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Microbial Genomics

NGS Aids Researchers in the Ebola Fight

Genomic studies are enabling researchers to track outbreaks and understand the virus’s rapid mutation rate

NGS Aids Researchers in the Ebola Fight
May 14, 2015

The work to halt the transmission of the Ebola virus has required input from a wide range of experts, including clinicians, public health engineers, and epidemiologists. Yet, stopping the Ebola virus in its tracks will require an understanding of the virus at its most basic level. Researchers are now using next-generation sequencing (NGS) platforms like Illumina’s HiSeq and MiSeq Systems to understand the genetic structure of the virus. Deep sequencing of samples from people infected with the virus has revealed some of its many secrets, including a rapid mutation rate.

Pardis Sabeti, PhD, a computational geneticist at Harvard University, and Christian Happi, PhD, a visiting professor of infectious disease at Harvard School of Public Health and Director of the African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria, have spent much of the last year using the HiSeq System to understand how this virus spreads and changes over time.

Their results revealed that Ebola first moved to West Africa from its historic home in Central and East Africa in 2004. There was substantial genetic variation as the virus moved from human to human, and even as it multiplied within the same host.

“Rather than one consensus viral sequence, we found thousands of different genetic snapshots of the virus as it mutated in an individual,” Dr. Sabeti said.

The study also revealed that this strain of the virus likely only jumped to humans from its animal reservoir one time, but that one spillover event created a sustained chain of human-to-human transmission. In October 2014, a separate group of scientists traced the Ebola transmission chain back to a toddler in Guinea.

“If we had seen that each of these outbreaks was independent, and that they weren’t genetically related and coming from the same evolutionary tree, then we might have thought these were different infections from a natural reservoir and the result of different entries from the environment,” Dr. Sabeti said. “However, these outbreaks were closely related in time and the contact tracing supported that. It suggested that this was a single event in one long viral transmission chain.”

These results confirmed the importance of contact tracing to prevent the spread of disease. Because the virus wasn’t being continually reintroduced from the environment, epidemiologists knew that if they could stop people from passing the virus to each other, then they could stop the outbreak.

Read more about the groundbreaking research in this in-depth interview.

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