Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellanii

Abstract

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs ofPleurochrysisendemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.

The origin and evolution of viruses inferred from fold family structure

“…Virus genes without any detectable cellular homolog or ORFans, virus-specific genes, constitute >90% of the genes in the proposed family “ Pandoraviridae ” [ 78 ], whose members possess the largest virus genomes ever discovered [ 14 ]. A very recent study identified an amoeba virus (Yaravirus) with a nearly complete ‘ORFan genome’ [ 79 ]. These virus-specific genes are starkly different even among members of the same virus family [ 14 , 32 ].…”

Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation

“…2). For the a newly described amoeba-tropic virus called Yaravirus 30 (Fig. 2A), only Cenote-Taker2 could discern an annotation for any genes, with the major capsid protein (MCP), packaging ATPase, and replicative helicase all being recognizable.…”

Investigating the Concept and Origin of Viruses

“…This is especially true when the objective is to place fast-evolving organisms and viruses in the tree of life [ 64 ]. First, the subset of virus genes for which reliable homologs can be found is extremely small [ 48 ]. This fact greatly limits the choice and the number of available orthologous genes to be used in phylogeny reconstruction.…”

“…Moreover, regular and recent gene uptake from cells is expected to leave detectable similarity traces in the viral genomes. However, >90% of Pandoravirus genes show no similarity to cellular genes [ 24 ] (a feature conserved in many viruses [ 41 ], see also [ 48 ]) and viruses encode several protein fold structures that have never been detected in cells [ 41 ]. It is strange to think that regularly and recently captured viral genes are no longer recognizable whereas presumably ancient ‘core’ genes used to build virus phylogenies are readily recognizable.…”