Related Experiment Video

Updated: Sep 30, 2025

High-throughput Screening for Broad-spectrum Chemical Inhibitors of RNA Viruses
11:34

High-throughput Screening for Broad-spectrum Chemical Inhibitors of RNA Viruses

Published on: May 5, 2014

14.0K

Evitar: designing anti-viral RNA therapies against future RNA viruses

Dingyao Zhang1,2, Jingru Tian1,2, Yadong Wang1,2,3

  • 1Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.

Bioinformatics (Oxford, England)
|March 16, 2022
PubMed
Abstract

Insights

We developed Evitar, a pipeline for designing RNA therapeutics like siRNAs and CRISPR guide RNAs against emerging viruses. Evitar can predict effective therapeutics for future outbreaks, accelerating pandemic response.

Area of Science:

  • Virology
  • Bioinformatics
  • RNA Therapeutics

Background:

  • Emerging RNA viruses pose significant threats, as demonstrated by the COVID-19 pandemic.
  • Current therapeutic options for novel RNA viruses are limited, highlighting the need for rapid development tools.

Purpose of the Study:

  • To develop a computational pipeline (Evitar) for designing RNA-targeting therapeutics (siRNAs and CRISPR Cas13a gRNAs) against emerging RNA viruses.
  • To enable pre-outbreak design of therapeutics for potential future viral threats.

Main Methods:

  • Developed the Evitar pipeline incorporating Greedy Algorithm with Redundancy and Similarity-weighted Greedy Algorithm with Redundancy.
  • Utilized historical coronavirus genomes for pre-outbreak siRNA and gRNA design simulations.
  • Validated designed siRNAs through in vitro reporter assays against SARS-CoV-2 sequences.

Main Results:

  • Evitar successfully identified potential SARS-CoV-2 targeting siRNAs and CRISPR Cas13a gRNAs using genomic data predating the COVID-19 outbreak.
  • Pre-outbreak therapeutic designs were feasible for MERS-CoV and 2009-H1N1 swine flu viruses.
  • In vitro assays confirmed the ability of designed siRNAs to suppress SARS-CoV-2 viral sequences.

Conclusions:

  • The Evitar pipeline is effective for designing anti-viral siRNAs and gRNAs against future RNA viruses.
  • Propose creating a collection of pre-designed, off-the-shelf siRNA/CRISPR therapeutics to expedite responses to future viral outbreaks.

More Related Videos

Evaluation of the Efficacy And Toxicity of RNAs Targeting HIV-1 Production for Use in Gene or Drug Therapy12:03

Evaluation of the Efficacy And Toxicity of RNAs Targeting HIV-1 Production for Use in Gene or Drug Therapy

Published on: September 5, 2016

8.0K
Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds09:29

Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds

Published on: October 29, 2015

30.4K

Related Concept Videos

Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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...
180
Retrovirus Life Cycles01:10

Retrovirus Life Cycles

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...
47.2K
siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the...
17.1K
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
26.5K
Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

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...
186
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.3K