Friday, December 5, 2014

How is Bioinformatics Helping the Ebola Outbreak?

In recent months, Ebola has moved from a winning disease on the popular Plague Lab and Epidemic phone apps to a very serious global health issue. According to the Center for Disease Control (CDC), as of November 11, 2014, the total cases of the Ebola virus totaled 14413; 8920 of those were confirmed laboratory cases, and 5177 constitute total deaths. Though there have been a few well-documented cases in the United States and Spain, the vast majority of these cases have occurred in West Africa, in the countries of Guinea, Sierra Leone, Liberia, and Mali.

            Many reasons can be cited for the spread of the Ebola. West Africa lacks proper infrastructure, facilities, and resources to handle the disease. In addition, Ebola doesn’t show symptoms until at least two weeks after contraction of the disease, and the first symptoms manifest in the same manner symptoms from a common cold or flu do; by this time, everyone that person has come in contact with has been exposed to the virus. Further, once the affected have passed away, most villages do not have proper disposal techniques, and in many areas, burning the body (the most sanitary and available means of disposal) is seen culturally as an improper means of burial.


            Though all of the problems mentioned above (and the problems Ebola poses are by no means limited to those) do not have a panacea, there are things being done to combat aspects of the unprecedented difficulty Ebola has posed to West Africa and to the world. In addition to all of the humanitarian and medical aid needed, aid is also being given in the form of bioinformatics. Bioinformatics is the field that combines technological methods and software programs in an effort to develop more tools for understanding biological data. Scientists of bioinformatics must be versed in computer science, mathematics, and engineering, amongst other fields.

            Dr. Ketan Patel, of the US Naval Medical Research Center and former postdoctoral fellow in bioinformatics at the University of North Carolina at Charlotte, has used his experience in bioinformatics to assist in the establishment of a high-technology mobile laboratory in Liberia, a project located near a treatment unit that is supported by the World Health Organization (WHO).

Ketan Patel in the laboratory separating genomic material. (Photo courtesy of WHO).

            This laboratory, situated in what was previously an abandoned house of sorts, is meant to speed up the time for diagnosis. As can be inferred from the earlier explanation of Ebola symptoms, early diagnosis is key for control. Prior to the establishment of Patel’s lab, even preliminary Ebola diagnosis took anywhere from two to five days. Because of the advanced bioinformatics technology in this fledgling laboratory, results can be rendered in just three to five hours; a significant decrease in time and the effective elimination of days of potential exposure of Ebola victims to those uninfected.

            To diagnose, the laboratory follows three steps. First, the Ebola virus within the sample is inactivated, allowing for safety of testing. Secondly, all genetic material is extracted from the blood sample- by doing this, doctors can identify unique ribonucleaic acid (RNA) associated with Ebola. Once this is identified, copies of the RNA are made through a process called polymerase chain reaction (PCR). Depending on the prevalence of the virus in the provided blood sample, this last step (the actual diagnosis step) can take anywhere from just a few cycles to very many cycles. The entire process is streamlined and carefully monitored for cleanliness and safety; workers use biological safety hoods and suits, in addition to chlorine “dunk tanks” to avoid direct contact and eliminate any potential or accidental contamination.

Ketan Patel prepares to work in the laboratory. (Photo courtesy of WHO). 


            Amalgamated, these steps take anywhere from three to five hours, with a maximum of sixteen samples in a rotation. The laboratory was established in October and, since then, over 500 blood samples have been processed and, of those, approximately fifty percent identified as positive for Ebola. Thanks to Dr. Patel and the help that his bioinformatics experience has aided to the laboratory in Liberia, the fight against Ebola has advanced that much more.

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