News Feature | November 20, 2014

Enhancing Ebola Surveillance With Faster, More Accurate Genome Sequencing

By Chuck Seegert, Ph.D.

Ebola Virus 450x300

A new method of genomic sequencing has been developed that could provide efficient and affordable Ebola surveillance for West African nations. The process enables shorter test times and allows viruses to be tracked in populations where it may be spreading.

The current West African Ebola outbreak has been the worst epidemic for this disease to date, and it is also unique in that it is the first to affect highly populated urban centers. The virus has spread through many African nations, Europe, and the United States, which has highlighted the need for rapid and accurate testing to identify those who are infected and isolate them appropriately.

Genomic sequencing is an important tool in these surveillance efforts, but historically it has been constrained by many factors, according to a recent press release from BioMed Central. Taking a blood sample and sequencing viral genomes directly from the sample is often difficult because the sample contains so much human RNA, the molecule that is studied in genomic sequencing. Additionally, warm temperatures and the precautions required to deal with these contaminated samples can cause the Ebola RNA to break down.

A new method developed by a team from the Broad Institute uses “H-based digestion” (the “H” stands for a hydrolysis mechanism), which is a targeted RNase that specifically eliminates poly(rA) carrier and ribosomal RNA from the biological sample, according to an open access article published by the team in Genome Biology. The new method is capable of sequencing genomes of the Ebola virus more accurately by reducing the contaminating human RNA in blood samples from 80 percent to 0.5 percent, leaving Ebola RNA behind for testing.

“We were surprised that our strategy worked so well with such diverse, and often difficult samples of undefined quality and quantity,” said Christian Matranga, a researcher at the Broad Institute and the lead author of the study, in the press release. “And because of the speed of our approach, we were rapidly able to make the viral genetic data available to the scientific community to provide timely insights for ongoing surveillance and control efforts in the area.”

Unlike many sequencing approaches, this new method does not rely on having a previously known Ebola viral sample to test against, according to the press release. Instead it can sequence completely unknown samples and has been able to identify new strains of viruses and uncommon genetic variants. This may help develop a better understanding of viral evolution and enable researchers to learn more about how viruses spread. The method is also general and can be applied to many different viruses, not just Ebola. In fact, it was originally developed for Lassa fever, another hemorrhagic fever common in Africa.

Rapid test methods for Ebola have recently been under intense investigation. Rapid tests that are used in a way that is analogous to pregnancy tests have been developed. These tests can identify the presence of Ebola in as little as 15 minutes with just a drop or two of blood.