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Complete comparative genomic analysis of two field isolates of Mamestra configurata nucleopolyhedrovirus-A

Lulin Li^1,

Qianjun Li^2,

¹ Pacific Agri-Food Research Centre, AAFC, Summerland, BC, Canada
² Saskatoon Research Centre, AAFC-Saskatoon, SK, Canada
³ Southern Crop Protection and Food Research Centre, AAFC, London, ON, Canada

Correspondence
Cam Donly
donlyc{at}agr.gc.ca

A second genotype of Mamestra configurata nucleopolyhedrovirus-A (MacoNPV-A), variant 90/4 (v90/4), was identified due to its altered restriction endonuclease profile and reduced virulence for the host insect, M. configurata, relative to the archetypal genotype, MacoNPV-A variant 90/2 (v90/2). To investigate the genetic differences between these two variants, the genome of v90/4 was sequenced completely. The MacoNPV-A v90/4 genome is 153 656 bp in size, 1404 bp smaller than the v90/2 genome. Sequence alignment showed that there was 99·5 % nucleotide sequence identity between the genomes of v90/4 and v90/2. However, the v90/4 genome has 521 point mutations and numerous deletions and insertions when compared to the genome of v90/2. Gene content and organization in the genome of v90/4 is identical to that in v90/2, except for an additional bro gene that is found in the v90/2 genome. The region between hr1 and orf31 shows the greatest divergence between the two genomes. This region contains three bro genes, which are among the most variable baculovirus genes. These results, together with other published data, suggest that bro genes may influence baculovirus genome diversity and may be involved in recombination between baculovirus genomes. Many ambiguous residues found in the v90/4 sequence also reveal the presence of 214 sequence polymorphisms. Sequence analysis of cloned HindIII fragments of the original MacoNPV field isolate that the 90/4 variant was derived from indicates that v90/4 is an authentic variant and may represent approximately 25 % of the genotypes in the field isolate. These results provide evidence of extensive sequence variation among the individual genomes comprising a natural baculovirus outbreak in a continuous host population.

The GenBank/EMBL/DDBJ accession number for the sequence reported in this paper is AF539999.

Figures showing mutations in the promoter regions of lef-7 (orf16) and orf25, an alignment of the LEF-9 C-terminal amino acid sequences of v90/4 and v90/2 with those of 13 lepidopteran baculoviruses and an alignment of the 5'-end sequences of bro-b between v90/4 and v90/2 are available as supplementary material in JGV Online.

Present address: Animal Disease Research Institute, 3851 Fallowfield Rd, Ottawa, ON, Canada, K2H 8P9.

Present address: Department of Medicine/Division of Geographic Medicine, University of Alabama at Birmingham, BBRB 203, 845 South 19th Street, Birmingham, AL 35294-2170, USA.

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