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

Abstract

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.

Genome assembly and annotation of Spilosoma obliqua multicapsid nucleopolyhedrovirus from Bihar hairy caterpillar, an agriculturally important insect pest

“…Similar results were reported recently when two newly identified isolates of HycuNPV (HycuNPV‐BJ and HycuNPV‐HB) from China were compared with the Japanese isolate HycuNPV‐N9 and SpobMNPV (Peng et al., 2022). The same study utilized genomes of only alphabaculoviruses in addition to one deltabaculovirus as an outgroup for the phylogenetic analysis (Peng et al., 2022), whereas we utilized 84 baculoviruses representing all four genera. Using 80 baculoviruses from four genera, the SpobNPV–Manipur isolate was shown to be closely related to SpobMNPV phylogenetically (Paul et al., 2021).…”

“…Peng et al. (2022) while analysing the hrs , also confirmed the presence of seven hrs in the SpobMNPV isolate. However, in HycuNPV‐BJ and HycuNPV‐HB isolates only six hrs were reported (Peng et al., 2022).…”

“…The present virus clustered in clade Ia of alphabaculovirus group I comprising baculoviruses such as ChmuNPV, CfMNPV, ChroMNPV, OpMNPV, HycuNPV, AnpeNPV, EppoNPV, CoveMNPV, CfDEFMNPV and AgMNPV. Baculovirus core genes have been used for phylogenetic analysis (Herniou et al., 2003, 2004; Jehle et al., 2006; Paul et al., 2021; Peng et al., 2022) and found to be the source of reliable baculovirus markers to identify lepidopteran baculoviruses and genetic diversity monitoring (Chen et al., 1999).…”

“…et al, 2022). The same study utilized genomes of only alphabaculoviruses in addition to one deltabaculovirus as an outgroup for the phylogenetic analysis (Peng et al, 2022), whereas we utilized 84 baculoviruses representing all four genera. Using 80 baculoviruses from four genera, the SpobNPV-Manipur isolate was shown to be closely related to SpobMNPV phylogenetically (Paul et al, 2021).…”

A gut‐isolated Enterococcus strain (HcM7) triggers the expression of antimicrobial peptides that aid resistance to nucleopolyhedrovirus infection of Hyphantria cunea larvae

“…Nucleopolyhedrovirus (NPV) is an ecologically safe and highly pathogenic agent that can be used to control agricultural and forest pests 10,11 . A species‐specific NPV has been isolated from H. cunea larvae [referred to as H. cunea nucleopolyhedrovirus (HycuNPV)], and several strains have been applied as biopesticides 12–15 . However, a higher killing rate of HycuNPVs is required for successful application of the virus and this remains an area of intense research.…”