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Related Concept Videos

Viral Mutations00:36

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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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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When a pathogen enters the body and reproduces, it can cause an infection, damage body cells, and cause illness symptoms that eventually lead to disease. Therefore, its prevention requires breaking the chain of infection.
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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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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...
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Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

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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...
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Updated: Jul 12, 2025

Single-cell Quantitation of mRNA and Surface Protein Expression in Simian Immunodeficiency Virus-infected CD4+ T Cells Isolated from Rhesus macaques
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Inferring Viral Transmission Pathways from Within-Host Variation.

Ivan O A Specht1,2, Brittany A Petros1,3,4,5, Gage K Moreno1

  • 1The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Medrxiv : the Preprint Server for Health Sciences
|October 24, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a new evolutionary model for reconstructing viral transmission, improving accuracy by analyzing within-host genetic data. The method enhances understanding of pathogen spread, including SARS-CoV-2.

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Area of Science:

  • Virology
  • Epidemiology
  • Computational Biology

Background:

  • Existing viral transmission inference methods often use simplified evolutionary models and incomplete genetic data, limiting accuracy.
  • Understanding pathogen spread during outbreaks requires robust methods for reconstructing transmission histories.

Approach:

  • Developed a novel evolutionary model to track within-host viral population genetics and transmitted lineages.
  • Validated the model's accuracy in describing within-host variant frequencies using a large SARS-CoV-2 genome dataset.
  • Compared reconstruction accuracy against leading methods using synthetic data, a bovine respiratory syncytial virus outbreak, and a SARS-CoV-2 outbreak.

Key Points:

  • The model accurately represents within-host variant frequencies in SARS-CoV-2 genomes.
  • Transmission reconstruction was more accurate than existing methods on diverse datasets.
  • Successfully applied the tool to analyze 5,692 SARS-CoV-2 outbreaks in Massachusetts.

Conclusions:

  • Within-host genetic variation is crucial for accurate transmission inference in SARS-CoV-2 and other pathogens.
  • The developed mathematical framework provides an adaptable tool for tracking pathogen evolution and transmission dynamics.