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. 2010 Feb 9;8(2):e1000301.
doi: 10.1371/journal.pbio.1000301.

Paleovirology--modern consequences of ancient viruses

Michael Emerman  1 , Harmit S Malik
Affiliations

Paleovirology--modern consequences of ancient viruses

Michael Emerman et al. PLoS Biol. .
No abstract available

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Time-line of paleoviruses in the human lineage.
The dashed line at the top line represents the time period for paleoviruses. The red lightning bolts represent dates of known recent and ancient viruses based either on historical records, molecular clocks, or on endogenous retroviruses in the human genome for SARS-Co , HIV-1 and -2 , dengue (DEN) , measles , smallpox , HERV-K(HML2) , or PtERV , and older endogenous retroviruses shared among all hominoids or all primates . The blue, green, and orange lightning bolts represent inferred viruses based on positive selection of TRIM5 , and the brown line is an inferred virus based on positive selection of ZAP simplified for representation, here. Each color corresponds to inferred paleoviruses based on positive selection on a particular antiviral gene calculated on the phylogenetic tree in the bottom of the figure where the lineage under selection has the same color coding, and the dates correspond to dates of the ancestors . Although one virus is shown per episode of selection, there could be many different waves of similar viruses during that time period. Purple branches refer to selections due to inferred paleoviruses in lineages that do not lead directly to humans. There is considerable uncertainty associated with most of the dates referred to in this figure.
Figure 2
Figure 2. TRIM5 restriction of HIV-1 has decreased during evolution leading to humans.
The shading of the rectangle represents the degree that TRIM5 will limit infection of HIV-1 (darker color means TRIM5 decreases HIV-1 infection more) and the X-axis indicates time in millions of years from the present. Each dotted line represents the reconstruction of TRIM5 as it likely existed at a node of a phylogenetic tree indicating a common ancestor of humans with chimpanzees, gorillas, orangutans, gibbons, and Old World monkeys (rhesus). Original data is found in and shows that the antiviral gene TRIM5 restricted HIV-1 better at points in evolution earlier than the chimp–human common ancestor than it does after that. On the right shows an amino acid sequence of a region of TRIM5 containing amino acids that confer resistance or susceptibility to HIV-1 with the amino acids that are under the strongest positive selection in red . Changes in this region cause a gain of restriction to some viruses, while causing a loss to others ,–. The R332 amino acid, which represents the single largest determinant of loss of resistance to HIV-1 ,, was fixed before the chimp–human common ancestor, but positive selection has continued in TRIM5 along the human lineage beyond this point.
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