Evolutionary Insights into the Ecology of Coronaviruses

Abstract

Although many novel members of the Coronaviridae 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. 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. 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. These results indicate that diverse coronaviruses are endemic in different bat species, with repeated introductions to other animals and occasional establishment in other species. Our findings suggest that bats are likely the natural hosts for all presently known coronavirus lineages and that all coronaviruses recognized in other species were derived from viruses residing in bats. Further surveillance of bat and other animal populations is needed to fully describe the ecology and evolution of this virus family.

Circulation of Group 2 Coronaviruses in a Bat Species Common to Urban Areas in Western Europe

“…The finding of group 2 CoVs in bats outside Asia supports the opinion that group 1 and 2 bat-CoVs will circulate worldwide, since recent evidence suggests that bat-CoVs are the gene pools for all the mammalian CoVs in groups 1 and 2 (Vijaykrishna et al 2007, Woo et al 2009). Whether this particular virus circulating in the Netherlands can cause zoonotic disease is not known.…”

“…Roost sites include locations in proximity to humans like houses (cellars and cavity walls), stables, bridges, mines, and wells; frequent contact with intermediate hosts like domestic cats enlarge the possibility of transmission of virus from bats (Calisher et al 2006). Recent studies indicate that bats are the natural hosts for all mammalian CoVs and that the circulation of CoVs in other mammals is the result of occasional introductions from bats (Vijaykrishna et al 2007, Woo et al 2009). Genetic analyses show that bat CoVs belong to groups 1 and 2.…”

Detection of bat coronaviruses from Miniopterus fuliginosus in Japan

“…BtCoV HKU8-1, which was isolated from M. pusillus in Hong Kong in 2006 [18], was the second related strain, but fewer nucleotides were identified (80%) than in HKU7-1. In the S protein region, M.ful./Japan/03/2009 showed 92% identity relative to BtCoV Fujian/773/2005 (GenBank EF434379), which was isolated in the Fujian province in China in 2005 [20]. In contrast, M.ful./Japan/04/2010 showed about 70% similarity with the HKU8 strain and other group 1 BtCoVs (1a and 1b), which were isolated in Hong Kong from 2004 to 2005 [21].…”

Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives

“…In fact, there are many works reporting the jumping of viral species between host species. These events are commonly called viral-host switches (Gibbs and Weiller 1999; Nemirov et al 2002; Vijaykrishna et al 2007; Kang et al 2010; Liu et al. 2010, 2011; Longdon et al 2011) or species jumps.…”