DOI: 10.5061/dryad.9w0vt4bqq
title: EVE: Software to identify novel viral insertions in wild-caught arthropod hosts from next-generation short read data

description: Eukaryotic genomes harbor sequences derived from non-retroviral RNA
 viruses, known as endogenous viral elements (EVEs) or non-retroviral
 integrated RNA virus sequences (NIRVS). These sequences represent a record
 of past infections and have been implicated in host anti-viral response.
 We have created a program to identify viral sequences integrated in a host
 genome.  It begins with a specimen BAM file and outputs candidate
 NIRVS, along with putative host insertion sites and overlapping genomic
 features of the host genome in XML and visual formats, with minimal
 intermediary intervention.  We ran through this software
 short-read data derived from the genomes of 222 wild-caught Aedes aegypti
 mosquitoes, from a dozen geographical regions, and located putative NIRVS
 from seven virus families. This program is as accurate as currently
 available software for NIRVS detection and represents a significant
 improvement in adaptability and user-friendliness. Furthermore, the
 flexibility of this pipeline allows the user to search for sequence
 integrations across the genome of any organism, as long as a query
 sequence database and a reference genome is provided.  Potential
 extended applications include the identification of integrated transgenic
 sequences used for research or vector control strategies.
description: # EVE-X: Software to Identify Novel Viral Insertions in Wild-Caught
 Arthropod Hosts from Next-Generation Short Read Data *Molecular Ecology
 Resources*, to appear ## Authors Jessen Havill Dept. of Computer Science,
 Bucknell University Lewisburg, PA 17837 Olivia Strasburg Dept. of
 Biomedical Engineering, University of Virginia Charlottesville, VA 22904
 Tessy Udoh Dept. of Computer Science, Denison University Granville, OH
 43023 Jacob E. Crawford Verily Life Sciences Mountain View, CA 94043
 Andrea Gloria-Soria Dept. of Entomology, The Connecticut Agricultural
 Experiment Station New Haven, CT 06511 ## blastdb.zip The blastdb
 directory contains sample BLAST databases to demo the EVE-X software. The
 data is geared toward the discovery of NIRVS in specimen *Aedes aegypti*
 genomes. ### virusdb.\* This BLAST viral database (named virusdb) contains
 complete sequences for all known RNA virus families that contain
 arboviruses. Specifically, it contains sequences from the families/orders
 in the following table: | Family/Order | NCBI taxid | | ---------------- |
 ---------- | | Bromoviridae | 39740 | | Chrysoviridae | 249310 | |
 Flaviviridae | 11050 | | Nodaviridae | 12283 | | Orthomyxoviridae | 11308
 | | Partitiviridae | 11012 | | Picornaviridae | 12058 | | Sedoreovirinae |
 689832 | | Togaviridae | 11018 | | Totiviridae | 11006 | | Tymoviridae |
 249184 | | Mesoniviridae | 1312872 | | Bunyavirales | 1980410 | |
 Mononegavirales | 11157 | It was created using the following command: ```
 makeblastdb -in virusdb_no_retro_or_unverified.fasta -dbtype nucl
 -parse_seqids -title "virusdb" -out virusdb ``` ###
 virusdb\_no\_retro\_or\_unverified.fasta This is the source FASTA file
 from which the viral database was created. ### aegyptidb.\* This BLAST
 database was created from the *Aedes aegypti* AaegL5.0 reference genome
 with accession numbers NC_035107.1, NC_035108.1, and NC_035109.1. ## EVE-X
 software The software, written in Python, is available on
 [GitHub](https://github.com/havillj/eve-x) and a snapshot of the software
 has been uploaded to Zenodo. ## Specimen files We have also deposited all
 222 of the specimen BAM files used in our analysis in the SRA with
 BioProject accession number PRJNA1158798.  These BAM files contain only
 the unmapped reads and their paired-end mates from the original specimen
 files.  EVE-X will recognize this from the filename format and skip the
 first stage of the program that would otherwise extract the unmapped reads
 from the original files.