Identification and genomic sequence analysis of a new Spodoptera exigua multiple nucleopolyhedrovirus, SeMNPV-QD, isolated from Qingdao, China

A new beet armyworm (Spodoptera exigua) multiple nucleopolyhedrovirus SeMNPV-QD was isolated from dead larvae in the field in Qingdao, Shandong, China. The virus has a polyhedron size of 1.39 ± 0.28 μm, and typical virions contain one to seven nucleocapsids per envelope. SeMNPV-QD only infects the larvae of S. exigua; it does not infect larvae of S. litura, Agrotis ipsilon, A. segetum, Bombyx mori, Hyphantria cunea, or Stilpnotia salicis, and thus, has higher host specificity. SeMNPV-QD has a circular double-stranded DNA genome of 128,525 bp with a GC content of 37.41% and 127 putative open reading frames (ORF), each of which encodes more than 50 amino acids. These were identified and annotated in the SeMNPV-QD genome, accounting for 87.53% of the whole genome. Phylogenetic analysis of 38 core genes of the baculovirus confirmed that SeMNPV-QD is a Group II Alphabaculovirus and is most closely related to SeMNPV American isolate (SeMNPV-US1), S. litura nucleopolyhedrovirus II (SpliNPV-II), S. frugiperda multiple nucleopolyhedrovirus (SfMNPV), A. segetum nucleopolyhedrovirus (AgseNPV), A. segetum nucleopolyhedrovirus B (AgseNPV-B) and A. ipsilon multiple nucleopolyhedrovirus (AgipNPV). The pairwise distance of the nucleotide sequences of lef-8, lef-9, polh and concatenated lef-8/lef-9/polh fragments between SeMNPV-QD and several sister viruses mentioned above were all above 0.05 substitutions/site. SeMNPV-QD has 123 ORFs similar to those of SeMNPV-US1, and the genomic similarity was 45.8%. Compared to SeMNPV-US1, SeMNPV-QD has four additional ORFs such as two baculovirus repeat ORF (bro) genes, bro-1, bro-2, orf39 and orf95, but lacks 17 ORFs that have no effect on viral transcription and replication. The above results indicate that SeMNPV-QD is a new species of S. exigua multiple nucleopolyhedrovirus.