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. To date, SfMNPV genomic diversity of different isolates has been mainly studied by means of restriction pattern analyses and by sequencing of the egt region. 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.
Highlights
Through molecular evolution studies we provide evidence of diversifying selection acting on sf29, a putative collagenase which could contribute to the oral infectivity of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV)
Analysis of residue conservation revealed that the HEXXH motif, involved in zinc binding and a common feature of metalloproteases (Rawlings et al 2013), is conserved in most of the sequences of our dataset, suggesting that sf29 could be a functional collagenase (Fig. 4c). It is increasingly recognized the relevance of genomic diversity as a key determinant of viral evolutionary dynamics and virulence (Geoghegan and Holmes 2018), specially in large DNA viruses (Renner and Szpara 2017)
This work presents a snapshot of the underlying genomic diversity present inside a natural isolate of SfMNPV, expanding previous studies of isolates for which only a consensus sequence has been reported (Harrison, Puttler, and Popham 2008; Wolff et al 2008; Simón et al 2011; Simón, Palma, et al 2012; Barrera et al 2015)
Summary
The fall armyworm, Spodoptera frugiperda (J.E. Smith, Lepidoptera: Noctuidae), is an invasive agricultural pest that attacks a variety of crops and is naturally distributed across the Americas. Traditional control methods for this pest involve the use of chemical products or crops expressing Bt toxins (Bernardi et al 2015). Cases of field-evolved resistance to Bt toxins and environmental impact of chemical pesticides are forcing the development of novel control strategies (Harrison et al 2019). Baculoviruses are insect-specific large DNA viruses (Harrison et al 2018) with a narrow host range and high virulence, which make them potentially safe candidates to develop biopesticides (Haase, Sciocco-Cap, and Romanowski 2015). A nucleopolyhedrovirus infecting S. frugiperda (SfMNPV) has been implemented for the biological control of fall armyworm populations (Bentivenha et al 2018)
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