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Related Concept Videos

Retroviruses02:33

Retroviruses

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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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Viral Mutations

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Retrovirus Life Cycles01:10

Retrovirus Life Cycles

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Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
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Non-LTR Retrotransposons03:18

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Viral Recombination00:57

Viral Recombination

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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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Updated: Jun 30, 2025

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A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.

Nadja Brait1, Thomas Hackl, Côme Morel2

  • 1Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands.

Virus Evolution
|March 22, 2024
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Summary

Endogenous viral elements (EVEs) in host genomes can be mistaken for active viral infections in RNA-Seq data. This study shows EVEs impact virus discovery accuracy, necessitating better methods to distinguish them from true viral sequences.

Keywords:
endogenous viral elementmosquitoorthomyxovirusvirus discovery

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Area of Science:

  • Virology
  • Genomics
  • Bioinformatics

Background:

  • Metagenomic and transcriptomic studies have expanded knowledge of viral diversity.
  • Endogenous viral elements (EVEs), integrated into host genomes, are often overlooked in virus discovery, particularly in RNA-Seq data.
  • Distinguishing EVEs from active viral infections poses a significant challenge, potentially biasing analyses and classification.

Purpose of the Study:

  • To systematically assess the impact of EVEs on virus discovery pipelines.
  • To evaluate how EVEs affect data integrity and classification accuracy.
  • To provide recommendations for improved practices in virus discovery from transcriptomic data.

Main Methods:

  • Analysis of EVEs and exogenous viral sequences related to Orthomyxoviridae.
  • Examination of 13 genomic and 538 transcriptomic datasets from Culicinae mosquitoes.
  • Evaluation of a prototypical virus discovery pipeline's performance in the presence of EVEs.

Main Results:

  • A significant portion of viral sequences detected in transcriptomic data were identified as transcripts from EVEs, not active viruses.
  • Distinguishing transcribed EVEs from exogenous viruses was challenging, especially in samples with low viral abundance.
  • Mapping reads to host genomes with EVEs reduced the EVE burden but decreased viral hit counts and assembly quality.

Conclusions:

  • The presence of EVEs can alter perceived viral genetic diversity, leading to false positives and inaccurate sequence information.
  • Accurate identification and management of EVEs are crucial for reliable virus discovery and understanding viral diversity.
  • Improved bioinformatics strategies are needed to differentiate EVE transcripts from genuine viral sequences in transcriptomic datasets.