Coronaviruses are found in a diverse array of bat and bird species, which are believed to act as natural hosts. Molecular clock dating analyses of coronaviruses suggest that the most recent common ancestor of these viruses existed around 10,000 years ago. This relatively young age is in sharp contrast to the ancient evolutionary history of their putative natural hosts, which began diversifying tens of millions of years ago. Here, we attempted to resolve this discrepancy by applying more realistic evolutionary models that have previously revealed the ancient evolutionary history of other RNA viruses. By explicitly modeling variation in the strength of natural selection over time and thereby improving the modeling of substitution saturation, we found that the time to the most recent ancestor common for all coronaviruses is likely far greater (millions of years) than the previously inferred range.
INTRODUCTION
Coronaviruses (family Coronaviridae, subfamily Coronavirinae) are important pathogens of birds and mammals. Coronaviruses are positive-sense RNA viruses and are currently classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (1). Alphacoronaviruses and betacoronaviruses are found exclusively in mammals, whereas gammacoronaviruses and deltacoronaviruses primarily infect birds. The identification of severe acute respiratory syndrome (SARS) coronavirus in 2003 (2) prompted an intensive search for novel coronaviruses, resulting in the detection of a number of novel coronaviruses in humans, domesticated animals, and wildlife (3–7). Interestingly, surveillance of coronaviruses in wild animals has led to the discovery of the greatest diversity of coronaviruses in bat and avian species, which suggests that these animals are the natural reservoirs of the viruses (8–10). Indeed, phylogenetic studies of bat and avian coronaviruses suggest an ancient relationship with possible codivergence and coevolution with their hosts. Conversely, many coronaviruses found in bats and other mammals diverged near the tips of coronavirus phylogeny, suggesting that these viruses were the result of recent cross-species transmission events
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676139/
INTRODUCTION
Coronaviruses (family Coronaviridae, subfamily Coronavirinae) are important pathogens of birds and mammals. Coronaviruses are positive-sense RNA viruses and are currently classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (1). Alphacoronaviruses and betacoronaviruses are found exclusively in mammals, whereas gammacoronaviruses and deltacoronaviruses primarily infect birds. The identification of severe acute respiratory syndrome (SARS) coronavirus in 2003 (2) prompted an intensive search for novel coronaviruses, resulting in the detection of a number of novel coronaviruses in humans, domesticated animals, and wildlife (3–7). Interestingly, surveillance of coronaviruses in wild animals has led to the discovery of the greatest diversity of coronaviruses in bat and avian species, which suggests that these animals are the natural reservoirs of the viruses (8–10). Indeed, phylogenetic studies of bat and avian coronaviruses suggest an ancient relationship with possible codivergence and coevolution with their hosts. Conversely, many coronaviruses found in bats and other mammals diverged near the tips of coronavirus phylogeny, suggesting that these viruses were the result of recent cross-species transmission events
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676139/
