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Open AccessArticle

Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing

1
Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), 6708PB Wageningen, The Netherlands
2
Laboratory of Virology, Wageningen University and Research, 6708PD Wageningen, The Netherlands
3
Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708PD Wageningen, The Netherlands
4
Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
5
Centre for Crop Systems Analysis, Wageningen University and Research, 6708PD Wageningen, The Netherlands
*
Author to whom correspondence should be addressed.
Current affiliation: Air University Multan Campus, Islamabad 66000, Pakistan.
Viruses 2019, 11(9), 872; https://doi.org/10.3390/v11090872
Received: 17 July 2019 / Revised: 26 August 2019 / Accepted: 11 September 2019 / Published: 17 September 2019
(This article belongs to the Special Issue Insect Viruses and Pest Management)
Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere. View Full-Text
Keywords: Spodoptera litura nucleopolyhedrovirus; SpltNPV; virulence; deep sequencing; Illumina; genomics Spodoptera litura nucleopolyhedrovirus; SpltNPV; virulence; deep sequencing; Illumina; genomics
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Zwart, M.P.; Ali, G.; van Strien, E.A.; Schijlen, E.G.W.M.; Wang, M.; van der Werf, W.; Vlak, J.M. Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing. Viruses 2019, 11, 872.

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