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

Zwart, Mark P.; Ali, Ghulam Muhammad; Strien, E.A. van; Schijlen, Elio; Wang, Manli; Werf, Wopke Van der; Vlak, Just M.

doi:10.3390/v11090872

Cited by 12 publications

(8 citation statements)

References 32 publications

(60 reference statements)

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“…The genetic diversity found in SfMNPV ARG-M (5.3 x 10 -3 iSNV per bp) is similar to previous reports of other baculovirus species (Brito et al 2015(Brito et al , 2018Alletti et al 2017;Zwart et al 2019). Because nonsynonymous variants have the potential to introduce drastic changes on protein structure, we focused much of our analyses on this type of mutation.…”

Section: Discussionsupporting

confidence: 89%

Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

Masson

Fabre

Pidre

et al. 2020

Preprint

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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.

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Section: Discussionsupporting

confidence: 89%

Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

Masson

Fabre

Pidre

et al. 2020

Preprint

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“…For intra-populational genetic variants, we found limited non-synonymous substitutions within each Chinese isolate, this may be due to the single and highly pure genotype of the two Chinese isolates. There are very limited within-isolate polymorphisms in each Pakistani Spodoptera litura NPV [ 27 ], and a similar situations has been reported in Spodoptera frugiperda MNPV [ 28 ] and AcMNPV [ 29 ]. For inter-isolate non-synonymous mutations, the most variable genes were hycu78 , desmop , p15 , hycu36 , hycu118 , etm , me53 and ep32 , having genetic diversity levels greater than 40 × 10 − 3 NSS/bp, whereas most of the genes had values lower than the average diversity of the whole genome (23.28 × 10 − 3 NSS/bp).…”

Section: Discussionmentioning

confidence: 64%

Genomic analysis of two Chinese isolates of hyphantria cunea nucleopolyhedrovirus reveals a novel species of alphabaculovirus that infects hyphantria cunea drury (lepidoptera: arctiidae)

Peng

Zhang²,

Lei

et al. 2022

BMC Genomics

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Background Baculoviruses act as effective biological control agents against the invasive pest Hyphantria cunea Drury. In this study, two Chinese Hyphantria cunea nucleopolyhedrovirus (HycuNPV) isolates, HycuNPV-BJ and HycuNPV-HB, were deep sequenced and compared with the Japanese isolate, HycuNPV-N9, to determine whole-genome level diversity and evolutionary history. Results The divergence of the phylogenetic tree and the K2P distances based on 38 core-gene concatenated alignment revealed that two Chinese HycuNPV isolates were a novel species of Alphabaculovirus that infected Hyphantria cunea in China. The gene contents indicated significant differences in the HycuNPV genomes between the Chinese and Japanese isolates. The differences included gene deletions, acquisitions and structural transversions, but the main difference was the high number of single nucleotide polymorphisms (SNPs). In total, 10,393 SNPs, corresponding to approximately 8% of the entire HycuNPV-N9 genome sequence, were detected in the aligned reads. By analyzing non-synonymous variants, we found that hotspot mutation-containing genes had mainly unknown functions and most were early expressing genes. We found that the hycu78 gene which had early and late promoter was under positive selection. Biological activity assays revealed that the infectivity of HycuNPV-HB was greater than that of HycuNPV-BJ, and the killing speed of HycuNPV-HB was faster than that of HycuNPV-BJ. A comparison of molecular genetic characteristics indicated that the virulence differences between the two isolates were affected by SNP and structural variants, especially the homologous repeat regions. Conclusions The genomes of the two Chinese HycuNPV isolates were characterized, they belonged to a novel species of Alphabaculovirus that infected Hyphantria cunea in China. We inferred that the loss or gain of genetic material in the HycuNPV-HB and HycuNPV-BJ genomes resulted in new important adaptive capabilities to the H. cunea host. These results extend the current understanding of the genetic diversity of HycuNPV and will be useful for improving the applicability of this virus as a biological control agent.

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“…One-thousand bootstrapped datasets were used to obtain fiducial limits for the mutation rate estimates. dI/dS and dN/dS analyses Estimates of dN/dS (i.e., the normalized rate of nonsynonymous mutations, here made for authentic viral genes) were made using standard methods [46,47]. As we are not aware of any estimates of the mutation spectrum for insect DNA viruses and our own data suggest these biases may not be very strong (Table 2), we assume no mutation bias is present (i.e., a transition to transversion ratio of 1).…”

Section: Mutation Rate Estimates With Established Approachesmentioning

confidence: 99%

Empirical estimates of the mutation rate for an alphabaculovirus

Boezen

Ali

Wang

et al. 2021

Preprint

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Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical estimates of mutation rate are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication machinery. Here, we report an empirical estimate of the mutation rate per base per strand copying (s/n/r) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV). To avoid biases due to selection, we analyzed mutations that occurred in a stable, non-functional genomic insert after five serial passages in Spodoptera exigua larvae. Population bottlenecks, viral mode of replication and thresholds for mutation detection likely affect mutation rate estimates, and we therefore used population genetic models that account for these processes to infer the mutation rate. We estimated a mutation rate of 1 X 10-7 s/n/r. This estimate was not sensitive to different model assumptions or including whole genome data. The rates at which different classes of mutations accumulate provide good evidence for neutrality of mutations occurring within the inserted region. We therefore present a robust approach for mutation rate estimation for viruses with stable genomes, and strong evidence of a much lower alphabaculovirus mutation rate than supposed based on the high levels of polymorphism observed.

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

Cited by 12 publications

References 32 publications

Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

Genomic analysis of two Chinese isolates of hyphantria cunea nucleopolyhedrovirus reveals a novel species of alphabaculovirus that infects hyphantria cunea drury (lepidoptera: arctiidae)

Empirical estimates of the mutation rate for an alphabaculovirus

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