Spodoptera frugiperda multiple nucleopolyhedrovirus isolate:ARG-M Raw sequence reads. Spodoptera frugiperda multiple nucleopolyhedrovirus isolate:ARG-M

Despite the availability of consensus sequences for each Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) isolate, we lack information about the genetic diversity levels present at the population level, mainly because most strains were sequenced using Sanger technology. Intrahost single nucleotide variants (iSNV) specific to each isolate are a relevant source of variability and could contribute to SfMNPV adaptability, as demonstrated for other baculoviruses. In this work, we characterized the genome-wide diversity present in a natural population of SfMNPV using High-Throughput Sequencing (HTS) with deep coverage. We found low diversity levels across SfMNPV genome, which is congruent with previous reports for other baculoviruses. Patterns of iSNVs and single nucleotide polymorphisms (SNP) between isolates suggest that the adaptive process in SfMNPV is driven by a small group of genes. Additionally, we found evidence of structural variation affecting large portions of the viral genome, which highlights a more drastic scenario than previously reported. We believe that our data will help to better understand the adaptation process of SfMNPV to the fall armyworm.