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Updated: Aug 17, 2025

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A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression

Zachary T Neeb1, Alexander J Ritter2, Lokendra V Chauhan3

  • 1Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.

Scientific Reports
|December 15, 2022
PubMed

Insights

This study reveals novel small viral RNAs (svRNAs) produced by SARS-CoV-2 that interact with host gene expression. These svRNAs may influence viral propagation and offer potential therapeutic targets for COVID-19.

Area of Science:

  • Molecular Biology
  • Virology
  • Genomics

Background:

  • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, but its impact on host RNA machinery is unclear.
  • Understanding viral-host interactions at the molecular level is crucial for developing effective treatments.

Purpose of the Study:

  • To investigate the effects of SARS-CoV-2 infection on host mRNA and small RNA (sRNA) expression.
  • To identify and characterize SARS-CoV-2-derived small viral RNAs (svRNAs) and their potential interactions with host molecules.

Main Methods:

  • Comparative transcriptomics analysis of infected human lung (Calu-3) and monkey kidney (Vero-E6) cell lines.
  • Identification and sequencing of host and viral small RNAs.
  • Bioinformatic prediction of interactions between svRNAs and host mRNAs/miRNAs.

Main Results:

  • SARS-CoV-2 infection caused global changes in host gene expression and differential expression of host microRNAs (miRNAs).
  • Over a hundred novel svRNAs were discovered, originating from various viral genome regions via a non-canonical pathway.
  • A significant number of svRNAs were predicted to interact with differentially expressed host miRNAs and mRNAs, suggesting a role in post-transcriptional regulation.

Conclusions:

  • SARS-CoV-2 infection profoundly alters host gene expression and produces unique svRNAs.
  • These svRNAs may modulate host post-transcriptional gene regulation, potentially aiding viral propagation.
  • Targeting these svRNAs could represent a novel therapeutic strategy against COVID-19.

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