Tagged: Lassa virus Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 8:52 pm on June 1, 2017 Permalink | Reply
    Tags: Assembled arenavirus glycoprotein, , Hemorrhagic fever viruses, Lassa virus, , , , Tripod Shape Key to Future Vaccine Design, Up to 90 percent fatal in pregnant women,   

    From SLAC: “SLAC X-Ray Beam Helps Uncover Blueprint for Lassa Virus Vaccine” 

    SLAC Lab

    June 1, 2017

    The molecular structure of a Lassa virus protein provides the blueprints for vaccine design. (Ollmann Saphire Lab/The Scripps Research Institute)

    Erica Ollmann Saphire, professor of Immunology and Microbial Science at The Scripps Research Institute, during a visit of the Kenema Government Hospital, Sierra Leone, to study Lassa virus. (Kathryn Hastie/The Scripps Research Institute)

    An antibody from a human survivor (turquoise) is shown inactivating a Lassa virus surface protein. (Ollmann Saphire Lab/The Scripps Research Institute)

    A decade-long search ends at the Stanford Synchrotron Radiation Lightsource, where researchers from The Scripps Research Institute emerge with a clear picture of how the deadly Lassa virus enters human cells.


    Before Ebola virus ever struck West Africa, locals were continually on the lookout for another deadly pathogen: Lassa virus. With thousands dying from Lassa every year – and the potential for the virus to cause even larger outbreaks – researchers are committed to designing a vaccine to stop it.

    Now a team of scientists from The Scripps Research Institute (TSRI) has solved the structure of the viral machinery that Lassa virus uses to enter human cells.

    X-ray beams from the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory gave the team the final piece in a puzzle they sought to solve for over 10 years.

    Their study, published today in Science, is the first to show a key piece of the viral structure, called the surface glycoprotein, for any member of the deadly arenavirus family, and the new structure provides a blueprint to design a Lassa virus vaccine.

    “This was a tenacious effort – over a decade – to conquer a global threat,” said Erica Ollmann Saphire, a professor of Immunology and Microbial Science from TSRI and senior author of the new study.

    X-ray data for this study was collected at SLAC and the DOE’s Argonne National Laboratory.

    For the SLAC experiments, the researchers used a station at SSRL, a DOE Office of Science User Facility that has a strong program in biological X-ray crystallography. In this method, scientists prompt biological molecules to align and form a crystal, which they then study with powerful X-rays. The way the X-rays scatter off the crystal reveals the structure of the molecules inside – in 3-D and with atomic detail.

    “I am proud of SSRL’s strong partnership with TSRI and our involvement in this project that utilized the bright X-ray microbeams and high level of automation at Beam Line 12-2 to obtain the necessary data,” said SSRL senior staff scientist Aina Cohen. “This structure provides key information towards engineering an effective vaccine against Lassa, enabling the infected to combat the immunosuppressive traits of this virus, which is estimated to kill tens of thousands of people each year.”

    It Started with a Thesis

    The effort began with TSRI staff scientist Kathryn Hastie, the lead author of the study. In 2007, then a grad student in Ollmann Saphire’s lab, she told her thesis committee she wanted to solve the structure of the assembled arenavirus glycoprotein, something never done before. She hoped to create a map of the target on the virus where antibodies need to attack – a key step in developing a vaccine.

    Such maps can be obtained with X-ray crystallography, but the method depends on having a stable protein. Yet, all the Lassa virus glycoprotein wanted to do was fall apart.

    The problem was that glycoproteins are made up of smaller subunits. Other viruses have bonds that hold the subunits together, “like a staple,” Hastie said. Arenaviruses don’t have that staple; instead, the subunits just floated away from each other whenever Hastie tried to work with them.

    Another challenge was to recreate part of the viral lifecycle in the lab – a stage when Lassa’s glycoprotein gets clipped into two subunits. “We had to figure out how to get the subunits to be sufficiently clipped, which is necessary to make the biologically functional assembly, and also where to put an engineered staple to make sure they stayed together,” Hastie said.

    Partnering with West Africa

    As Hastie tackled those challenges from her lab bench in San Diego, staff at the Kenema Government Hospital in Sierra Leone labored on the front lines of the ongoing fight against Lassa.

    Until the 2014–15 Ebola virus outbreak, Kenema was the only hospital in the world to have a special ward dedicated to treating hemorrhagic fever viruses. Staff at the clinic – from the nurses to the ambulance drivers – are all Lassa survivors, which gives them immunity to the disease. The TSRI scientists have a long-term collaboration with Kenema as part of a research program run by Tulane University that provided them with antibodies from survivors of Lassa fever. These antibodies could inactivate the virus, and they provided lifesaving protection to animal models. These were the kinds of antibodies researchers are hoping to elicit with a future Lassa virus vaccine.

    In 2009, Hastie got to visit Kenema on a trip with Ollmann Saphire.

    “I had been working on the project for two years with very little success at that point,” Hastie said. “Going to West Africa showed me how important it was to keep going.”

    Like Ebola virus, Lassa fever starts with flu-like symptoms and can lead to debilitating vomiting, neurological problems and even hemorrhaging from the eyes, gums and nose. The disease is 50 to 70 percent fatal—and up to 90 percent fatal in pregnant women.

    “Studying Lassa is critically important. Hundreds of thousands of people are infected with the virus every year, and it is the viral hemorrhagic fever that most frequently comes to the United States and Europe,” said Ollmann Saphire. “Kate’s study needed to be done.”

    Tripod Shape Key to Future Vaccine Design

    By creating mutant versions of important parts of the molecule, Hastie engineered a version of the Lassa virus surface glycoprotein that didn’t fall apart. She then used this model glycoprotein as a sort of magnet to find antibodies in patient samples that could bind with the glycoprotein to neutralize the virus.

    With this latest study she solved the structure of the Lassa virus glycoprotein, bound to a neutralizing antibody from a human survivor.

    Her structure showed that the glycoprotein has two parts. She compared the shape to an ice cream cone and a scoop of ice cream. A subunit called GP2 forms the cone, and the GP1 subunit sits on top. They work together when they encounter a host cell. GP1 binds to a host cell receptor, and GP2 starts the fusion process to enter that cell.

    The new structure also showed a long structure hanging off the side of GP1—like a drip of melting ice cream running down the cone. This “drip” holds the two subunits together in their pre-fusion state.

    Zooming in even closer, Hastie discovered that three of the GP1-GP2 pairs come together like a tripod. This arrangement appears to be unique to Lassa virus. Other viruses, such as influenza and HIV, also have three-part proteins (called trimers) at this site, but their subunits come together to form a pole, not a tripod. The structure is also important because it can be used as a model to conquer related viruses throughout the Americas, Europe and Africa for which no equivalent structure yet exists.

    “It was great to see exactly how Lassa was different from other viruses,” said Hastie. “It was a tremendous relief to finally have the structure.”

    This tripod arrangement offers a path for vaccine design. The scientists found that 90 percent of the effective antibodies in Lassa patients targeted the spot where the three GP subunits came together. These antibodies locked the subunits together, preventing the virus from gearing up to enter a host cell.

    A future vaccine would likely have the greatest chance of success if it could trigger the body to produce antibodies to target the same site.

    Ollmann Saphire explained that Hastie accomplished something unique in structural biology. “The research started from scratch with the native, wild-type viruses in patients in a remote clinic—and went all the way to developing a basis for vaccine design. And the work was done almost entirely by one woman.”

    Moving Forward with a Lassa Vaccine

    The next step is to test a vaccine that will prompt the immune system to target Lassa’s glycoprotein.

    As director of the Viral Hemorrhagic Fever Immunotherapeutic Consortium, Ollmann Saphire is already coordinating with her partners at Tulane and Kenema to bring a vaccine to patients.

    The Coalition for Epidemic Preparedness Innovations, an international collaboration that includes the Wellcome Trust and the World Health Organization as partners, has recently named a vaccine for Lassa virus as one of its three top priorities. “The community is keenly interested in making a Lassa vaccine, and we think we have the best template to do that,” said Ollmann Saphire.

    She added that with Hastie’s techniques for solving arenavirus structures, researchers can now get a closer look at other hemorrhagic fever viruses, which cause death, neurological diseases and even birth defects around the world.

    Ollmann Saphire added that beamlines such as 12-2 at SSRL, which provided the X-ray beam used to finally determine the Lassa virus glycoprotein structure, along with its recent detector upgrades, are essential for ongoing advances in structural biology.

    “This research highlights the power of crystallographic techniques that rely on advanced synchrotron facilities to combat the most challenging biological problems. The support of the DOE’s Office of Science Biological and Environmental Research, the National Institutes of Health and private institutions such as TSRI enables us to make these resources available to the wider biomedical community,” Cohen said.

    In addition to Ollmann Saphire and Hastie, the following authors contributed: Michelle A. Zandonatti of TSRI; James E. Robinson and Robert F. Garry of Tulane University; Lara M. Kleinfelter and Kartik Chandran of the Albert Einstein College of Medicine; and Megan L. Heinrich, Megan M. Rowland and Luis M. Branco of Zalgen Labs.

    The new study included (left to right) first author Kathryn M. Hastie, senior author Erica Ollmann Saphire and co-author Michelle A. Zandonatti of The Scripps Research Institute. (Photo by Madeline McCurry-Schmidt.)

    The study was supported by the National Institutes of Health and an Investigators in Pathogenesis of Infectious Diseases Award from the Burroughs Wellcome Fund. Research funding for the SSRL Structural Molecular Biology Program was provided by the DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here .

    See the Scripps press release here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 11:13 am on August 15, 2015 Permalink | Reply
    Tags: , , Lassa virus,   

    From Broad Institute at Harvard: “New insights on an old virus 

    Harvard University

    Harvard University

    Harvard Broad Institute
    Broad Institute of Harvard and MIT

    August 13th, 2015
    Angela Page

    New research from Broad scientists lends new understanding to Lassa virus, which kills at least 5,000 people every year. Pictured are Pardis Sabeti and Edwin Konuwa of the Kenema Government Hospital.Photo courtesy of the Sabeti Lab.

    Between 2013 and 2015, an outbreak of Ebola virus killed more than 11,000 people. Broad Institute researchers quickly deployed real-time sequencing efforts that confirmed that the virus was primarily spreading through human-to-human contact rather than between animals and humans and that the viral genome was mutating. This work had a profound impact on how public health officials diagnosed the disease and developed strategies to contain it.

    That research was feasible largely because institute member Pardis Sabeti and her team had already been working on another deadly virus affecting West Africa: Lassa virus. In 2007, the Sabeti lab discovered genetic evidence that humans might be able to develop resistance to Lassa. They quickly set up a field site in Nigeria at the Irrua Specialist Teaching Hospital and formed collaborations with researchers from Tulane University working in Sierra Leone. Since then, the group has been sequencing the genomes of Lassa viral content in human blood samples. Those data now collectively form the largest catalog of information to date on Lassa Virus (LASV) available in the world. They were published this week, along with the team’s analyses, in the August issue of the journal Cell.

    Like Ebola, Lassa is a fatal, hemorrhagic fever virus. It kills at least 5,000 people each year, most of whom live in Sierra Leone, Nigeria, Liberia, and Guinea. Despite its impact, little research had been done on the virus until 2009. The same was true of Ebola before the recent outbreak. “Lassa and Ebola are not only potential global threats, but have likely been circulating in communities for many years,” said Sabeti. “It is a greatly overlooked public health challenge but also an opportunity to set up capacity to diagnose, treat and research these viruses now, before the next major outbreak.””Because of the potential for such large and severe outbreaks, it’s important that we perform research that allows us to better understand how these viruses transmit, how they evolve, how long they’ve been with us—we need to answer very fundamental questions and sequencing can help us address some of them,” said Kristian Andersen, one of three co-first authors on the new Cell paper. Andersen—now an assistant professor at the Scripps Research Institute in La Jolla, California—led the Lassa work while a post-doctoral researcher in Sabeti’s lab.

    This was a massive, international collaborative effort involving researchers from 19 different institutions across the academic, government, non-profit, medical, and commercial sectors. “It took many years to form this consortium and set up the infrastructure and many months to develop the sequencing protocols,” said fellow co-first author Christian Matranga, a research scientist at Broad. “But these efforts led to many technical leaps, which enabled discoveries that would not have been otherwise possible.”

    Mambu Momoh of Kenema Government Hospital and Kristian Andersen. Photo courtesy of the Sabeti Lab

    Andersen and his colleagues sequenced 196 LASV genomes, including 11 collected from the rodent species that serves as the virus’ natural reservoir. The data allowed them to confirm that, in contrast to Ebola, Lassa patients typically contract the disease through individual “spillover” events from the animal to human population—that is, the virus is rarely transmitted between human patients.

    “Lassa is probably less transmissible than Ebola—either from rodent to human, or from human to human,” Andersen explained. “Presumably, however, since many rodents are infected and live in households, there may be more ‘opportunities’ for transmission from rodent to human to occur.” This means that strategies for containing Lassa could be fundamentally different from those used to contain Ebola and would focus more on the rodent reservoir population rather than minimizing human-to-human contact.

    The data also allowed the team to determine the most recent common ancestor of all modern Lassa virus strains: it existed more than 1,000 years ago. This calculation support Sabeti’s original suspicion that humans have been under natural selection to evolve resistance to the virus. “If that’s the case,” Andersen said, “the virus would need to have been around for quite a long time.”

    The team also examined the diversity of viral species infecting humans and rodents and found much more diversity among the latter. Because the rodents can be infected without becoming ill or dying, they are considered chronic carriers in whom there is more opportunity for the virus to mutate and evolve. Surprisingly, the researchers also saw a few human samples containing more diverse viral strains than normal, suggesting that some people might be infected for longer than previously thought.

    Andersen and his team at Scripps, as well as researchers at Broad, Tulane, and Irrua are now launching an effort to sequence healthy individuals across West Africa to determine whether the virus is present as a chronic, symptom-free infection in many more people than are typically diagnosed. “We’re also looking at how many people have antibodies to these viruses—both to Ebola and Lassa,” Andersen said, explaining that antibodies are developed whenever an individual becomes infected, even if they don’t present any symptoms.

    The diversity findings may also point to an immune escape mechanism wherein the virus develops mutations that allow it to evade an infected host’s immune response. “We found that, of the within-host mutations that affect protein structure, a surprisingly high number fall in parts of a Lassa surface protein targeted by the human immune system,” said Jesse Shapiro, a co-first author based at the University of Montreal. “This could have implications for vaccine design because it might mean that the virus is able to evade vaccine-induced immunity.” But the team also found that these particular mutations are rarely passed from one host to another, suggesting that, while they do provide adaptive immune escape within the host, “they may be evolutionary dead-ends that are unfit to transmit,” Shapiro said. The team is now undertaking further research to follow up on the immune escape hypothesis.

    While the research is exciting from a scientific perspective, Andersen said, “People are dying every day.” He noted that work like this is critical to better understanding the disease in order to someday make a real difference for patients and their families.

    Paper Cited: Andersen, Shapiro, Matranga, et al. Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus. Cell. DOI: 10.1016/j.cell.2015.07.020

    Other Broad Researchers: Aaron M. Berlin, Bruce Birren, James Bochicchio, Eleina M. England, Hilary K. Finucane, Michael Fitzgerald, Stephen K. Gire, Andreas Gnirke, Andrea Ireland, Eric Lander, Niall J. Lennon, Joshua Z. Levin, Aaron E. Lin, Christian B. Matranga, Caryn McCowan, Mahan Nekoui, Eric Phelan, Elizabeth M. Ryan, Stephen F. Schaffner, B. Jesse Shapiro, Rachel Sealfon, Matthew Stremlau, Shervin Tabrizi, Ridhi Tariyal, Barbara Tazon-Vega, Ryan Tewhey, Sarah Winnicki.

    See the full article here.

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

Compose new post
Next post/Next comment
Previous post/Previous comment
Show/Hide comments
Go to top
Go to login
Show/Hide help
shift + esc
%d bloggers like this: