The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa

Authors: ESCASA, SHANNON - Algoma University; Harrison, Robert - Bob; Mowery, Joseph; Bauchan, Gary; CORY, JENNY - Simon Frasier University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/13/2018
Publication Date: 2/8/2019
Citation: Escasa, S.R., Harrison, R.L., Mowery, J.D., Bauchan, G.R., Cory, J.S. 2019. The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa. PLoS One. 14(2):e0209937.

Interpretive Summary: The African armyworm is a pest of important grasses and cereal crops in southern and eastern Africa, and poses a significant invasive threat to agriculture in the USA. Chemical insecticides used to kill this pest come with negative consequences, and are not an option for organic agriculture. Naturally occurring insect viruses have been used in the past to kill insect pests like the African armyworm without the problems of chemical insecticides. In this study, the virus particles and molecular sequence of a virus that infects and kills the African armyworm was determined. The features of the sequence and virus particles were characterized and described. This information will be of interest to those in academia, government, and industry who are trying to develop environmentally-friendly forms of insect control.

Technical Abstract: Spodoptera exempta nucleopolyhedrovirus (SpexNPV) is a viral pathogen of the African armyworm, Spodoptera exempta (Lepidoptera: Noctuidae), a significant agricultural pest of cereal crops in Africa. SpexNPV has been evaluated as a potential biopesticide for control of this pest and has served as the subject research on baculovirus pathology and transmission. In this study, the occlusion bodies (OBs) of SpexNPV isolate 244.1 were examined, and the nucleotide sequence of the genome was determined and characterized. SpexNPV-244.1 OBs consisted of irregular polyhedra with a size and appearance typical for alphabaculoviruses. Virions within the polyhedra contained 1-8 nucleocapsids per unit envelope. The SpexNPV-244.1 genome was comprised of a 129,528 bp circular sequence, in which 139 ORFs were annotated. Five homologous regions (hrs) consisting of a variable number of 28-bp imperfect palindromes were identified in the genome. The genome sequence contained the 38 core genes of family Baculoviridae, as well as three ORFs unique to the SpexNPV sequence and one ORF that was apparently acquired by horizontal gene transfer with a betabaculovirus ancestor. Phylogenetic inference with core gene amino acid sequence alignments placed SpexNPV-244.1 in a lineage containing alphabaculoviruses of Spodoptera frugiperda and Spodopotera exigua which in turn is part of a larger group of alphabaculoviruses from subfamily Noctuinae in the lepidopteran family Noctuidae. Kimura-2-parameter pairwise nucleotide distances indicated that SpexNPV-244.1 represented a different and previously unlisted species of genus Alphabaculovirus. Gene parity plots indicated that the gene order of SpexNPV-244.l was extensively collinear with that of Spodoptera exigua NPV (SeMNPV). These plots also revealed a group of 17 core genes whose order was conserved in other alpha- and betabaculoviruses.