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A Novel, 3D-Printed Virus

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In the blog post “3D Printing the Novel Coronavirus,” I mentioned receiving my very own 3D-printed model of the novel coronavirus SARS-CoV-2, the cause of COVD-19. I shared this impressive model, created by the NIH 3D Print Exchange, with viewers during our third virtual NIH Town Hall meeting. The one-hour meeting was held on May 21, 2020 for employees, contractors, fellows, and trainees now sheltering at home to discuss the multi-phased return to the NIH workplace that will begin in June. Credit: NIH


3D Printing the Novel Coronavirus

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Credit: 3D Print Exchange, NIAID, NIH

The coronavirus disease 2019 (COVID-19) pandemic has truly been an all-hands-on-deck moment for the nation. Among the responders are many with NIH affiliations, who are lending their expertise to deploy new and emerging technologies to address myriad research challenges. That’s certainly the case for the dedicated team from the National Institute of Allergy and Infectious Diseases (NIAID) at the NIH 3D Print Exchange (3DPX), Rockville, MD.

A remarkable example of the team’s work is this 3D-printed physical model of SARS-CoV-2, the novel coronavirus that causes COVID-19. This model shows the viral surface (blue) and the spike proteins studded proportionally to the right size and shape. These proteins are essential for SARS-CoV-2 to attach to human cells and infect them. Here, the spike proteins are represented in their open, active form (orange) that’s capable of attaching to a human cell, as well as in their closed, inactive form (red).

The model is about 5 inches in diameter. It takes more than 5 hours to print using an “ink” of thin layers of a gypsum plaster-based powder fused with a colored binder solution. When completed, the plaster model is coated in epoxy for strength and a glossy, ceramic-like finish. For these models, NIAID uses commercial-grade, full-color 3D printers. However, the same 3D files can be used in any type of 3D printer, including “desktop” models available on the consumer market.

Darrell Hurt and Meghan McCarthy lead the 3DPX team. Kristen Browne, Phil Cruz, and Victor Starr Kramer, the team members who helped to produce this remarkable model, created it as part of a collaboration with the imaging team at NIAID’s Rocky Mountain Laboratories (RML), Hamilton, MT.

The RML’s Electron Microscopy Unit captured the microscopic 3D images of the virus, which was cultured from one of the first COVID-19 patients in the country. The unit handed off these and other data to its in-house visual specialist to convert into a preliminary 3D model. The model was then forwarded to the 3DPX team in Maryland to colorize and optimize in preparation for 3D printing.

This model is especially unique because it’s based exclusively on SARS-CoV-2 data. For example, the model is assembled from data showing that the virus is frequently oval, not perfectly round. The spike proteins also aren’t evenly spaced, but pop up more randomly from the surface. Another nice feature of 3D printing is the models can be constantly updated to incorporate the latest structural discoveries.

That’s why 3D models are such an excellent teaching tools to share among scientists and the public. Folks can hold the plaster virus and closely examine its structure. In fact, the team recently printed out a model and delivered it to me for exactly this educational purpose.

In addition to this complete model, the researchers also are populating the online 3D print exchange with atomic-level structures of the various SARS-CoV-2 proteins that have been deposited by researchers around the world into protein and electron microscopy databanks. The number of these structures and plans currently stands at well over 100—and counting.

As impressive as this modeling work is, 3DPX has found yet another essential way to aid in the COVID-19 fight. In March, the Food and Drug Administration (FDA) announced a public-private partnership with the NIH 3D Print Exchange, Department of Veterans Affairs (VA) Innovation Ecosystem, and the non-profit America Makes, Youngstown, OH [1]. The partnership will develop a curated collection of designs for 3D-printable personal protective equipment (PPE), as well as other necessary medical devices that are in short supply due to the COVID-19 pandemic.

You can explore the partnership’s growing collection of COVID-19-related medical supplies online. And, if you happen to have a 3D printer handy, you could even try making them for yourself.

Reference:

[1] FDA Efforts to Connect Manufacturers and Health Care Entities: The FDA, Department of Veterans Affairs, National Institutes of Health, and America Makes Form a COVID-19 response Public-Private Partnership (Food and Drug Administration)

Links:

Coronavirus (COVID-19) (NIH)

NIH 3D Print Exchange (National Institute of Allergy and Infectious Diseases/NIH, Rockville, MD)

Rocky Mountain Laboratories (NIAID/NIH, Hamilton, MT)

Department of Veterans Affairs (VA) Innovation Ecosystem (Washington, D.C.)

America Makes (Youngstown, OH)

NIH Support: National Institute of Allergy and Infectious Diseases


Enlisting Monoclonal Antibodies in the Fight Against COVID-19

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B38 Antibody and SARS-CoV-2 wtih ACE2 Receptor
Caption: Antibody Binding to SARS-CoV-2. Structural illustration of B38 antibody (cyan, green) attached to receptor-binding domain of the coronavirus SARS-CoV-2 (magenta). B38 blocks SARS-CoV-2 from binding to the ACE2 receptor (light pink) of a human cell, ACE2 is what the virus uses to infect cells. Credit: Y. Wu et a. Science, 2020

We now know that the immune system of nearly everyone who recovers from COVID-19 produces antibodies against SARS-CoV-2, the novel coronavirus that causes this easily transmitted respiratory disease [1]. The presence of such antibodies has spurred hope that people exposed to SARS-CoV-2 may be protected, at least for a time, from getting COVID-19 again. But, in this post, I want to examine another potential use of antibodies: their promise for being developed as therapeutics for people who are sick with COVID-19.

In a recent paper in the journal Science, researchers used blood drawn from a COVID-19 survivor to identify a pair of previously unknown antibodies that specifically block SARS-CoV-2 from attaching to human cells [2]. Because each antibody locks onto a slightly different place on SARS-CoV-2, the vision is to use these antibodies in combination to block the virus from entering cells, thereby curbing COVID-19’s destructive spread throughout the lungs and other parts of the body.

The research team, led by Yan Wu, Capital Medical University, Beijing, first isolated the pair of antibodies in the laboratory, starting with white blood cells from the patient. They were then able to produce many identical copies of each antibody, referred to as monoclonal antibodies. Next, these monoclonal antibodies were simultaneously infused into a mouse model that had been infected with SARS-CoV-2. Just one infusion of this combination antibody therapy lowered the amount of viral genetic material in the animals’ lungs by as much as 30 percent compared to the amount in untreated animals.

Monoclonal antibodies are currently used to treat a variety of conditions, including asthma, cancer, Crohn’s disease, and rheumatoid arthritis. One advantage of this class of therapeutics is that the timelines for their development, testing, and approval are typically shorter than those for drugs made of chemical compounds, called small molecules. Because of these and other factors, many experts think antibody-based therapies may offer one of the best near-term options for developing safe, effective treatments for COVID-19.

So, what exactly led up to this latest scientific achievement? The researchers started out with a snippet of SARS-CoV-2’s receptor binding domain (RBD), a vital part of the spike protein that protrudes from the virus’s surface and serves to dock the virus onto an ACE2 receptor on a human cell. In laboratory experiments, the researchers used the RBD snippet as “bait” to attract antibody-producing B cells in a blood sample obtained from the COVID-19 survivor. Altogether, the researchers identified four unique antibodies, but two, which they called B38 and H4, displayed a synergistic action in binding to the RBD that made them stand out for purposes of therapeutic development and further testing.

To complement their lab and animal experiments, the researchers used a particle accelerator called a synchrotron to map, at near-atomic resolution, the way in which the B38 antibody locks onto its viral target. This structural information helps to clarify the precise biochemistry of the complex interaction between SARS-CoV-2 and the antibody, providing a much-needed guide for the rational design of targeted drugs and vaccines. While more research is needed before this or other monoclonal antibody therapies can be used in humans suffering from COVID-19, the new work represents yet another example of how basic science is expanding fundamental knowledge to advance therapeutic discovery for a wide range of health concerns.

Meanwhile, there’s been other impressive recent progress towards the development of monoclonal antibody therapies for COVID-19. In work described in the journal Nature, an international research team started with a set of neutralizing antibodies previously identified in a blood sample from a person who’d recovered from a different coronavirus-caused disease, called severe acute respiratory syndrome (SARS), in 2003 [3]. Through laboratory and structural imaging studies, the researchers found that one of these antibodies, called S309, proved particularly effective at neutralizing the coronavirus that causes COVID-19, SARS-CoV-2, because of its potent ability to target the spike protein that enables the virus to enter cells. The team, which includes NIH grantees David Veesler, University of Washington, Seattle, and Davide Corti, Humabs Biomed, a subsidiary of Vir Biotechnology, has indicated that S309 is already on an accelerated development path toward clinical trials.

In the U.S. and Europe, the Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) partnership, which has brought together public and private sector COVID-19 therapeutic and vaccine efforts, is intensely pursuing the development and testing of therapeutic monoclonal antibodies for COVID-19 [4]. Stay tuned for more information about these potentially significant advances in the next few months.

References:

[1] Humoral immune response and prolonged PCR positivity in a cohort of 1343 SARS-CoV 2 patients in the New York City region. Wajnberg A , Mansour M, Leven E, Bouvier NM, Patel G, Firpo A, Mendu R, Jhang J, Arinsburg S, Gitman M, Houldsworth J, Baine I, Simon V, Aberg J, Krammer F, Reich D, Cordon-Cardo C. medRxiv. Preprint Posted May 5, 2020.

[2] A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. Wu Y. et al., Science. 13 May 2020 [Epub ahead of publication]

[3] Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Pinto D, Park YJ, Beltramello M, Veesler D, Cortil D, et al. Nature. 18 May 2020 [Epub ahead of print]

[4] Accelerating COVID-19 therapeutic interventions and vaccines (ACTIV): An unprecedented partnership for unprecedented times. Collins FS, Stoffels P. JAMA. 2020 May 18.

Links:

Coronavirus (COVID-19) (NIH)

Monoclonal Antibodies (National Cancer Institute/NIH)

Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV)

NIH Support: National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences


My Virtual Greeting to X-STEM All Access Conference

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The USA Science & Engineering Festival just held its X-STEM All Access conference, though this year in a virtual format. It was my pleasure to videotape some brief remarks for the conference, and I offer them here to share the excitement and encourage young people to consider careers in the sciences. The opportunities that await in the biomedical sciences in particular are unprecedented, and there are lots of great jobs to be had. X-STEM All Access is an interactive online experience for kids. Through a series of daily livestream events, students will hear from an exclusive group of visionaries about careers in science, technology, engineering, and mathematics. My videotaped remarks were shown on May 18, 2020.


Bringing Out the Best in Us During the Pandemic

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Pablo Vidal-Ribas Belil at the grocery store
Caption: Pablo Vidal-Ribas visiting a supermarket to pick up groceries for four neighbors. Credit: Pablo Vidal-Ribas

Sheltering at home for more than two months has made many of us acutely aware of just how much we miss getting out and interacting with other human beings. For some, the coronavirus disease 2019 (COVID-19) pandemic has also triggered a more selfless need: to be a good neighbor to the most vulnerable among us and help them stay well, both mentally and physically, during this trying time.

The term “good neighbor” definitely applies to Pablo Vidal-Ribas Belil, a postdoctoral fellow at NIH’s Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). Though Vidal-Ribas has his hands full caring for his 4-year-old son in their condo, which is located near NIH’s main campus in Bethesda, MD, he wasn’t too busy to notice that some of his neighbors were in need of help.

Vidal-Ribas extended a helping hand to pick up groceries and prescriptions for the older woman downstairs, as well as several more of his elderly neighbors. He and other concerned neighbors also began enlisting more volunteers to join a neighborhood coronavirus task force. There are now up to 30 volunteers and sometimes hold virtual meetings.

To try to reach everyone in the more than 950-unit Parkside Condominium community, the group coordinated its activities with the help of the management office. They also issued flyers and email messages via the neighborhood list serv, offering to assist people at greatest risk for COVID-19, including seniors and those with compromised immune systems or other serious conditions, by shopping for essential items and dropping the items off at their doors.

The personal interest and care of Vidal-Ribas also comes with medical expertise: he’s a clinical psychologist by training. Vidal-Ribas, who is originally from Barcelona, Spain, came to the United States four years ago to work with an NIH lab that specializes in the study of depression and related conditions in young people. Last year, Vidal-Ribas moved to NICHD as a Social and Behavioral Sciences Branch Fellow, where he now works with Stephen Gilman. There, he explores prenatal and early developmental factors that contribute to attempts at suicide later in life.

His expertise as a psychologist has come in handy. Vidal-Ribas has found that many of the individuals requesting help with grocery items or prescriptions also want to talk. So, the team’s efforts go a long way toward providing not only basic necessities, but also much-needed social and emotional support.

In recognition of this need, the group has expanded to offer virtual chats and other community activities, such as physically distanced games, conversations, or story times. One talented young volunteer has even offered to give music concerts remotely by request. Folks know they can call on Vidal-Ribas and some of the most active task force volunteers at any time.

Vidal-Ribas reports that they’ve taken great care to follow the latest guidelines from the Centers for Disease Control and Prevention on how to protect yourself and others from COVID-19 to ensure that those volunteering their time do so safely. He and other volunteers typically buy for multiple neighbors at once while they do their own personal shopping to reduce the number of outings. They then leave the bags with groceries or prescriptions at their neighbors’ doors with no direct contact. As far as he knows, none of his vulnerable neighbors have come down with COVID-19.

Vidal-Ribas says he’s prepared to continue his volunteer outreach for as long as it takes. And, even when the threat of COVID-19 subsides, he’ll keep on lending a hand to his neighbors. It’s one of the ways he stays connected to his community and grounded within himself during this difficult time. By sharing his story, he hopes it will inspire others to do what they can to help others in need to stay safe and well.

Links:

Coronavirus (COVID-19) (NIH)

Social and Behavioral Sciences Branch Fellows (National Institute of Child Health and Human Development/NIH)

Stephen Gilman ((National Institute of Child Health and Human Development/NIH)


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