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Related Experiment Video

Updated: Jul 12, 2025

Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm

Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm

Published on: April 12, 2017

Untangling an insect's virome from its endogenous viral elements.

Paula Rozo-Lopez¹, William Brewer², Simon Käfer³

¹Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA. plopez2@utk.edu.

|October 24, 2023

Summary

This summary is machine-generated.

Endogenous viral elements (EVEs) in insect genomes can be mistaken for new viruses when using RNA sequencing. This study highlights EVEs as a significant challenge for accurately discovering insect viral diversity.

Keywords:

Aphids Endogenous viral elements Insects RNAseq Viral discovery

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Last Updated: Jul 12, 2025

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Published on: December 22, 2014

Area of Science:

Virology
Genomics
Entomology

Background:

Insects harbor vast undiscovered viral biodiversity.
High-throughput RNA sequencing advances insect virome studies.
Endogenous viral elements (EVEs) in insect genomes complicate viral discovery using RNA sequencing.

Purpose of the Study:

To investigate the virome of the potato aphid, Macrosiphum euphorbiae, a significant agricultural pest and plant pathogen vector.
To identify and differentiate exogenous viruses from endogenous viral elements (EVEs) in the aphid's genome.

Main Methods:

Utilized rRNA-depleted RNA sequencing to profile microbial communities in individual aphids.
Employed PCR screening to assess the prevalence of specific heritable viruses in a local aphid population.
Generated a draft genome assembly of M. euphorbiae using Nanopore sequencing with Illumina correction to detect transcriptionally active EVEs.

Main Results:

Detected reads from insect-specific viruses, a parasitoid virus, a plant pathogenic virus, and phages via RNAseq.
The genome assembly revealed that some identified viral sequences were actually endogenous viral elements (EVEs) present in the aphid's genome.
Demonstrated that EVEs contributed to the misidentification of aphid viruses in RNA sequencing data.

Conclusions:

Endogenous viral elements (EVEs) can lead to misidentification of viruses in insect RNA sequencing studies.
The presence of EVEs poses a widespread challenge for accurately characterizing insect viral diversity.
Recommends careful consideration of EVEs in future insect virome research.