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United States Department of Agriculture

Agricultural Research Service


Location: Imported Fire Ant and Household Insects Research

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

item Valles, Steven
item Varone, Laura
item Briano, Juan

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2009
Publication Date: 1/5/2010
Publication URL:
Citation: Valles, S.M., Allen, C., Varone, L., Briano, J. 2010. Complete genome sequence of an Argentinean isolate of Solenopsis invicta virus 3. Virus Genes. 40:293-297.

Interpretive Summary: The red imported fire ant was introduced into the United States in the 1930s and currently infests about 300 million acres. It causes economic losses that exceed 6 billion dollars annually in the United States and poses a threat to human health. USDA-ARS scientists at the Center for Medical, Agricultural and Veterinary Entomology (Gainesville, FL) and the South American Biological Control Laboratory, Buenos Aires, Argentina, have discovered a recently described new species of virus (SINV-3) in Argentina. The genome of the Argentinean isolate was sequenced in entirety and compared with the North American isolate. The virus is associated with fire ant colony mortality and may find utility as a biological control agent (or microbial insecticide) for fire ants.

Technical Abstract: The genome of an Argentinean isolate of Solenopsis invicta virus 3 (SINV-3ArgSF) obtained from the Santa Fe region of Argentina was sequenced in entirety. Assembly of 9 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-3ArgSF was identical to the North American isolate (SINV-3USDM). The SINV-3ArgSF genome possessed 3 major ORFs (comprised of =100 codons) in the sense orientation; SINV-3USDM 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-3ArgSF recognized conserved domains for helicase, protease, and RNA-dependent RNA polymerase. These domains and their corresponding positions were identical to those reported for SINV-3USDM. ORF2a, unique to the SINV-3ArgSF 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 ORF2a 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.

Last Modified: 06/25/2017
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