from one human to another, human MERS infections were generally a result of independent zoonoses (animal to human transmissions) from camels (see Dudas et al. for more information). This has lead to a self-limiting outbreak largely restricted to the Arabian Peninsula.
However, not all coronaviruses are as deadly as SARS-CoV and MERS-CoV. There are four “seasonal” coronaviruses that commonly infect humans each year. Compared with SARS, these seasonal coronavirus strains are “much more prevalent, much less severe, and common causes of influenza‐like illness (ILI)”. In fact, 5–12% of all ILI cases test positive for coronaviruses, so they are rather common, resulting in millions of infections every year with low severity. These seasonal coronaviruses are the results of separate spillovers from the bat animal reservoir into humans in the past ~100 years, in which after spillover, each seasonal virus established itself and spread widely in the human population.
Coronaviruses infect a wide range of animals, and the human outbreaks described above are a result of one or more “jumps” from these animal reservoirs into the human population. SARS is believed to have arrived in the human population from horseshoe bats via a masked palm civet intermediary.
The ability for different lineages to be transmitted between humans is extremely important to understand the potential development of an outbreak. Due to the ability of SARS to spread between humans and the high case fatality rate, SARS (or a SARS-like virus) is considered a global public health threat by the WHO.
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.