Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations

Abstract

Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential.

How to maintain a high virulence: evolution of a killer in hosts of various susceptibilities

“…We previously described our generation 0 virus population (Chateigner et al 2015), obtained by in vivo amplification of an archival sample. AcMNPV-WP10 was extracted from a one-cycle infection of a large number of highly susceptible hosts (Trichoplusia ni), minimizing the selection pressure on viral genomes.…”

“…For baculoviruses, which infect pest caterpillars, transmission mainly occurs via direct ingestion of viral particles, on the form of occlusion bodies (OBs), which are released after the death and liquefaction of the previous host (Slack and Arif 2006). An individual baculovirus particle, such as the natural isolate of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) carries many genetically diverse genomes, harboring different single nucleotide variations (SNVs), insertions or deletions (INDELs) (Chateigner et al 2015;Gilbert et al 2014Gilbert et al , 2016. It is thus a population of individual virus genotypes.…”

MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data

“…Shotgun sequencing and partial genome assembly is biased towards identification of dominant genotypes or taxa as a result of the limited read depth across multiple whole genomes [10,12,13]. Amplicon sequencing introduces bias resulting from gene copy number, selection of primers, and classification based on limited span of the genome [2,7,12,14].…”

“…Shotgun data can also be used to infer an approximate total number of strains within an isolate and the relative abundance of taxonomic clusters of strains within this population [13,19], but cannot determine the relative abundance of individual strains or abundance of strains that may contain multiple polymorphisms distributed across fragmented reads.…”

Comparative Analysis of HaSNPV-AC53 and Derived Strains

“…Baculovirus species have been described using restriction endonuclease digestion profile and Sanger sequencing, and more recently by Next Generation Sequencing (NGS) [10,11,16,17,23,26,27,28,29]. Previous research has shown that HaSNPV and HzSNPV share sequence similarity of up to 99.9%, but could be distinguished by a small number of nucleotide substitutions and by open reading frame (ORF) insertions and deletions in the published consensus genome [17,30,31].…”