Faustovirus, an asfarvirus-related new lineage of giant viruses infecting amoebae

Abstract

Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of ≈ 200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes ≈ 3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy.

Importance: By using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is ≈ 3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database).

FIG 1

Electron microscopy imaging of the faustovirus replication cycle in V. vermiformis. (A) A faustovirus particle being phagocytosed by an amoeba at 0 h p.i. (B) Virus factory at 8 h p.i., with a dense replication center surrounded by empty capsids. (C) Higher-magnification view of a virus factory, showing the empty particles. (D) Virus factory at 8 h p.i., showing the donut-type morphology with both empty and DNA-filled particles. (E) Virus factory at 14 h p.i., showing the increased number of viral particles at different stages of morphogenesis. (F) Higher-magnification view of the boxed area in panel E. (G) Virus factory at 16 h p.i., with the new viral community occupying the entire cell cytoplasm area. (H and I) Higher-magnification views of panel G, demonstrating the honeycomb stitches. (J) Negative staining of a purified viral suspension showing a faustovirus in the typical aspect of Megavirales, with an icosahedral capsid and a size of 200 nm without fibrils. (K) Cryo-electron micrograph of faustovirus particles at different stages of maturation. The empty particles are 1,600 Å in diameter, whereas the full particles are 1,750 Å in diameter, vertex to vertex (n = 660). (L) Cryo-EM reconstruction of full faustovirus particles.

FIG 2

Circular representation of the faustovirus E12 genome. The circles show the following, from the center to the outside: GC skew (green/purple), GC content (black), best-hit taxonomy (black, Archaea; green, Bacteria; purple, Eukarya; and blue, viruses), proteins in the virions as identified by proteomics (red), and ORFs on the plus and minus strands (blue).

FIG 3

Phylogeny reconstruction based on the family B DNA polymerase. Phylogenetic analyses were performed using the maximum likelihood method, based on the family B DNA polymerases from faustoviruses (including the faustovirus E12 strain) and representative members of the different families or new putative families of the proposed order Megavirales.