Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses

Authors: OLENDRAITE, INGRIDA - University Of Cambridge; LUKHOVITSKAYA, NINA - University Of Cambridge; Porter, Sanford; Valles, Steven; FIRTH, ANDREW - University Of Cambridge

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2017
Publication Date: 8/31/2017
Citation: Olendraite, I., Lukhovitskaya, N.I., Porter, S.D., Valles, S.M., Firth, A.E. 2017. Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses. Journal of General Virology. 98(6):2368-2378.

Interpretive Summary: The red imported fire ant is a highly invasive species that was introduced into the United States in the 1930s. The ant causes approximately $6 billion in damage annually to livestock and agricultural production and poses a serious threat to human health. In cooperation with scientists at the University of Cambridge, UK, USDA-ARS scientists at the Center for Medical, Agricultural and Veterinary Entomology (Gainesville, FL) have discovered a new RNA virus in the fire ant, named Solenopsis invicta virus 4 (SINV-4). This new virus is part of new virus family, which has been named Polycipiviridae, and is proposed in this manuscript. Two members of this family infect the fire ant, Solenopsis invicta (SINV-2 and SINV-4). SINV-2 has been shown to cause reductions in colony fecundity and appears to be an important natural control organism for fire ants.

Technical Abstract: Solenopsis invicta virus 2 is a single-stranded positive-sense picorna-like RNA virus with an unusual genome structure. The monopartite genome of approximately 11 kb contains four short open reading frames in its 5' one third, three of which encode proteins with homology to picornavirus-like jelly-roll fold capsid proteins. These are followed by an intergenic region, and then a single long open reading frame that covers the 3' two thirds of the genome. The polypeptide translation of this 3' open reading frame contains motifs characteristic of picornavirus-like helicase, protease and RNA-dependent RNA polymerase domains. Inspection of public transcriptome shotgun assembly sequences revealed five related apparently nearly complete virus genomes isolated from ant species and one from a dipteran insect. By high-throughput sequencing and in silico assembly of RNA isolated from Solenopsis invicta and four other ant species, followed by targeted Sanger sequencing, we obtained nearly complete genomes for four further viruses in the group. Four further sequences were obtained from a recent large-scale invertebrate virus study. The 15 sequences are highly divergent (pairwise amino acid identities as low as 17% in the non-structural polyprotein), but possess the same overall polycistronic genome structure distinct from all other characterized picorna-like viruses. Consequently we propose the formation of a new virus family, Polycipiviridae, to classify this clade of arthropod-infecting polycistronic picorna-like viruses. We further propose that this family be divided into three genera: Spipolycivirus (2 species), Hupolycivirus (2 species), and Sopolycivirus (11 species), with the latter infecting ants in at least three different subfamilies.