Evolutionary insights into the ecology of coronaviruses - PubMed (original) (raw)

Evolutionary insights into the ecology of coronaviruses

D Vijaykrishna et al. J Virol. 2007 Apr.

Erratum in

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.

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Figures

FIG. 1.

FIG. 1.

Phylogenetic relationships of helicase (A), spike (B), and nucleocapsid (C) genes based on alignments of 1,797, 2,204, and 1,812 nucleotides, respectively. Breda virus (AY427798) was used to root the trees. Numbers at branch nodes indicate neighbor-joining bootstrap values of ≥50%. Nodes with Bayesian posterior probabilities of ≤95% are indicated with asterisks. Bar, 0.1 nucleotide substitution per site (A) or 100 nucleotide substitutions per site (B and C).

FIG. 2.

FIG. 2.

Divergence dates of coronavirus lineages represented on a phylogenetic tree generated based on 1,797 nucleotides of the complete HEL domain sequence. Breda virus (AY427798) was used to root the tree. Numbers at branch nodes indicate the times of divergence, calculated using the uncorrelated exponential relaxed-clock model in BEAST v1.4. For an explanation of the letters at branch nodes, see Table 2.

FIG. 3.

FIG. 3.

Detection of recombination (A) and lineage-specific selection pressure (B) on the spike genes of SARS-CoVs. Mean ω values calculated using GA are presented above branches, with ω values of >1 shown in bold. Numbers below branches indicate an averaged model probability of >1 along specific lineages. Branches with P values of ≥95% are highlighted in gray. The Akaike information criterion (c-AIC) for the best-fitting model was 23,557.

FIG. 4.

FIG. 4.

Postulated ecology of coronaviruses. Solid and dashed lines represent confirmed and hypothetical interspecies transmission pathways, respectively, and arrows represent evolutionary pathways.

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