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Updated: Jul 7, 2026
Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
Genomic sequence analysis of a fast-killing isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus
Robert L Harrison1, Benjamin Puttler2, Holly J R Popham3
1Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Plant Sciences Institute, 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
Abstract:
Six clones of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) were plaque-purified from field isolates collected in Missouri, USA. In bioassays, four of the plaque-purified isolates killed neonate S. frugiperda larvae more rapidly than the field isolates from which they were derived, with LT(50) values (mean time to kill 50 % of the test larvae) ranging from 34.4 to 49.7 h post-infection. The complete genomic sequence of one of these isolates, SfMNPV-3AP2, was determined and analysed. The SfMNPV-3AP2 genome was 131 330 bp with a G+C content of 40.2 %. A total of 144 open reading frames (ORFs) was identified and examined, including the set of 62 genes in common among lepidopteran nucleopolyhedrovirus genomes. Comparisons of ORF content, order and predicted amino acid sequences with other nucleopolyhedoviruses indicated that SfMNPV is part of a cluster of viruses within NPV group II that includes NPVs isolated from Spodoptera, Agrotis and Mamestra host species. SfMNPV-3AP2 shared a high degree of nucleotide sequence similarity with partial sequences from other SfMNPV isolates. Comparison of the SfMNPV-3AP2 genome sequence with a partial sequence from a Brazilian isolate of SfMNPV revealed that SfMNPV-3AP2 contained a deletion that removed parts of ORF sf27 and the gene encoding ecdysteroid UDP-glucosyltransferase (egt). An examination of the egt region in the other isolates revealed that the other five SfMNPV clones also contained deletions of varying length in this region. Variant genotypes with deletions extending around the egt gene have been reported previously from a Nicaraguan field isolate of SfMNPV, suggesting that the presence of such variants is a common feature of SfMNPV populations.
Insights
Six Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) clones were isolated and sequenced. Four isolates showed faster larval kill rates, and genomic analysis revealed deletions in the egt gene, common in SfMNPV populations.
Area of Science:
- Virology
- Insect Pathology
- Genomics
Background:
- Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) is an important insect pathogen.
- Understanding SfMNPV genetic diversity is crucial for its application in pest control.
Purpose of the Study:
- To isolate and characterize virulent SfMNPV strains from field populations.
- To determine the complete genome sequence of a highly virulent SfMNPV isolate.
- To investigate genetic variations, particularly deletions in the egt gene, within SfMNPV populations.
Main Methods:
- Plaque purification of SfMNPV from field isolates.
- Bioassays to determine larval mortality and LT50 values.
- Whole-genome sequencing and bioinformatic analysis of SfMNPV-3AP2.
- Comparative genomic analysis with other nucleopolyhedroviruses.
Main Results:
- Four of six plaque-purified SfMNPV isolates exhibited enhanced virulence, with LT50 values as low as 34.4 h.
- The complete genome of SfMNPV-3AP2 was 131,330 bp with 144 ORFs.
- SfMNPV-3AP2 and other isolates showed deletions in the ecdysteroid UDP-glucosyltransferase (egt) gene.
- Genomic analysis placed SfMNPV within NPV group II, clustering with related Spodoptera, Agrotis, and Mamestra NPVs.
Conclusions:
- Highly virulent SfMNPV strains can be isolated and characterized.
- The SfMNPV-3AP2 genome provides a reference for this virus group.
- Deletions in the egt gene are common in SfMNPV populations and may influence virulence.
