Clean Cells, a GMP biologics quality control (QC) CRO, has launched next-generation sequencing (NGS)-based viral safety testing for viral vectors and recombinant preparations. Simultaneously, the CRO has acquired Xegen—a French bioinformatics CRO—to secure the analytical backbone the method requires.
Key Insights: European Pharmacopoeia chapter 2.6.41 formally recognizes NGS for adventitious virus detection in biological products, alongside ICH Q5A(R2). Programs still relying on classical assays alone face a documented gap in regulatory alignment that widens with each guidance cycle. Labs sourcing a single-partner NGS solution must confirm that wet-lab testing, sequencing, and GMP-auditable bioinformatics all operate under one quality system.
Safety Testing for Viral Vectors Has No Classical Assay Solution
Classical adventitious virus assays cannot cover viral matrices where no neutralizing antiserum exists for the vector itself, leaving a detection gap that regulators now expect developers to close with sequencing-based methods. Clean Cells’ R&D deputy director, Elodie Ribert, highlights that “a signal still must be investigated and confirmed,” emphasizing the need for comprehensive QC alongside NGS.
ICH Q5A(R2) and European Pharmacopoeia chapter 2.6.41 together establish NGS as a recognized, operationally defined method for adventitious virus detection, each covering distinct scope and implementation requirements.
| Framework | Scope | NGS/HTS Status | Effective Date |
| ICH Q5A(R2) | Biotechnology products from cell lines (human/animal); expanded to include certain viral vectors and viral vector-derived products | Formally incorporated as a recognized method for adventitious virus detection | 14 June 2024 |
| European Pharmacopoeia 2.6.41 | Biological products including vaccines, recombinant proteins, viral vectors, cell-based preparations | Defines HTS workflow, validation criteria, and controls | 1 April 2026 |
Before outsourcing NGS testing, confirm the CRO’s quality system explicitly covers HTS method validation under both frameworks.
Validated Bioinformatics Is the GMP Bottleneck
GMP-compliant NGS for viral safety depends on validated bioinformatics pipelines, as reads alone do not constitute a regulatory finding. A valid GMP submission requires version-controlled, traceable pipelines operating under the same quality system as the wet-lab stages.
Julien Paganini, PhD, MBA, Xegen’s co-founder, states: “Sequencing is the technology but turning it into a QC solution involves much more than simply generating reads.” Xegen’s PolyPhemeDiag, a modular platform for NGS data analysis, forms the software layer of the combined offering.
QA teams evaluating genomics and sequencing-based testing should verify the CRO integrates wet-lab testing, sequencing, and bioinformatics under one validated quality system. Clean Cells’ current offering covers several categories of acellular viral matrices:
- Viral vectors: Gene therapy programs where classical assays cannot cover the matrix due to absent antiserum
- Recombinant preparations: mRNA and recombinant protein programs requiring broad adventitious agent detection
- Vaccines: Biologics subject to the EMA, FDA, and ICH Q5A(R2) biosafety expectations
The matrix scope distinction carries real procurement weight for programs developing gene therapy or cell-based products. Because cell bank validation relies on highly specific genetics and genomics testing applications, this coverage requires separate verification rather than a simple assumption. Broader adoption of molecular biopharma QC methods means classical-assay-only programs are moving out of step with current regulatory norms. Laurent Claisse, CEO of Clean Cells, notes: “We provide a strong and secure analytical pipeline, with greater control of the full workflow from sample to interpreted result.”
Outsourcing NGS Viral Safety Testing: Key Verification Steps
Any outsourcing partner must hold a validated NGS method meeting ICH Q5A(R2) and EP 2.6.41 requirements, with GMP-compliant bioinformatics operating under the same quality system as its wet-lab stages. The Contract Laboratory network of biopharmaceutical testing partners provides a starting point for identifying qualified GMP NGS providers across biologics viral safety programs.
The original press release can be found here.
This article was created with the assistance of Generative AI and has undergone editorial review before publishing.