Sequence comparison between three geographically distinct Spodoptera frugiperda multiple nucleopolyhedrovirus isolates: Detecting positively selected genes

Abstract

The complete genomic sequence of a Nicaraguan plaque purified Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) genotype SfMNPV-B was determined and compared to previously sequenced isolates from United States (SfMNPV-3AP2) and Brazil (SfMNPV-19). The genome of SfMNPV-B (132,954bp) was 1623bp and 389bp larger than that of SfMNPV-3AP2 and SfMNPV-19, respectively. Genome size differences were mainly due to a deletion located in the SfMNPV-3AP2 egt region and small deletions and point mutations in SfMNPV-19. Nucleotide sequences were strongly conserved (99.35% identity) and a high degree of predicted amino acid sequence identity was observed. A total of 145 open reading frames (ORFs) were identified in SfMNPV-B, two of them (sf39a and sf110a) had not been previously identified in the SfMNPV-3AP2 and SfMNPV-19 genomes and one (sf57a) was absent in both these genomes. In addition, sf6 was not previously identified in the SfMNPV-19 genome. In contrast, SfMNPV-B and SfMNPV-19 both lacked sf129 that had been reported in SfMNPV-3AP2. In an effort to identify genes potentially involved in virulence or in determining population adaptations, selection pressure analysis was performed. Three ORFs were identified undergoing positive selection: sf49 (pif-3), sf57 (odv-e66b) and sf122 (unknown function). Strong selection for ODV envelope protein genes indicates that the initial infection process in the insect midgut is one critical point at which adaptation acts during the transmission of these viruses in geographically distant populations. The function of ORF sf122 is being examined.

Superinfection Exclusion in Alphabaculovirus Infections Is Concomitant with Actin Reorganization

“…The egfp gene is inserted into the polyhedrin locus under the control of the polyhedrin promoter in this virus, resulting in an occlusion-negative virus. The SfMNPV used in this study was a plaque-purified variant (genotype B) of a Nicaraguan isolate of SfMNPV (34). All viruses were propagated in Sf9 cells at 28°C using standard methods (32).…”

Analysis of a naturally-occurring deletion mutant of Spodoptera frugiperda multiple nucleopolyhedrovirus reveals sf58 as a new per os infectivity factor of lepidopteran-infecting baculoviruses

“…The genome of the defective genotype SfMNPV-G is 128,034 bp, which is 4920 bp smaller than the genome of the reference genotype SfMNPV-B (Simón et al, 2011). This size difference between the two genotypes was accounted for almost entirely by a deletion of 4860 bp located between nucleotides (nt) 29,654), reducing its length by 207 nucleotides.…”

“…The reaction products were loaded in an automated DNA sequencer ABI PRISM. The genomic sequence of SfMNPV-G (GenBank accession number JF899325) was compared with that of SfMNPV-B published previously (accession number HM595733; Simón et al, 2011) using the Clone Manager program (Scientific & Educational Software, 1994. Sequence alignments and gene-parity plots were performed using NCBI BLAST alignment tools (Altschul et al, 1990;Pearson, 1990) to examine genome organization and order of homologous ORFs.…”

“…Analysis of the translated sf58 gene revealed that the QLVSRN sequence of the SfMNPV-B genotype is conserved with 100% identity with other alphabaculoviruses such as SfMNPV-3AP2, SpltNPV, SeMNPV, AgseNPV or AgipNPV (Fig. 1) (Harrison et al, 2008;Simón et al, 2011). The sf58 ORF is 345 nt long and encodes a protein of 114 amino acids with a predicted molecular weight of 12.88 kDa.…”

“…The SfMNPV-B genotype with the largest genome, 132,954 bp (accession number HM595733; Simón et al, 2011), is the predominant genotype in the wild-type population. All the other genotypes present one or more deletions compared to SfMNPV-B (Simón et al, 2005).…”