Comparison of a Modern and Fossil Pithovirus Reveals Its Genetic Conservation and Evolution

Abstract

Most theories on viral evolution are speculative and lack fossil comparison. Here, we isolated a modern Pithovirus-like virus from sewage samples. This giant virus, named Pithovirus massiliensis, was compared with its prehistoric counterpart, Pithovirus sibericum, found in Siberian permafrost. Our analysis revealed near-complete gene repertoire conservation, including horizontal gene transfer and ORFans. Furthermore, all orthologous genes evolved under strong purifying selection with a non-synonymous and synonymous ratio in the same range as the ratio found in the prokaryotic world. The comparison between fossil and modern Pithovirus species provided an estimation of the cadence of the molecular clock, reaching up to 3 × 10(-6) mutations/site/year. In addition, the strict conservation of HGTs and ORFans in P. massiliensis revealed the stable genetic mosaicism in giant viruses and excludes the concept of a bag of genes. The genetic stability for 30,000 years of P. massiliensis demonstrates that giant viruses evolve similarly to prokaryotes by classical mechanisms of evolution, including selection and fixation of genes, followed by selective constraints.

Keywords: evolution; fossil; giant viruses; mosaicism.

Fig. 1.—

Pithovirus massiliensis. (A) Negative staining of the newly isolated P. massiliensis culture supernatant, showing the virus in its typical aspect of a thick electron dense envelope composed of stripes perpendicular to the surface. (B) Higher magnification of a P. massiliensis particle showing the particularity of its “cork”, composed of a highly regular hexagonal honeycomb-like grid.

Fig. 2.—

Comparison of the genome organization between P. massiliensis and P. sibericum.

Fig. 3.—

Estimation of the dN/dS ratio between closely related strains.