Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

Abstract

Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) represents a strong candidate to develop environmental-friendly pesticides against the fall armyworm (Spodoptera frugiperda), a widespread pest that poses a severe threat to different crops around the world. However, little is known regarding the genomic diversity present inside SfMNPV isolates and how it shapes the interactions between virus and host. Here, the genomic diversity present inside an isolate of SfMNPV was explored using high-throughput sequencing for the first time. We identified 704 intrahost single nucleotide variants, from which 184 are nonsynonymous mutations distributed among 82 different coding sequences. We detected several structural variants affecting SfMNPV genome, including two previously reported deletions inside the egt region. A comparative analysis between polymorphisms present in different SfMNPV isolates and our intraisolate diversity data suggests that coding regions with higher genetic diversity are associated with oral infectivity or unknown functions. In this context, through molecular evolution studies we provide evidence of diversifying selection acting on sf29, a putative collagenase which could contribute to the oral infectivity of SfMNPV. Overall, our results contribute to deepen our understanding of the coevolution between SfMNPV and the fall armyworm and will be useful to improve the applicability of this virus as a biological control agent.

Generation of Variability in Chrysodeixis includens Nucleopolyhedrovirus (ChinNPV): The Role of a Single Variant

“…In contrast, the ChinNPV-K reads had to be assembled in six contigs and had up to 394 variations in comparison to the consensus sequence that were distributed throughout the genome. The mutation rate for ChinNPV-K (2 × 10 −3 substitutions/nt) was similar to that of another NPV (~1 × 10 −3 substitutions/nt [12]), but higher than for other dsDNA viruses (~10 −6 substitutions/nt) [2]. Furthermore, the presence of these SNPs at restriction sites is likely to be the origin of some of the variability observed.…”

“…It appears likely, therefore, that variants were generated during replication in cell culture, principally by point mutation. Recent studies in different baculoviruses using deep sequencing seem to indicate that point mutations are a frequent source of diversity in this virus family [12,25,29,36]. Therefore, genetic variability within natural baculovirus isolates is probably far higher than that observed with techniques, such as REN profiles or the DGGE (denaturing gradient gel electrophoresis) analysis used by Baillie and Bouwer [16].…”

“…The presence of high diversity within baculoviruses is particularly evident when sequencing these viruses. Two recent examples, a study carried out on Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) [12] and another on Autographa californica multiple nucleopolyhedrovirus (AcMNPV) [13], revealed the high variability present in natural baculovirus isolates and the mechanisms likely to be involved in its generation. Factors such as food plants or host genetic heterogeneity can also directly influence the genetic variability present in baculovirus isolates [14,15].…”