PDA Letter Article

PDA IG Explores Next-Gen Sequencing for Viruses

by Rebecca Stauffer, PDA

PDA’s Advanced Virus Detection Technologies Interest Group convened during the virtual 2020 PDA Europe Virtual Virus Forum, June 23, providing an update on the group’s workstreams. Jean-Pol Cassart, PhD, Director, Viral Safety, GSK, covered the interest group’s activities, and Maria Bednar, Scientist II, Biogen focused on two collaborative, next-generation sequencing studies.

Established in 2014, the interest group’s mission is to advance next generation tools for viral risk evaluation by providing an informal, scientific forum for discussions and scientific collaborations. Subgroups within the interest group are involved in studies on sample selection/preparation/processing, virus standards and reference materials, a virus reference database, bioinformatics pipelines analysis and follow-up strategies to confirm the identity of a “hit.”

Cassart outlined four studies conducted by the group. A study to evaluate the potential sensitivity for different viruses by comparing different sample preparation approaches and technology platforms found that a comparable virus detection was obtained in the three laboratories involved. Another study is an ongoing virus spiking study exploring the impact of sample preparation methods on the sensitivity of NGS technology for adventitious virus detection. A third is looking into transcriptomics while a fourth is looking at long-read sequencing technology.

Bednar provided further details the spiking studies. A 2017 study evaluated an adventitious virus known to infect Chinese hamster ovary cells. All study groups detected mouse minute virus with coverage between 8% to 91%. The other spiking study looked at the performance of next-generation sequencing for adventitious virus detection in a mixed virus sample, mimicking a virus seed. At this time, all laboratory participants have completed their work and discussion is currently in progress.

The work of the Advanced Virus Detection Technologies Interest Group’s studies will be submitted for eventual peer review in a publication.

About the Experts

Cassart Jean PolJean-Pol Cassart, PhD, is responsible for the development and the implementation of novel analytical methods for QC testing at GSK Vaccines.

Maria BednarMaria Bednar, PhD, is a scientist at Biogen, located in Research Triangle Park, North Carolina. She is responsible for the development and validation of next-generation sequencing methods and implementing new assays for the global Quality Control Virology group