Genomic sequence analysis of a fast-killing isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus

Abstract

Six clones of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) were plaquepurified 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.

Analagous Population Structures for Two Alphabaculoviruses Highlight a Functional Role for Deletion Mutants

“…Although SfNIC and SeUS2 populations are clearly similar in terms of genotypic structure and diversity, the functional importance of their deletion variants appears to encompass different aspects of virus transmissibility in each virus population, ranging from OB pathogenicity effects (39) and speed-of-kill characteristics (17) to the quantities of OBs produced in each infected insect (as in this study). The three phenotypic traits analyzed here provide a broader picture of the functional significance of the defective genotype SeUS2-C.…”

“…The genetic basis for this is presently unclear, but it may be related to the absence of one or more of the genes of unknown function that are present in the SeUS2-C deleted region. One such gene is Se28, the homolog of which is partially deleted in SfMNPV (sf27) in a fastkilling variant of this virus (SfMNPV-3AP2), although its influence on OB production has not been determined (17).…”

“…Five samples from Japan and Thailand show restriction endonuclease profiles (10) with signs of deletion genotypes, characterized by submolar PstI-C and PstI-D fragments. Finally, in SfMNPV isolates from the United States (17) and Colombia (G. Barrera, O. Simón, and P. Caballero, unpublished data), the presence of genotypes with sizable genomic deletions in the same genomic region has been reported recently. The host ranges of these viruses differ.…”

“…The genomes of SfMNPV and SeMNPV are strikingly similar (14,15), with 72 to 85% nucleotide homology in colinear regions covering 30% of the genome, and with Ͼ85% of genes being shared; this has led researchers to suggest that these two viruses are closely related (16,17). The large-deletion genotypes present in a Floridan SeMNPV isolate, SeMNPV-US2 (SeUS2), were observed to share parallel genetic and phenotypic characteristics with an SfMNPV isolate from Nicaragua, SfMNPV-NIC (SfNIC) (18).…”

Stability of a Spodoptera frugiperda Nucleopolyhedrovirus Deletion Recombinant during Serial Passage in Insects

“…Natural populations of the fall armyworm Spodoptera frugiperda (Lepidoptera) suffer S. frugiperda multiple nucleopolyhedrovirus (SfMNPV) disease, and some SfMNPV isolates have the potential to control this pest (12,16,33,44). The complete genome sequences of two isolates have been published (16,44).…”