A new positive-strand RNA virus with unique genome characteristics from the red imported fire ant, Solenopsis invicta

• Published in: Virology (New York, N.Y.) Vol. 365; no. 2; pp. 457 - 463
• Main Authors: Valles, Steven M, Strong, Charles A, Hashimoto, Yoshifumi
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2007
• Subjects: Amino Acid Sequence; amino acid sequences; Animals; Ants - virology; consensus sequence; Dicistroviridae; DNA, Complementary - biosynthesis; Formicidae; Genome sequence; Genome, Viral; genomics; Iflavirus; Infectious Disease; insect viruses; invasive species; Molecular Sequence Data; Open Reading Frames; Peptide Hydrolases - genetics; Phylogeny; Picornaviridae; positive sense, single-stranded RNA viruses; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleases - metabolism; RNA helicases; RNA Helicases - chemistry; RNA Helicases - genetics; RNA Replicase - chemistry; RNA Replicase - genetics; RNA virus; RNA Viruses - classification; RNA Viruses - genetics; RNA Viruses - isolation & purification; RNA, Messenger - genetics; RNA, Viral - metabolism; RNA-directed RNA polymerase; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Solenopsis invicta; Solenopsis invicta virus 2; Viral Proteins - chemistry; Viral Proteins - genetics; Iflavirus; Genome sequence; RNA virus; Solenopsis invicta; Dicistroviridae
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1016/j.virol.2007.03.043

Abstract We report the discovery of a new virus with unique genome characteristics from the red imported fire ant, Solenopsis invicta . This virus represents the second identified from this ant species. It is provisionally named Solenopsis invicta virus 2 (SINV-2). The SINV-2 genome was constructed by compiling sequences from successive 5′ RACE reactions, a 3′ RACE reaction, and expressed sequence tag, c246 (accession number EH413675 ), from a fire ant expression library. The SINV-2 genome structure was monopartite, polycistronic and RNA-based. The genome consensus sequence ( EF428566 ) was 11,303 nucleotides in length, excluding the poly(A) tail present on the 3′ end. Analysis of the genome revealed 4 major open reading frames (ORFs; comprised of ≥ 100 codons) and 5 minor ORFs (comprised of 50–99 codons) in the sense orientation. No large ORFs were found in the inverse orientation suggesting that the SINV-2 genome was from a positive-strand RNA virus. Further evidence for this conclusion includes abolished RT–PCR amplification by RNase treatment of SINV-2 nucleic acid template, and failure to amplify without first conducting cDNA synthesis. Blastp analysis indicated that ORF 4 contained conserved domains of an RNA-dependent RNA polymerase, helicase, and protease, characteristic of positive-strand RNA viruses. However, the protease domain and putative structural proteins (ORFs 1, 2, and 3) were less well conserved. Phylogenetic analysis of the RdRp, helicase, and ORF 1 indicate unique placement of SINV-2 exclusive from the Dicistroviridae , iflaviruses, Picornaviridae , and plant small RNA viruses.