Two previously unpublished coronavirus sequences from a Chinese ferret badger and raccoon dog (CFBCo V/DM95/2003 and RDCo V/GM43/2003, respectively) were also included in the analysis.
The helicase (HEL) domain of the replicase gene, the spike protein (S) gene, and the nucleocapsid protein (N) gene were chosen for analysis based on function and the availability of Bt Co V sequences.
The identification of closely related viruses in animal hosts is a prerequisite for establishing the ecology of viral emergence along with reconstruction of evolutionary pathways; however, complex ecosystems make this difficult (41).
For the reconstruction of evolutionary pathways of coronaviruses isolated from bats, coronaviruses representing the three traditional viral groups, SARS-Co Vs from humans and civets (group 4), and coronaviruses from bats (group 5) were included in analyses.
Analysis of lineage-specific selection pressure also indicated that only SARS coronaviruses in civets and humans were under significant positive selection, also demonstrating a recent interspecies transmission.
Analysis of population dynamics revealed that coronavirus populations in bats have constant population growth, while viruses from all other hosts show epidemic-like increases in population.
Dating of different coronavirus lineages suggests that bat coronaviruses are older than those recognized in other animals and that the human severe acute respiratory syndrome (SARS) coronavirus was directly derived from viruses from wild animals in wet markets of southern China.
Furthermore, the most closely related bat and SARS coronaviruses diverged in 1986, an estimated divergence time of 17 years prior to the outbreak, suggesting that there may have been transmission via an unknown intermediate host.
have recently been recognized in different species, the ecology of coronaviruses has not been established.
Our study indicates that bats harbor a much wider diversity of coronaviruses than any other animal species.
Since the onset of the SARS epidemic in early 2003, intense scientific effort has focused on identifying the zoonotic source of SARS-Co V and its transmission route to humans (11, 31, 38, 46).
Surveys of domestic and wild animals in southern China revealed that civet cats, raccoon dogs, and ferret badgers from wet markets were vectors for SARS-Co V outbreaks in 20 (11, 31).
Lineage-specific positive selection analysis also suggests that the SARS-Co V precursor has not been identified.
Our findings suggest that bats are the natural hosts for all coronavirus lineages and that all coronaviruses recognized in other species were derived from viruses residing in bats.