Virus detection by short read high throughput sequencing in a high virus low cellular background

The safety of all biological products includes demonstrating the absence of adventitious viruses by testing various types of samples at different stages of the manufacturing process. Seven laboratories evaluated short-read high-throughput sequencing (HTS) for sensitivity and breadth of adventitious virus detection using viruses with distinct physicochemical and genome properties. These five viruses are currently designated as CBER NGS Virus Reagents and include: Epstein-Barr virus (EBV; or human herpes virus 4), feline leukemia virus (FeLV), respiratory syncytial virus (RSV), mammalian orthoreovirus type 1 (Reo1), and porcine circovirus type 1 (PCV1). To evaluate adventitious virus detection in a biological material with a high production virus titer and low cellular background, the 5 viruses were mixed and different copies of the viral genomes spiked into 1 - 5 × 10⁹ genome copies per mL (GC/mL) of purified adenovirus 5. Independent protocols were used by each laboratory for the entire HTS workflow. All laboratories detected 10⁴ GC/mL of the five viruses by both targeted and non-targeted bioinformatic analyses. Additionally, the limit of detection of squirrel monkey retrovirus and porcine endogenous retrovirus, which pre-existed in EBV and PCV1 virus stocks, respectively, was evaluated. The five laboratories that tested 10³ GC/mL, detected all 5 viruses with the targeted analysis, and Reo1 and EBV with the non-targeted analysis. It was noted that some laboratories achieved a better sensitivity for detection of the five viruses ( ≤10² GC/mL). This study presents an approach for HTS validation for viral safety testing of vaccines and other biologics using a panel of reference viruses. The results highlight that optimization of steps in the HTS workflow can improve the limit of detection for adventitious viruses.