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Related Experiment Video

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LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data.

Izabela Fabiańska1, Stefan Borutzki1, Benjamin Richter1

  • 1IDT Biologika GmbH, Am Pharmapark, 06861 Dessau-Roßlau, Germany.

Viruses
|December 28, 2021
PubMed
Summary

High-throughput sequencing (HTS) offers a powerful method for adventitious virus detection in biological products. The LABRADOR pipeline provides a standardized bioinformatics approach for reliable virus identification, enhancing vaccine safety testing.

Keywords:
adventitious virus testingbioinformatics workflowhigh-throughput sequencingvirus classification

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Area of Science:

  • Virology
  • Bioinformatics
  • Molecular Biology

Background:

  • High-throughput sequencing (HTS) is crucial for detecting adventitious viruses in biological products.
  • Current bioinformatics methods for HTS data analysis are complex and lack standardization.
  • Ensuring the safety of biologicals requires reliable detection of viral contaminants.

Purpose of the Study:

  • To develop a standardized and reliable bioinformatics pipeline for adventitious virus detection using HTS data.
  • To address the complexities of managing and analyzing HTS-generated data in the field of biological product safety.
  • To create a tool that can support or replace traditional in vitro and in vivo assays for adventitious agent testing.

Main Methods:

  • Development of LABRADOR, an analysis pipeline integrating third-party programs.
  • Implementation of direct reads classification using characteristic profiles and sequence alignment.
  • Utilizing de novo assembly of contigs with nucleotide and amino acid level classification.
  • Generation of a custom nucleotide database with viral sequences to meet regulatory guidelines.

Main Results:

  • LABRADOR demonstrated reliable detection of viruses in various HTS datasets.
  • The pipeline successfully identified viruses in mixtures of model viruses.
  • Validation on vaccine and clinical samples confirmed the pipeline's effectiveness.
  • The custom database enhanced the accuracy of viral sequence identification.

Conclusions:

  • The LABRADOR pipeline offers a standardized and reliable method for adventitious virus detection.
  • This bioinformatics tool can significantly improve the safety assessment of biological products.
  • LABRADOR has the potential to streamline and enhance viral safety testing protocols.