Complete genome sequence of an Argentinean isolate of Solenopsis invicta virus 3

Abstract

Solenopsis invicta virus 3 (SINV-3) is a recently described positive-strand RNA virus that infects the red imported fire ant, S. invicta. The genome of an Argentinean isolate of Solenopsis invicta virus 3 (SINV-3(ArgSF )) obtained from the Santa Fe region of Argentina was sequenced in entirety. Assembly of nine overlapping fragments yielded a consensus genome sequence 10,386 nucleotides long, excluding the poly(A) tail present on the 3' end (Genbank accession number GU017972). With the exception of the poly(A) tail, the genome length of SINV-3(ArgSF ) was identical to the North American isolate (SINV-3(USDM )). The SINV-3(ArgSF ) genome possessed three major open reading frames (ORFs) (comprised of >or=100 codons) in the sense orientation; SINV-3(USDM ) possessed only two. ORFs 1 and 2 had identical start and stop genome positions for both isolates. Blastp analysis of the translated ORF 1 of SINV-3(ArgSF ) recognized conserved domains for helicase, protease, and RNA-dependent RNA polymerase. These domains and their corresponding positions were identical to those reported for SINV-3(USDM ). ORF 2a, unique to the SINV-3(ArgSF ) genome, was also found in frame 2 and had a canonical start codon located at nucleotide position 8,351 and a stop codon ending at position 8,827. Blastp analysis of the translated amino acid sequence of ORF 2a revealed no significant similarity in the Genbank database. The two SINV-3 isolates exhibited 96.2% nucleotide sequence identity across the entire genome. The amino acid sequences of ORFs 1 and 2 exhibited higher identities (99.0 and 98.2%, respectively) than the corresponding nucleotide regions within the genome. These data indicated that the nucleotide differences between the SINV-3 isolates were largely synonymous. This observation was corroborated by codon substitution rate analysis. Thus, the majority of the SINV-3 codon changes were silent in the two polyproteins, indicating purifying selection pressure on the viral genome.