Related Experiment Video
Updated: Dec 11, 2025
09:13
Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy
Published on: November 1, 2011
17.8K
Differential Alphavirus Defective RNA Diversity between Intracellular and Extracellular Compartments Is Driven by
R M Langsjoen1, A E Muruato2, S R Kunkel1
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.
Mbio
|August 21, 2020
Summary
Defective RNAs (D-RNAs) in alphaviruses arise newly within cells and are not always packaged into new viruses. This study reveals a novel subgenomic D-RNA type conserved across arthritogenic alphaviruses.
Area of Science:
- Virology
- Molecular Biology
Background:
- Alphaviruses are RNA arboviruses causing arthritis or encephalitis.
- Defective RNAs (D-RNAs) with large deletions are produced during alphavirus replication.
- Previous studies focused on D-RNAs from passaged viruses or packaged virions.
Purpose of the Study:
- To characterize intracellular and packaged D-RNA populations during early alphavirus infections.
- To investigate the de novo intracellular generation of D-RNAs.
- To identify novel D-RNA subtypes and their packaging behavior.
Main Methods:
- Next-generation sequencing of RNA from chikungunya virus (CHIKV) passage 1 stock, intracellular virus, and passage 2 virions.
- Diversity and differential expression analyses of D-RNA populations.
- Validation in murine models and in vitro studies with related alphaviruses (Mayaro, Sindbis, Aura).
- Direct RNA nanopore sequencing for confirmation of recombination events.
Main Results:
- Intracellular D-RNA populations exhibit higher diversity than packaged D-RNAs.
- Specific D-RNA populations are differentially expressed between intracellular and extracellular compartments.
- A novel subgenomic D-RNA (sgD-RNA) subtype, conserved across arthritogenic alphaviruses, was identified.
- sgD-RNAs arise from recombination events in the subgenomic region and are enriched intracellularly.
- D-RNAs arise de novo intracellularly, with only a subset being packaged.
Conclusions:
- Alphavirus D-RNAs arise de novo intracellularly, and their detection is limited by packaging.
- A transmission bottleneck exists for D-RNAs due to selective packaging.
- Novel intracellularly enriched sgD-RNAs are conserved across arthritogenic alphaviruses.
- The role and influence of D-RNAs during infection may be constrained by packaging requirements.
Related Concept Videos
00:57Viral Recombination
24.6K
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.
24.6K
01:29Viruses with RNA Genomes
531
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
531
01:26Size and Structure of Viral Genomes
514
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
514
02:32Exon Recombination
3.9K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...
Exon shuffling follows “splice frame rules.” Each exon...
3.9K
02:33Retroviruses
14.3K
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’...
14.3K
01:29Viruses of Archaea
342
Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...
342