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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.

SUBMITTER: Vijaykrishna D

PROVIDER: S-EPMC1866124 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature

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Evolutionary insights into the ecology of coronaviruses.

Vijaykrishna D D Smith G J D GJ Zhang J X JX Peiris J S M JS Chen H H Guan Y Y

Journal of virology 20070131 8

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 wil ...[more]

PMID: 17267506

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Project description:BackgroundFloral nectar is an important determinant of plant-pollinator interactions and an integral component of pollination syndromes, suggesting it is under pollinator-mediated selection. However, compared to floral display traits, we know little about the evolutionary ecology of nectar. Combining a literature review with a meta-analysis approach, we summarize the evidence for heritable variation in nectar traits and link this variation to pollinator response and plant fitness. We further review associations between nectar traits and floral signals and discuss them in the context of honest signalling and targets of selection.ScopeAlthough nectar is strongly influenced by environmental factors, heritable variation in nectar production rate has been documented in several populations (mean h2 = 0.31). Almost nothing is known about heritability of other nectar traits, such as sugar and amino acid concentrations. Only a handful of studies have quantified selection on nectar traits, and few find statistically significant selection. Pollinator responses to nectar traits indicate they may drive selection, but studies tying pollinator preferences to plant fitness are lacking. So far, only one study conclusively identified pollinators as selective agents on a nectar trait, and the role of microbes, herbivores, nectar robbers and abiotic factors in nectar evolution is largely hypothetical. Finally, there is a trend for positive correlations among floral cues and nectar traits, indicating honest signalling of rewards.ConclusionsImportant progress can be made by studies that quantify current selection on nectar in natural populations, as well as experimental approaches that identify the target traits and selective agents involved. Signal-reward associations suggest that correlational selection may shape evolution of nectar traits, and studies exploring these more complex forms of natural selection are needed. Many questions about nectar evolution remain unanswered, making this a field ripe for future research.

Project description:Community protective immunity can affect RNA virus evolution by selecting for new antigenic variants on the scale of years, exemplified by the need of annual evaluation of influenza vaccines. The extent to which this process termed antigenic drift affects coronaviruses remains unknown. Alike the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), seasonal human coronaviruses (HCoV) likely emerged from animal reservoirs as new human pathogens in the past. We therefore analyzed the long-term evolutionary dynamics of the ubiquitous HCoV-229E and HCoV-OC43 in comparison with human influenza A virus (IAV) subtype H3N2. We focus on viral glycoprotein genes that mediate viral entry into cells and are major targets of host neutralizing antibody responses. Maximum likelihood and Bayesian phylogenies of publicly available gene datasets representing about three decades of HCoV and IAV evolution showed that all viruses had similar ladder-like tree shapes compatible with antigenic drift, supported by different tree shape statistics. Evolutionary rates inferred in a Bayesian framework were 6.5 × 10-4 (95% highest posterior density (HPD), 5.4-7.5 × 10-4) substitutions per site per year (s/s/y) for HCoV-229E spike (S) genes and 5.7 × 10-4 (95% HPD, 5-6.5 × 10-4) s/s/y for HCoV-OC43 S genes, which were about fourfold lower than the 2.5 × 10-3 (95% HPD, 2.3-2.7 × 10-3) s/s/y rate for IAV hemagglutinin (HA) genes. Coronavirus S genes accumulated about threefold less (P < 0.001) non-synonymous mutations (dN) over time than IAV HA genes. In both IAV and HCoV, the average rate of dN within the receptor binding domains (RBD) was about fivefold higher (P < 0.0001) than in other glycoprotein gene regions. Similarly, most sites showing evidence for positive selection occurred within the RBD (HCoV-229E, 6/14 sites, P < 0.05; HCoV-OC43, 23/38 sites, P < 0.01; IAV, 13/15 sites, P = 0.08). In sum, the evolutionary dynamics of HCoV and IAV showed several similarities, yet amino acid changes potentially representing antigenic drift occurred on a lower scale in endemic HCoV compared to IAV. It seems likely that pandemic SARS-CoV-2 evolution will bear similarities with IAV evolution including accumulation of adaptive changes in the RBD, requiring vaccines to be updated regularly, whereas higher SARS-CoV-2 evolutionary stability resembling endemic HCoV can be expected in the post-pandemic stage.

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Evolutionary insights into the ecology of coronaviruses.

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Evolutionary insights into the ecology of coronaviruses.

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