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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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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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Host-Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression

Athok Shofiudin Maarif1, Yukari Nishikawa1, Miyako Takata2

  • 1Division of Infectious Diseases, Graduate School of Medicine, Faculty of Medicine, Tottori University, Nishi-cho 86, Yonago 683-8503, Tottori, Japan.

International Journal of Molecular Sciences
|July 12, 2025
PubMed
Summary
This summary is machine-generated.

Persistent SARS-CoV-2 infections show evolving virus infectivity and immune responses. Mutations in the virus may drive immune escape, highlighting the need for monitoring prolonged infections.

Keywords:
GO enrichmentSARS-CoV-2gene expressionhost–virus interactionimmune responsepersistent infectionviral evolution

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Area of Science:

  • Virology
  • Immunology
  • Genomics

Background:

  • Persistent SARS-CoV-2 infections involve prolonged viral replication and host immune interactions.
  • These interactions can drive viral evolution and immune escape.
  • Understanding these dynamics is crucial for managing long-term COVID-19.

Purpose of the Study:

  • To investigate viral characteristics and host gene expression changes in persistent SARS-CoV-2 infections.
  • To identify mutations associated with prolonged infection and potential immune escape mechanisms.
  • To analyze the host's immune response during persistent infection phases.

Main Methods:

  • Analysis of nasopharyngeal samples from patients with persistent SARS-CoV-2 infection.
  • Viral isolation, culturing, and infectivity assessment using TCID50 assays.
  • RNA sequencing (RNA-seq) for differential gene expression analysis and Gene Ontology (GO) enrichment.
  • Viral genome sequencing to detect mutations.

Main Results:

  • Significant differences in viral infectivity were observed between early and late phases of infection.
  • Host gene expression showed an initial pro-inflammatory response (e.g., IL6, TNF) followed by immune suppression.
  • GO analysis revealed enrichment in inflammation and cytokine-mediated immune pathways.
  • Genomic sequencing identified mutations in ORF1ab and the spike (S) protein, potentially linked to immune escape.

Conclusions:

  • SARS-CoV-2 demonstrates adaptation during persistent infections, altering its infectivity and modulating host immune responses.
  • Mutations arising during prolonged infection may facilitate viral immune escape.
  • Continuous monitoring of persistent SARS-CoV-2 infections is essential to address viral evolution and immune evasion.