FDA moves to accept high throughput sequencing to identify viral contamination

Results of FDA study supports development of high throughput sequencing for viral safety evaluation of biologic materials

High throughput sequencing could become an important tool for ensuring product safety

The findings of a study1 led by scientists at the US Food and Drug Administration (FDA) suggest that a highly sensitive, but complex, new technology to sequence the genetic material of viruses could be standardised and used for rapid screening of biologic products, including vaccines, to demonstrate absence of contamination.

The technology, called high throughput sequencing (HTS) (or more commonly, next generation sequencing), enables scientists to sequence hundreds of millions of DNA molecules at a time. Sequencing is the process of determining the order in which DNA building blocks are linked together.

The results of the study support the development of standard reference virus reagents that can be used to validate the performance of their HTS procedures to demonstrate absence of viral contamination for product safety. This would enable the use of somewhat different HTS methods and bioinformatics pipelines while still getting reliably similar results.

The discoveries of unexpected viruses and novel viruses by HTS suggests that this new technology could become a broadly-used method for screening biological materials, such as novel cell substrates used to make vaccines.

However, the complexity of this technique and the fact that there are different types of equipment, sample processing methods and data analysis tools for performing these studies, means that screening results could vary among laboratories. However, if HTS screening results obtained for the same virus and biologic material by independent laboratories were closely comparable, the technique could become an important tool for ensuring product safety by supplementing the methods currently used, or possibly replacing some in the future.

To determine if HTS could produce reliably similar screening results in different laboratories, scientists at FDA and in two other industry laboratories, each independently used the technique to determine how well it could detect four model viruses, respiratory syncytial virus (RSV), Epstein-Barr virus (EBV), feline leukemia virus (FeLV), and human reovirus (REO).

The viruses were spiked into a human cell line called HeLa, using disrupted whole cell material or RNA extracted from the cells to represent potential types of samples that are tested for adventitious viruses in biologics (microorganisms that may have been unintentionally introduced into the manufacturing process of a biological medicinal product).

The results showed that regardless of the commercial gene analysis device used or the preparation techniques used to perform the screening processes, the results were comparable among the laboratories. That is, the laboratories identified about the same amount of each virus in the samples regardless of the differences in sample preparation and processing.

This finding supports the future development of reference virus materials that could be used to standardize their HTS methodologies and validate their findings.


  1. A. S. Khan, S.H.S. Ng, O. Vandeputte et al, "A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection," mSpehere, September/October 2017 Vol 2 Issue 5 https://doi.org/10.1128/mSphere.00307-17