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Open AccessArticle

Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses

Institute for Biological Control, Julius Kühn-Institut, Heinrichstraße 243, 64287 Darmstadt, Germany
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Viruses 2020, 12(6), 625; https://doi.org/10.3390/v12060625
Received: 28 April 2020 / Revised: 26 May 2020 / Accepted: 5 June 2020 / Published: 9 June 2020
Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool “bacsnp”, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample. View Full-Text
Keywords: genome sequencing; genetic variability; sequence heterogeneity; dsDNA viruses; Baculoviridae; Cydia pomonella granulovirus genome sequencing; genetic variability; sequence heterogeneity; dsDNA viruses; Baculoviridae; Cydia pomonella granulovirus
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Wennmann, J.T.; Fan, J.; Jehle, J.A. Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses. Viruses 2020, 12, 625.

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