Friday, October 31, 2014

Synthetic Gene Networks Printed on Paper for Rapid and Inexpensive Detection of Ebola

In their new paper in the journal Cell, Keith Pardee, James J. Collins and colleagues from Collins’ lab at Harvard’s Wyss Institute for Biological Inspired Engineering talk about networks, printing circuits, programming, and even orthogonality.

They’re not talking about electronics, though. They’re describing how they developed “paper-based synthetic gene networks” into a practical, and potentially revolutionary, diagnostic tool for detecting a wide range of biomolecular targets such as glucose and viruses.

It took them less than a day to produce a slip of paper that can detect the Ebola virus. Armed only with that slip and smartphone camera, a healthcare worker in the field could know within two hours—and sometimes in as little as 20 minutes—whether a patient is infected or not. And the doctor, nurse, or volunteer could do this without advanced skills, extensive sample preparation, expensive reagents, laboratory instruments, or even refrigeration.

“Our paper-based system could not only make tools currently only available in laboratory readily fieldable, but also improve the development of new tools and the accessibility of these molecular tools to educational programs for the next generation of practitioners,” wrote Collins.

To produce a synthetic gene network, selected chunks of DNA, RNA, proteins, organelles (including, importantly, the ribosomes that read messenger RNA, or mRNA, and translate it into proteins), and other biomolecules are freed from their cellular casings and isolated into a complete but non-living physiological pathway.

The Wyss researchers engineered their synthetic network, painted the stew onto paper (or cloth, or any other porous medium), and freeze-dried it into an inert dot. Add water and a bit of a triggering analyte—DNA from a suspicious virus, say—and the synthetic network goes to work, activating a cascade of reactions that causes the printed dot to change color. The approach could be used for detecting not just viruses, but a staggering variety of other targets.

A “toehold hairpin RNA” sensor is a key to the process. If a single strand of RNA includes complementary sequences at separated stretches along its length, it can fold back upon itself to form a hairpin. The Wyss researchers engineer an RNA sequence so that it includes: a stretch of detector RNA that will bind to messenger RNA produced by the target (a transcript Ebola virus produces to build coat proteins for new viruses, for example); a ribosome binding site sequence, which will prompt the ribosome to grab the molecule and start reading its instructions to make protein; a “closure” sequence that binds to the detector RNA, hiding the ribosome binding site in the loop of the hairpin; and mRNA instructions for an enzyme (such as beta-galactosidase) that will alter the structure of a reporter molecule (such as a yellow form of galactose) to change its color (say, to a purple). See the following video:

The design leaves the toehold, a short strip of detector RNA, dangling free at the bottom of the hairpin. The target RNA latches onto the toehold and starts zipping up along the rest of the detector sequence—and unzipping the closure sequence. This opens up the ribosome binding site in the hairpin. The unfolded mRNA then passes through the ribosome, and the ribosome produces the enzyme. The enzyme reacts with the reporter and, voila, the color changes.

The color changes can be seen with the naked eye or digitally quantified. Conventional laboratory plate readers will certainly do the job. But along the way, the Wyss team also developed algorithms that allow most digital color cameras, including those available in cellphones, to quantify color changes in the gene-network dots.

Pardee, Collins, and their colleagues report that paper-based synthetic gene networks offer a number of advantages, including cost, speed, and rapid development, over conventional diagnostic approaches.

Cost. Paper-based diagnostics could cost as little as US $0.02 to $0.04 per sensor, they say. This is dramatically lower than the $0.45 to $1.40 for familiar antibody-based rapid diagnostics tests (RDTs) like home pregnancy and glucose kits, and the $1.50 to $4.00 cost of the reagents used in a PCR (polymerase chain reaction) DNA assay.

Speed. The paper-based synthetic gene network diagnostics the Harvard team produced are about as fast as antibody-based home tests, a little faster than PCR, and much faster than the bacterial and viral culture methods that have been a diagnostic mainstay. The Wyss group’s paper diagnostics produce detectable color changes in 20 to 40 minutes (or perhaps longer, depending on the assay and the concentration of the target molecule). Antibody-based RDTs show results in about 20 minutes. And PCR assays require at least 60 minutes…and a well-equipped laboratory.

Rapid Development. As an exercise, the Wyss researchers gave themselves a day to develop an assay capable of detecting the Ebola virus, and of distinguishing between its Sudan and Zaire strains. They produced 24 Ebola sensors in less than 12 hours.

“Taken together,” the Wyss researchers conclude, “and considering the projected cost, reaction time, ease of use, and no requirement for laboratory infrastructure, we envision paper-based synthetic gene networks significantly expanding the role of synthetic biology in the clinic, global health, industry, research, and education.”

Source: IEEE Spectrum

Tuesday, October 28, 2014

Novel Biosensor Technology Could Allow Rapid Detection of Ebola Virus

In 2010, Ahmet Ali Yanik published his first paper on the rapid detection of Ebola virus using new biosensor technology he and colleagues at Boston University had invented. But he found there was little interest at the time in developing the technology further.

"People told me that there wasn't any profit in it because this disease only affects people in the developing world," Yanik said.

Now, however, Ebola hemorrhagic fever has captured the attention of first world countries in a big way. The current outbreak in West Africa began spreading out of control just as Yanik was setting up his lab as a new faculty member at UC Santa Cruz, where he is an assistant professor of electrical engineering. Yanik plans to resume his work on virus detection in addition to ongoing projects involving biosensors for other biomedical applications. The current Ebola crisis may subside before his technology can be perfected, since there are still many challenges to overcome, but the need will remain for simple and inexpensive virus detection techniques, he said.

"The truth is that Lassa virus, which is related to Ebola and also causes hemorrhagic fever, infects nearly half a million people every year in Africa and kills more people than Ebola, but it doesn't make the news. So there has been an ongoing crisis with hemorrhagic fever viruses, and now it's finally getting some serious attention," Yanik said.

His goal is to create a low-cost biosensor that can be used to detect specific viruses without the need for skilled operators or expensive equipment. "We need a platform for virus detection that is like the pregnancy tests you can use at home," Yanik said. "The initial symptoms of hemorrhagic fever are similar to the flu, and you just cannot treat every person with flu symptoms as a potential Ebola-infected patient. It needs to be simple and cheap."


Nanotechnology may provide a solution. Advances in nanotechnology have enabled researchers to fabricate novel materials with precise structures on the scale of nanometers (a nanometer is one billionth of a meter). A "plasmonic nanohole," for example, is a tiny hole a few hundred nanometers across. Yanik's 2010 paper described a biosensor based on arrays of nanoholes in a metallic surface that interact with light in predictable ways. Using antibodies on the sensor surface to bind specific viruses, the researchers showed that binding of the virus caused a detectable change in the color of light transmitted by the nanohole arrays.

Detecting the color change, however, required the use of a spectrometer. Yanik later figured out how to make a sensor that could be read with the naked eye, without any need for electronic instruments. "You can use sunlight as the light source and the human eye as the detector," he said.

He published that technique in a 2011 paper in the Proceedings of the National Academy of Sciences. The sensor technology involves realms of physics far more complex than the relatively straightforward enzymatic reactions involved in a pregnancy test. Light transmission through nanohole arrays occurs through a phenomenon known as "surface plasmon resonances," which involves the oscillations of free electrons in a metallic surface. Yanik's 2011 paper showed that light transmission could be greatly enhanced by exploiting a phenomenon called Fano resonances (named for Italian physicist Ugo Fano).

The transmission of light through plasmonic nanohole arrays changes with the binding of specific proteins or virus particles, as shown in the illustration above.

Label-free detection

"This effect causes a huge difference in light transmission that you can see with the naked eye," Yanik said. Unlike conventional laboratory tests such as PCR and ELISA (currently the standard tests for Ebola infection), Yanik's approach does not rely on labeling with fluorescent tags or other markers to see the results. "The results can be read immediately after the pathogen binds to the sensor," he said.

Further work is needed, however, to improve the sensitivity of the sensor to the point where it could be effective for virus detection in routine "point-of-care" clinical evaluations. Yanik plans to work with Jin Zhang, professor of chemistry and biochemistry at UC Santa Cruz, to develop a new version of the sensor. Zhang's research group works on advanced nanomaterials for a wide range of applications.

"He has the exact technology I need to make the biosensor more sensitive for virus detection, so we are working on a proposal to combine his approach with ours," Yanik said.

Another major focus of Yanik's research is the detection and isolation of circulating tumor cells (CTCs) in the blood of cancer patients. CTCs can spread cancer to other parts of the body (metastasis), and detecting them in blood samples can have important prognostic and therapeutic implications. Yanik is working on methods for capturing CTCs with high efficiency and isolating them for molecular analysis. He began this work as a research associate at Harvard University Medical School and Massachusetts General Hospital before coming to UC Santa Cruz. At UCSC, he is working with Zhu Wang, an assistant professor of molecular, cell, and developmental biology, who studies genetic alterations in prostate cancer.

"It was a natural match," Yanik said. "We met during an orientation meeting for new faculty, and our collaboration spun off from there."

Both plasmonic biosensors and CTC technology are crowded fields with lots of competition, but Yanik has confidence in the methods he has developed. "There are a lot of different approaches to these problems, but we have achieved some unprecedented results with our technology," he said. "I am pretty optimistic that we can make a difference in people's lives."

Source: University of California Santa Cruz

Friday, October 24, 2014

FDA Guidelines Restrict Use of Ebola Scanning Device at Hospitals

It took two days for the US Centers for Disease Control and the Texas Department of State Health Services to confirm that Thomas Eric Duncan, the first patient to be diagnosed with Ebola in the US during the current outbreak, had in fact tested positive for the hemorrhagic fever. For a virus that claimed the 42-year-old Liberian national's life in less than two weeks, two days might have made all the difference — and it appears that a device in Texas Health Presbyterian Hospital's arsenal could have turned around the results in less than an hour.

The device is called the FilmArray, a sleek diagnostic scanner that can identify more than a dozen different viruses and bacteria. With the right kit, these capabilities include testing for Ebola. In fact, healthcare workers at Emory University Hospital in Atlanta used the device to diagnose US aid workers Dr. Kent Brantley and Nancy Writebol after they contracted the disease in Liberia.

Another proponent of the device is the US military, which has funded the company behind the machine, BioFire, to tailor the device for testing diseases like Ebola — an investment that has proven worthwhile considering the military is utilizing the FilmArray as apart of its Ebola response efforts in West Africa.

BioFire confirmed to DefenseOne that the Dallas hospital does in fact have a FilmArray in its arsenal, begging the question as to why it wasn't used to test Duncan during his emergency room visit, instead of sending his samples to a CDC-sanctioned lab in Texas and the agency's Atlanta headquarters.

First and foremost, the hospital would have needed a special Ebola panel for the device — a panel that most hospitals probably don't have, Dr. Stephen Morse, an epidemiology professor at Columbia University, told VICE News. But perhaps the biggest obstacle is the fact that, despite military backing and high profile cases of use, the device is not technically approved by the Food and Drug Administration for diagnosing Ebola.

Currently, FilmArray is approved for diagnosing gastrointestinal and respiratory problems, but when it comes to Ebola the scanner must get special approval by the FDA, an allowance which falls under the agency's "research use only" guidelines. This means that even if the FDA gave a hospital the green light to use the Ebola panel for the FilmArray, it would have to be strictly for research, not simply for determining whether a patient has the disease.

According to Morse, once the hospital is given permission to use a device under the research guidelines, it would be up to clinicians to determine what that means — leaving a definite gray area in which testing could be done.

In the case of a potential Ebola patient, it may seem reasonable for healthcare workers to cite an emergency situation and use the diagnostic test. But Dr. Peter Jacobson, a health law and policy professor at the University of Michigan, told VICE News that using the test could open a hospital up to liability issues.

"If you're a hospital, before you use a device, you ask the FDA for a waiver because if you don't and you get it wrong, you have a liability issue," he said. "In an emergency situation, you've got to give healthcare administrators leeway, but you have to be careful and justify why it's an emergency."

Jacobson said there is a strong defense for allowing emergency use of FilmArray for Ebola diagnosis.

"Unchecked Ebola has obviously dire consequences," he said, explaining that if you can argue that something would work to prevent the spread of Ebola or cure someone, you would have a strong defense. "Particularly with this device, one argument could be that the only way to actually find out if it works is to use it during an outbreak." Jacobson noted an important caveat: FilmArray should not be used exclusively — its results should be backed up by other testing methods.

The FDA said it has been reaching out to commercial companies in order to encourage them to develop rapid diagnostic tests for Ebola, in addition to acknowledging the importance of such technologies. As Morse points out, diagnostic tests are especially important for tackling the outbreak at its source West Africa. He explained that rapid diagnostic capabilities are important on the ground in order to differentiate between Ebola and diseases with similar symptoms, especially Malaria, which is very common in the region.

Early diagnostics also help to jumpstart contact tracing efforts, ensuring that resources are not used to follow the contacts of someone who doesn't actually have the virus.

Regardless of the fervor surrounding the outbreak, the FDA sticks by its current use guidelines for FilmArray. The agency said it works to quickly decide on these cases once they receive a request.

"The FDA may not authorize the use of a diagnostic test before reviewing data about its performance in detecting Ebola virus in human specimens and determining that the standard for authorization is met. Doing so would also be irresponsible and potentially unsafe," the FDA said in a statement.

According to Jacobson, the FDA is constantly under attack for being to slow to respond or to slow to approve pharmaceutical and medical devices.

"But there's a reason why we have the FDA," he said. "FDA approval needs to be systematically thorough and robust so we don't have devices on the market that don't work and/or that cause more harm."

Jacobson said the debate brings up larger issues that the government will have to resolve going forward.

"We know that we need some type of policy to deal with this kind of outbreak," he said. "The way Ebola spreads and the fear it induces suggests we need to think differently about devices and pharmaceuticals in an outbreak."


Sunday, October 19, 2014

US Federal Government Sits on a Rapid Ebola Test While the Private Sector Ramps Up Its Efforts

Researchers at a government lab have developed a minimally invasive test for Ebola that could cut the time it takes to diagnose cases of the lethal virus from days and hours to minutes or even seconds, International Business Times has learned. The Department of Energy, which invented the procedure at its Oak Ridge National Laboratory in Knoxville, Tennessee, is now scrambling to find a partner to commercialize the technology.

The development comes amid fears that the Ebola virus may spread in the U.S. after the first cases appeared in Dallas in the past week. On Friday, President Obama named former vice presidential chief of staff Ron Klain as the nation’s first “Ebola czar.”

In a solicitation-for-contractors document, DOE describes its test as a “rapid, portable viral diagnostic for RNA viruses,” including, specifically, Ebola hemorrhagic fever. RNA viruses are made from genetic material comprising ribonucleic acid. In addition to Ebola, the DOE said the test can quickly detect Hanta, Dengue, West Nile and several other exotic viruses.

DOE posted its solicitation late Wednesday to a federal contracting database. A public records search showed that as of Friday one contractor had expressed interest: Healtheon Inc., of New Orleans, which manufacturers a range of diagnostic tools. Healtheon president Jasmeet Walia did not immediately respond to a request for more information.

A DOE spokesperson said the agency has been directed to refer all calls related to Ebola to the National Security Council. NSC officials did not immediately return phone calls.

In its solicitation, the DOE said rapid diagnostics “are critical elements of an effective response to viral outbreaks, but are limited by both available technology and implementation. ORNL researchers have developed a diagnostic for active, acute viral infections using a highly fieldable, and nearly reagentless system.”

A reagentless system would not require blood samples or other bodily fluids from suspected Ebola sufferers to be transported to a lab to be mixed with other chemicals.

An expert who viewed DOE patent documents on behalf of International Business Times said the technology appears to be a legitimate breakthrough. Dr. Amar Safdar, director for Transplant Infectious Diseases at New York University’s Langone Medical Center, said it could significantly reduce the time and cost of diagnosing new Ebola cases. “It’s cutting-edge,” said Safdar.

Health care facilities currently test for Ebola using a method known as polymerase chain reaction (PCR). The method requires several steps in a lab to isolate and then amplify the virus’ RNA.

DOE’s technology is “a major improvement on the existing, time-consuming PCR technology,” said Safdar, adding it could be used to conduct on-the-spot screenings at airports and other points of entry. Subjects could be asked to provide a drop of blood or nasal swab, which could then be checked using test strips that change color. “If there is a good, rapid test, then that is extremely desirable,” said Safdar.

Beyond speed, the technology could promote more widespread Ebola testing in developing nations in western Africa, where the current outbreak originated. PCR testing requires access to sophisticated and expensive lab equipment, which is not widely available in the region. Health care workers deployed to the area are in some cases shipping blood samples to Europe for testing.

Safdar cautioned, however, that rapid virus testing may not be as accurate as PCR. Rapid testing for human immunodeficiency virus (HIV), which has been available for several years, is known to deliver a very small percentage of false positives, though no false negatives. “This may be better at ruling people out than ruling them in,” said Safdar.

Positive results detected through rapid testing should be confirmed in a lab, Safdar added. He said that the DOE’s technology, as is the case with PCR testing, would only work on individuals who are symptomatic. Humans can harbor the Ebola virus for as long as three weeks before showing signs such as severe headaches, diarrhea and vomiting.

In the meantime, a number of private contractors are working on their own versions of the technology.

Colorado-based Corgenix has partnered with Tulane University to develop a rapid diagnostic kit. A production-ready version is several months in the offing, according to reports. Another vendor, Nanōmix, is also participating. It offers a device that can check for multiple infections at once. “We did do some field testing, but we need to do more,” Tulane scientist Dr. Robert Garry told The New Republic.

The U.S. military is also using commercially produced hardware in the fight to contain Ebola. Troops deployed to western Africa are screening suspected patients with a device called FilmArray, from BioFire Diagnostics of Salt Lake City. The box scans for the genetic markers of Ebola and a number of other viruses. “It will take the Ebola cells, break them open, expose the [ribonucleic acid] in the Ebola and match those with a target we’ve identified,” BioFire reps said in a statement to DefenseOne.

The New York Post reported on Thursday that startup Nanobiosym has “an iPhone-sized device” that can detect Ebola and other diseases in less than an hour. Numerous other companies are working on technologies that can be used to support Ebola containment efforts to the point at which investors are now tracking the market.

The 2014 Ebola outbreak has to date claimed about 4,500 lives, according to the Centers for Disease Control and Prevention in Atlanta. There has been one death in the U.S. Thomas Eric Duncan passed away after traveling from Liberia to a hospital in Dallas. Two nurses who treated Duncan were infected and are receiving treatment.

Source: International Business Times

Friday, October 10, 2014

This New Ebola Test Is As Easy As a Pregnancy Test, So Why Aren’t We Using It?

The best weapon against the outbreak may be one we’re not using: Scientists at Tulane University are sitting on millions of rapid diagnostic kits capable of spotting the virus instantly.

The story of Thomas Eric Duncan’s experience with Ebola is one that has played out thousands of times in West Africa. The patient fell ill with a fever. Doctors misdiagnosed him. A vial of his blood was shipped to a high-tech laboratory to be tested. By the time virologists confirmed it was Ebola—in this case, four days later—isolation was long overdue.

It’s a sequence of events that captures one of the biggest, and often overlooked obstacles to curbing the spread of the disease in West Africa: inefficient testing.

There is only one approved, working test that can detect whether or not Ebola is present in the blood. One. The powerful technology required is slow, complicated, and requires both a laboratory and equipment. It is not that more-efficient tests do not exist; it’s that we don’t yet have the permission needed to use them.

As Ebola cases in West Africa surpassed 6,000 last week, Dr. Bob Garry, a scientist at Tulane University, is working harder than ever to get one possible solution—a rapid diagnostic test—approved. Until that happens do, testing will remain the epidemic’s secret ally.

The vial of blood taken from Duncan in Dallas was sent to the Centers for Disease Control and Prevention’s Atlanta lab, where a single test was performed. It’s the same one used by doctors in West Africa, or anywhere in the world. The test, called polymerase chain reaction (PCR), uses a method to amplify the DNA to a point where the virus can actually be detected. But the technology, while powerful, is cumbersome and takes anywhere from 12 hours to four days to yield a result.

This isn’t the best test for this epidemic, but it’s the only one.

Garry says the biggest problem with this test is in its high-tech, time-consuming method.

For example, a vial of the patient’s blood is transported to one of the few laboratories in West Africa with the suitcase-size PCR equipment needed to test for the virus. These facilities, among other more sophisticated equipment, require central electricity. In many parts of West Africa, this is hard to find. The test can take anywhere from one day to four. Factoring in travel, an answer to a sick patient’s question could be as much as a week away.

At the outset of this process, the patient is told to remain at the treatment center until a diagnosis can be made. But by the time the test results come back, the vast majority are gone. Some have fled the hospital in fear. Some have gone into hiding. Some have gone home to die. All of those who are positive have now needlessly spread the virus to countless others.

It’s the breakdown in care caused by delay that Garry and his team are hoping to fix. The scientists began working in West Africa roughly 10 years ago on another fever called Lassa. Over the course of a few years, they developed a rapid diagnostic test that allowed doctors to give patients a diagnosis on the spot. When the first cases of Ebola began popping up in West Africa, Garry and his team began “fortifying” existing labs they had in the area. In the creation of the Lassa fever test strips, they had also made a similar, but separate, Ebola test. But without any presence of Ebola in the region until this year, they were unable to test them until now.

The value of the rapid diagnostic test lies in its simplicity. It consists of a small white lancet, which requires just a small drop of blood. In 15 minutes or less, a positive or negative line will appear on the test, indicating Ebola positive or negative. "They work like pregnancy tests except its blood," says Garry.

“What our tests would permit one to do is to basically see if a person has Ebola on the spot,” Garry tells me. “They are not perhaps as sensitive as a PCR. That’s a very sophisticated test, but they don’t really have to be. What we’re most interested in doing is coming out with a test that could detect when someone is infectious, immediately.”

Taken into a clinical setting in West Africa, the test would allow physicians to immediately determine the condition of their patient, improving both the health of that individual and the safety of those around them. By immediately isolating patients that test positive, Liberia, Guinea, and Sierra Leone could prevent infected patients from going back to their village and spreading the virus further.

Dr. Alan Wu, a chemistry lab director at San Francisco General and professor at lab medicine at University of California SF, said he believes the rapid diagnostic testing is necessary in the U.S. as well. At his hospital in San Francisco, he’s received CDC training in preparation for an outbreak. But if a case comes in that he suspects is Ebola, he won’t be able to test it himself. Wu has been instructed to send the vial to the CDC’s headquarters in Atlanta—one of 12 labs in the nation (according to the CDC) capable of performing the test. “Not everyone can do molecular tests, whereas anyone can do a finger stick,” he says. “This is not going to go away. This is not a handful of patients. It’s going to have an impact on Americans as other people interact with people from that part of Africa, so we need products and we need a nimble system that will allow products to be available in advance.”

So if the test is so promising, why aren’t we already using it? “We have to prove that it works,” says Garry. “The timing is what’s holding us up.” In July at the American Association for Clinical Chemistry (AACC)’s Annual Meeting and Clinical Lab Expo, Corgenix (the company behind the rapid test) and the Viral Hemorrhagic Fever Consortium were awarded $2.9 million in grant money by the National Institutes of Health to continue work on the development of the Ebola test kit.  [See our post on the Corgenix-Tulane project for more information.]

Three months later, Garry and his team are prepped and ready to have hundreds of thousands, “even millions,” of the rapid tests ready to send to West Africa. But without 100 percent proof that it works, they’re at a standstill. With the news of an American being diagnosed with Ebola on U.S. soil, Garry hopes the process may be sped along. Not only so the test can be used in the States—but on planes.

With Garry and Corgenix’s previous rapid tests for Lassa used extensively—and successfully—in Sierra Leone and elsewhere, the evidence is even more compelling that their Ebola test will get approval. In the eyes of Wu, the test should already be out in the field, despite a lack of 100 percent proof. “If you have a positive, even if it’s a false positive, you’re erring on the side of caution. That is good.”

But not all physicians see rapid diagnostic tests as the answer. Kent Sepkowitz, an infectious disease specialist from New York (and contributor to The Daily Beast) said he thinks the technology is simply coming too late. “It will be great when the Ebola outbreak starts in 2016, or whenever the next one is. Would have nipped that in the bud.” says Sepkowitz. “But I think they need gowns and hospital rooms much more than rapid tests.”

While the rapid diagnostic test could help this epidemic, it’s by no means a longterm solution West Africa, where thousands die of other viruses each year. "We will get to a point where Ebola is not the only thing people are thinking about,” says Doug Simpson, President and CEO of Corgenix. In effort to address the larger issue, Simpson’s company has teamed up with Nanomix, a a leading nanotechnology company focused on the development of next generation Point of Care diagnostic tests. The joint venture entails Corgenix migrating the rapid diagnostic tests into a handheld device designed by Nanomix. In a matter of minutes, using multiplex detection on a drop of blood, the handheld device can distinguish between at least five different common disease ranging from Malaria to Lassa Fever. "The longterm answer is you have to be able to differentiate between the diseases,” says Simpson. “I think that’s the answer."

As the epidemic rages on, Garry is working tirelessly to get the test through the U.S.’s clunky approval process. The delay, he says, is not for lack of backing. “At the very highest level of government they know about it,” says Garry. “We’re trying to work as quickly as we can.” While he stresses that the test isn’t scientifically smarter than the existing PCR, he’s aware of its power to potentially change the tide of the epidemic.  “If you could quarantine people on the spot… it would make a big difference in trying to shut this thing down.”

The response to the Ebola epidemic in West Africa has surged in the past few weeks, delivering more money, supplies, and doctors. As the region is flooded with goods, Garry and his team are stripping the virus testing process bare. It’s not another Ebola test that the world needs, but a simpler one.

Source: The Daily Beast and

Wednesday, October 1, 2014

Detecting Ebola with Nanotechnology

By late January, 1.4 million people in Liberia and Sierra Leone could be infected with the Ebola virus. That’s the worst-case scenario of the Ebola epidemic in West Africa recently offered by scientists at the US Centers for Disease Control and Prevention. The CDC warns that  those countries could now have 21,000 cases of the virus, which kills 70 percent of people infected.

One of the big problems hindering containment of Ebola is the cost and difficulty of diagnosing the disease when a patient is first seen. Conventional fluorescent label-based virus detection methods require expensive lab equipment, significant sample preparation, transport and processing times, and extensive training to use. One potential solution may come from researchers at the College of Engineering and the School of Medicine, who have spent the past five years advancing a rapid, label-free, chip-scale photonic device that can provide affordable, simple, and accurate on-site detection. The device could be used to diagnose Ebola and other hemorrhagic fever diseases in resource-limited countries.

The first demonstration of the concept, described in the American Chemical Society journal Nano Letters in 2010 and developed by an ENG research group led by Selim Ünlü, a professor of biomedical engineering, electrical and computer engineering, and materials science and engineering, in collaboration with Bennett Goldberg, a College of Arts & Sciences professor of physics, showed the ability to pinpoint and size single H1N1 virus particles. Now, after four years of refining the instrumentation with the collaboration of John Connor, a School of Medicine associate professor of microbiology, and other hemorrhagic fever disease researchers at the University of Texas Medical Branch, the team has demonstrated the simultaneous detection of multiple viruses in blood serum samples—including viruses genetically modified to mimic the behavior of Ebola and the Marburg virus.

Mentioned in Forbes magazine as a potentially game-changing technology for the containment of Ebola, the device identifies individual viruses based on size variations resulting from distinct genome lengths and other factors. Funded by the National Institutes of Health, the research appears in the May 2014 ACS Nano.

“Others have developed different label-free systems, but none have been nearly as successful in detecting nanoscale viral particles in complex media,” says Ünlü, who is also ENG associate dean for research and graduate programs, referring to typical biological samples that may have a mix of viruses, bacteria, and proteins. “Leveraging expertise in optical biosensors and hemorrhagic fever diseases, our collaborative research effort has produced a highly sensitive device with the potential to perform rapid diagnostics in clinical settings.”

Whereas conventional methods can require up to an hour for sample preparation and two hours or more for processing, the current BU prototype requires little to no sample preparation time and delivers answers in about an hour.

“By minimizing sample preparation and handling, our system can reduce potential exposure to health care workers,” says Connor, a researcher at the University’s National Emerging Infectious Diseases Laboratories (NEIDL). “And by looking for multiple viruses at the same time, patients can be diagnosed much more effectively.”

The shoebox-sized battery-operated prototype diagnostic device, known as the single particle interferometric reflectance imaging sensor (SP-IRIS), detects pathogens by shining light from multicolor LED sources on viral nanoparticles bound to the sensor surface by a coating of virus-specific antibodies. Interference of light reflected from the surface is modified by the presence of the particles, producing a distinct signal that reveals the size and shape of each particle. The sensor surface is very large and can capture the telltale responses of up to a million nanoparticles.

In collaboration with BD Technologies and NexGen Arrays, a start-up based at the Photonics Center and run by longtime SP-IRIS developers David Freedman (ENG’10) and postdoctoral fellow George Daaboul (ENG’13), the research team is now working on making SP-IRIS more robust, field-ready, and fast—ideally delivering answers within 30 minutes—through further technology development and preclinical trials.

SP-IRIS devices are now being tested in several labs, including a Biosafety Level-4 (BSL-4) lab at the University of Texas Medical Branch that’s equipped to work with hemorrhagic viruses. Other tests will be conducted at BU’s NEIDL once the facility is approved for BSL-4 research. Based on the team’s current rate of progress, a field-ready instrument could be ready to enter the medical marketplace in five years.

Source: BU Today