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COVID-19 testing

Pop-Up Testing Lab Shows Volunteer Spirit Against Deadly Pandemic

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Caption: Postdoc Jenny Hamilton volunteered to work on coronavirus testing at the Innovative Genomics Institute. Behind her is one of the lab’s liquid-handling systems, which robotically extracts RNA from patient samples before another machine can detect whether that RNA comes from the coronavirus. Credit: Max & Jules Photography.

On March 19, 2020, California became the first U. S. state to issue a stay-at-home order to halt the spread of SARS-CoV-2, the novel coronavirus that causes COVID-19. The order shuttered research labs around the state, and thousands of scientists began sheltering at home and shifting their daily focus to writing papers and grants, analyzing data from past experiments, and catching up on their scientific reading.

That wasn’t the case for everyone. Some considered the order as presenting a perfect opportunity to volunteer, sometimes outside of their fields of expertise, to help their state and communities respond to the pandemic.

One of those willing to pitch in is Jennifer Doudna, University of California, Berkeley (UC Berkeley) and executive director of the school’s Innovative Genomics Institute (IGI), a partnership with the University of California, San Francisco (UC San Francisco). She is also recognized as a pioneer in the development of the popular gene-editing technology called CRISPR.

Doudna, an NIH-supported structural biochemist with no experience in virology or clinical diagnostics, decided that she and her IGI colleagues could establish a pop-up testing lab at their facility. Their job: boost the SARS-CoV-2 testing capacity in her community.

It was a great idea, but a difficult one to execute. The first daunting step was acquiring Clinical Laboratory Improvement Amendments (CLIA) certification. This U. S. certification ensures that quality standards are met for laboratory testing of human blood, body fluid, and other specimens for medical purposes. CLIA certification is required not only to perform such testing in the IGI lab space, but for Doudna’s graduate students, postdocs, and volunteers to process patient samples.

Still, fate was on their side. Doudna and her team partnered with UC Berkeley’s University Health Services to extend the student health center’s existing CLIA certification to the IGI space. And because of the urgency of the pandemic, federal review of the extension request was expedited and granted in a few weeks.

The next challenge was technological. Doudna’s team had to make sure that its diagnostic system was as good or better than those of other SARS-CoV-2 testing platforms. With great care and attention to lab safety, the team began assembling two parallel workstreams: one a semi-manual method to get going right away and the other a faster, automated, robotic method to transition to when ready.

Soon, patient samples began arriving in the lab to be tested for the presence of genetic material (RNA) from SARS-CoV-2, an indication that a person is infected with the virus. The diagnostic system was also soon humming along, with Doudna’s automated workstream having the capacity to process 384 samples in parallel.

The pop-up lab—known formally as the IGI SARS-CoV-2 Diagnostic Testing Laboratory—is funded through philanthropy and staffed by more than 50 volunteers from IGI, UC Berkeley, UC San Francisco, and local data-management companies. Starting on April 6, the lab was fully operational, capable of running hundreds of tests daily with a 24-hour turnaround time for results. A positive test requires that at least two out of three SARS-CoV-2 genomic targets return a positive signal, and the method uses de-identified barcoded sample data to protect patient privacy.

Doudna intends to keep the pop-up lab open as long as her community needs it. So far, they’ve provided testing to UC Berkeley students and staff, first responders (including the entire Berkeley Fire Department), and several members of the city’s homeless population. She says that availability of samples will soon be the rate-limiting step in their sample-analysis pipeline and hopes continued partnerships with local health officials will enable them to work at full capacity to deliver thousands of test results rapidly.

Doudna says she’s been amazed by the team spirit of her lab members and other local colleagues who have come together around a crisis. They’ve gotten the job done by contributing their different skills and resources, including behind-the-scenes efforts by the university’s leadership and staff, philanthropists, city officials, and state government workers.

Although Doudna and her team intend to publish their work to help others follow suit [1], she says the experience has also provided her with many intangible rewards. It has highlighted the value of resilience and adaptation, as well as given her a newfound appreciation for the complexity and precision of operations in the commercial clinical labs that are a routine part of our medical care.

Although the COVID-19 pandemic seems to have thrust all of us into a time warp, in which weeks sometimes feel like months, there is much to do. The amount of work needed to tame this virus is significant and requires an all-hands-on-deck mentality, which NIH and the biomedical research community have embraced fully.

Doudna is not alone. Other labs around the country are engaged in similar efforts. At the NIH’s main campus in Bethesda, MD, staff at the clinical laboratory in the Clinical Center rapidly set up testing for SARS-CoV-2 RNA, and have now tested more than 1,000 NIH staff. Researchers at the Broad Institute of MIT and Harvard partnered with the city of Cambridge, MA, to pilot COVID-19 surveillance in homeless shelters and skilled nursing and assisted living facilities located there.

Hats off to everyone who goes the extra mile to get us through this tough time. I am so gratified when, guided by compassion and dogged determination of the human spirit, science leads the way and provides much needed hope for our future.

Reference:

[1] Blueprint for a Pop-up SARS-CoV-2 Testing Lab. Innovative Genomics Institute SARS-CoV-2 Testing Consortium, Hockemeyer D, Fyodor U, Doudna JA. 2020. medRxiv. Preprint posted on April 12, 2020.

Links:

Coronavirus (COVID-19) (NIH)

CLIA Law & Regulations (Centers for Disease Control and Prevention)

Innovative Genomic Institute (Berkeley, CA)

Doudna Lab (University of California, Berkeley)


Testifying in Congress During a Pandemic

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I testified before the Senate Committee on Health, Education, Labor, and Pensions as part of a hearing titled “Shark Tank: New Tests for COVID-19.” Also testifying was Gary Disbrow (left), Office of the Assistant Secretary for Preparedness and Responses, U.S. Department of Health and Human Services. We started the hearing wearing masks. But due to some technical difficulties with the sound system, we removed them to elevate our voices, while maintaining good physical distancing. I then presented some of the inspiring efforts now underway to combat the novel coronavirus. That includes the recently launched Rapid Acceleration of Diagnostics (RADx) Initiative and its national technology development competition to increase our nation’s testing capacity. This “shark tank”-like competition is now encouraging science and engineering’s most inventive minds to develop rapid, easy-to-use technologies to test for the presence of SARS-CoV-2. The hearing was held on May 7, 2020 in the Dirksen Senate Office Building, Washington, D.C. Credit: United States Senate


Study Finds Nearly Everyone Who Recovers From COVID-19 Makes Coronavirus Antibodies

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Credit: NIH

There’s been a lot of excitement about the potential of antibody-based blood tests, also known as serology tests, to help contain the coronavirus disease 2019 (COVID-19) pandemic. There’s also an awareness that more research is needed to determine when—or even if—people infected with SARS-CoV-2, the novel coronavirus that causes COVID-19, produce antibodies that may protect them from re-infection.

A recent study in Nature Medicine brings much-needed clarity, along with renewed enthusiasm, to efforts to develop and implement widescale antibody testing for SARS-CoV-2 [1]. Antibodies are blood proteins produced by the immune system to fight foreign invaders like viruses, and may help to ward off future attacks by those same invaders.

In their study of blood drawn from 285 people hospitalized with severe COVID-19, researchers in China, led by Ai-Long Huang, Chongqing Medical University, found that all had developed SARS-CoV-2 specific antibodies within two to three weeks of their first symptoms. Although more follow-up work is needed to determine just how protective these antibodies are and for how long, these findings suggest that the immune systems of people who survive COVID-19 have been be primed to recognize SARS-CoV-2 and possibly thwart a second infection.

Specifically, the researchers determined that nearly all of the 285 patients studied produced a type of antibody called IgM, which is the first antibody that the body makes when fighting an infection. Though only about 40 percent produced IgM in the first week after onset of COVID-19, that number increased steadily to almost 95 percent two weeks later. All of these patients also produced a type of antibody called IgG. While IgG often appears a little later after acute infection, it has the potential to confer sustained immunity.

To confirm their results, the researchers turned to another group of 69 people diagnosed with COVID-19. The researchers collected blood samples from each person upon admission to the hospital and every three days thereafter until discharge. The team found that, with the exception of one woman and her daughter, the patients produced specific antibodies against SARS-CoV-2 within 20 days of their first symptoms of COVID-19.

Meanwhile, innovative efforts are being made on the federal level to advance COVID-19 testing. The NIH just launched the Rapid Acceleration of Diagnostics (RADx) Initiative to support a variety of research activities aimed at improving detection of the virus. As I recently highlighted on this blog, one key component of RADx is a “shark tank”-like competition to encourage science and engineering’s most inventive minds to develop rapid, easy-to-use technologies to test for the presence of SARS-CoV-2.

On the serology testing side, the NIH’s National Cancer Institute has been checking out kits that are designed to detect antibodies to SARS-CoV-2 and have found mixed results. In response, the Food and Drug Administration just issued its updated policy on antibody tests for COVID-19. This guidance sets forth precise standards for laboratories and commercial manufacturers that will help to speed the availability of high-quality antibody tests, which in turn will expand the capacity for rapid and widespread testing in the United States.

Finally, it’s important to keep in mind that there are two different types of SARS-CoV-2 tests. Those that test for the presence of viral nucleic acid or protein are used to identify people who are acutely infected and should be immediately quarantined. Tests for IgM and/or IgG antibodies to the virus, if well-validated, indicate a person has previously been infected with COVID-19 and is now potentially immune. Two very different types of tests—two very different meanings.

There’s still a way to go with both virus and antibody testing for COVID-19. But as this study and others begin to piece together the complex puzzle of antibody-mediated immunity, it will be possible to learn more about the human body’s response to SARS-CoV-2 and home in on our goal of achieving safe, effective, and sustained protection against this devastating disease.

Reference:

[1] Antibody responses to SARS-CoV-2 in patients with COVID-19. Long QX, Huang AI, et al. Nat Med. 2020 Apr 29. [Epub ahead of print]

Links:

Coronaviruses (NIH)

NIH Begins Study to Quantify Undetected Cases of Coronavirus Infection,” NIH News Release, April 10, 2020.

NIH mobilizes national innovation initiative for COVID-19 diagnostics,” NIH News Release, April 29, 2020.

Policy for Coronavirus Disease-2019 Tests During the Public Health Emergency (Revised), May 2020 (Food and Drug Administration)


Rising to the COVID-19 Challenge: Rapid Acceleration of Diagnostics (RADx)

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NIH Rapid Acceleration of Diagnostics (RADx) Initiative for COVID-19
Credit: NIH

Step into any major medical center, and you will see the amazing power of technology at work. From X-rays to functional MRIs, blood typing to DNA sequencing, heart-lung machines to robotic surgery, the progress that biomedical technology has made over the past century or so stands as a testament to human ingenuity—and its ability to rise to the all-important challenge of saving lives and improving health.

Today, our nation is in the midst of trying to contain a most formidable health threat: the global coronavirus disease 2019 (COVID-19) pandemic. I’m convinced that biomedical technology has a vital role to play in this urgent effort, which is why the NIH today launched the Rapid Acceleration of Diagnostics (RADx) Initiative.

Fueled by a bold $1.5 billion investment made possible by federal stimulus funding, RADx is an urgent call for science and engineering’s most inventive and visionary minds—from the basement to the board room—to develop rapid, easy-to-use testing technologies for SARS-CoV-2, the novel coronavirus that causes COVID-19. To achieve this, NIH will work closely with our colleagues at the Biomedical Advanced Research and Development Authority, the Centers for Disease Control and Prevention, and the Food and Drug Administration.

If all goes well, RADx aims to support innovative technologies that will make millions more rapid SARS-CoV-2 tests available to Americans by late summer or fall. Such widespread testing, which will facilitate the speedy identification and quarantine of infected individuals and their contacts, will likely be a critical component of making it possible for Americans to get safely back into public spaces, including returning to work and school.

For history buffs and tech geeks, the RADx acronym might ring a bell. During the World War II era, it was the brainstorming of MIT’s “Rad Lab” that gave birth to radar—a groundbreaking technology that, for the first time, enabled humans to use radio waves to “see” planes, storm systems, and many other things. Radar played such a valuable role in finding bombing targets, directing gunfire, and locating enemy aircraft, ships, and artillery that some have argued that this technology actually won the war for the U.S. and its Allies.

As for NIH’s RADx, our aim is to speed the development and commercialization of tests that can rapidly “see” if people have been infected with SARS-CoV-2 with very high sensitivity and specificity, meaning there would be few false negatives and false positives. A key part of this effort, which started today, will be a national technology development competition that’s open to all comers. In this competition, which begins a bit like a “shark tank,” participants will vie for an ultimate share of an approximately $500 million fund that will be awarded to help advance the most-promising testing technologies.

The proposals will undergo an initial review for technical, clinical, commercial, and regulatory issues. For example, could the testing technology be easily scaled up? Would it provide clear advantages over existing approaches? And would the U.S. health-care system realistically be able to adopt the technology rapidly? If selected, the proposals will then enter a three-phase process that will run into summer. Each development team will receive its own initial budget, deadlines, and set of deliverables. Competitors must also work collaboratively with an assigned expert and utilize associated web-based tools.

As you see in the graphic above, each phase will whittle down the competition. Those testing technologies that succeed in making it to Phase 2 will receive an appropriate budget to enable full clinical deployment on an accelerated timeline. They will also be matched with technical, business, and manufacturing experts to boost their chances of success.

Of course, not all technologies will enter the competition at the same stages of development. Those that are already relatively far along will be “fast tracked” to a phase that corresponds with their place in the commercialization process. Our hope is that the winning technologies will feature patient- and user-friendly designs, mobile-device integration, affordable cost, and increased accessibility, for use at the point of care (or even at home).

To assist competitors in their efforts to accomplish these bold goals, RADx will expand the Point-of-Care Technologies Research Network, which was established several years ago by NIH’s National Institute of Biomedical Imaging and Bioengineering (NIBIB). The network supports hundreds of investigators through five technology hubs at: Emory University/Georgia Institute of Technology, Atlanta; Johns Hopkins University, Baltimore; Northwestern University, Evanston, IL; University of Massachusetts Medical School, Worcester; and the Consortia for Improving Medicine with Innovation & Technology at Harvard Medical School/Massachusetts General Hospital, Boston.

RADx is focused on diagnostic testing, but NIH is also intensely engaged in developing safe, effective therapies and vaccines for COVID-19. One innovative effort, called Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV), is a public-private partnership that aims to speed the development of ways to treat and prevent this disease that’s caused so much suffering and death around the globe.

So, to the U.S. science and engineering community, I have these words: Let’s get going—our nation has never needed your skills more!

Links:

Coronavirus (COVID-19) (NIH)

NIH mobilizes national innovation initiative for COVID-19 diagnostics, NIH news release, April 29, 2020

Point-of-Care Technologies Research Network (National Institute of Biomedical Imaging and Biotechnology/NIH)

NIH to launch public-private partnership to speed COVID-19 vaccine and treatment options, NIH news release, April 17, 2020.

We Need More COVID-19 Tests. We Propose a ‘Shark Tank’ to Get There, Lamar Alexander, Roy Blunt. Washington Post, April 20, 2020.


The Challenge of Tracking COVID-19’s Stealthy Spread

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Floating SARS-CoV-2 particles
Credit: CDC/ Alissa Eckert, MS; Dan Higgins, MAMS

As our nation looks with hope toward controlling the coronavirus 2019 disease (COVID-19) pandemic, researchers are forging ahead with efforts to develop and implement strategies to prevent future outbreaks. It sounds straightforward. However, several new studies indicate that containing SARS-CoV-2—the novel coronavirus that causes COVID-19—will involve many complex challenges, not the least of which is figuring out ways to use testing technologies to our best advantage in the battle against this stealthy foe.

The first thing that testing may help us do is to identify those SARS-CoV-2-infected individuals who have no symptoms, but who are still capable of transmitting the virus. These individuals, along with their close contacts, will need to be quarantined rapidly to protect others. These kinds of tests detect viral material and generally analyze cells collected via nasal or throat swabs.

The second way we can use testing is to identify individuals who’ve already been infected with SARS-CoV-2, but who didn’t get seriously ill and can no longer transmit the virus to others. These individuals may now be protected against future infections, and, consequently, may be in a good position to care for people with COVID-19 or who are vulnerable to the infection. Such tests use blood samples to detect antibodies, which are blood proteins that our immune systems produce to attack viruses and other foreign invaders.

A new study, published in Nature Medicine [1], models what testing of asymptomatic individuals with active SARS-CoV-2 infections may mean for future containment efforts. To develop their model, researchers at China’s Guangzhou Medical University and the University of Hong Kong School of Public Health analyzed throat swabs collected from 94 people who were moderately ill and hospitalized with COVID-19. Frequent in-hospital swabbing provided an objective, chronological record—in some cases, for more than a month after a diagnosis—of each patient’s viral loads and infectiousness.

The model, which also factored in patients’ subjective recollections of when they felt poorly, indicates:

• On average, patients became infectious 2.3 days before onset of symptoms.
• Their highest level of potential viral spreading likely peaked hours before their symptoms appeared.
• Patients became rapidly less infectious within a week, although the virus likely remains in the body for some time.

The researchers then turned to data from a separate, previously published study [2], which documented the timing of 77 person-to-person transmissions of SARS-CoV-2. Comparing the two data sets, the researchers estimated that 44 percent of SARS-CoV-2 transmissions occur before people get sick.

Based on this two-part model, the researchers warned that traditional containment strategies (testing only of people with symptoms, contact tracing, quarantine) will face a stiff challenge keeping up with COVID-19. Indeed, they estimated that if more than 30 percent of new infections come from people who are asymptomatic, and they aren’t tested and found positive until 2 or 3 days later, public health officials will need to track down more than 90 percent of their close contacts and get them quarantined quickly to contain the virus.

The researchers also suggested alternate strategies for curbing SARS-CoV-2 transmission fueled by people who are initially asymptomatic. One possibility is digital tracing. It involves creating large networks of people who’ve agreed to install a special tracing app on their smart phones. If a phone user tests positive for COVID-19, everyone with the app who happened to have come in close contact with that person would be alerted anonymously and advised to shelter at home.

The NIH has a team that’s exploring various ways to carry out digital tracing while still protecting personal privacy. The private sector also has been exploring technological solutions, with Apple and Google recently announcing a partnership to develop application programming interfaces (APIs) to allow voluntary digital tracing for COVID-19 [3], The rollout of their first API is expected in May.

Of course, all these approaches depend upon widespread access to point-of-care testing that can give rapid results. The NIH is developing an ambitious program to accelerate the development of such testing technologies; stay tuned for more information about this in a forthcoming blog.

The second crucial piece of the containment puzzle is identifying those individuals who’ve already been infected by SARS-CoV-2, many unknowingly, but who are no longer infectious. Early results from an ongoing study on residents in Los Angeles County indicated that approximately 4.1 percent tested positive for antibodies against SARS-CoV-2 [4]. That figure is much higher than expected based on the county’s number of known COVID-19 cases, but jibes with preliminary findings from a different research group that conducted antibody testing on residents of Santa Clara County, CA [5].

Still, it’s important to keep in mind that SARS-CoV-2 antibody tests are just in the development stage. It’s possible some of these results might represent false positives—perhaps caused by antibodies to some other less serious coronavirus that’s been in the human population for a while.

More work needs to be done to sort this out. In fact, the NIH’s National Institute of Allergy and Infectious Diseases (NIAID), which is our lead institute for infectious disease research, recently launched a study to help gauge how many adults in the U. S. with no confirmed history of a SARS-CoV-2 infection have antibodies to the virus. In this investigation, researchers will collect and analyze blood samples from as many as 10,000 volunteers to get a better picture of SARS-CoV-2’s prevalence and potential to spread within our country.

There’s still an enormous amount to learn about this major public health threat. In fact, NIAID just released its strategic plan for COVID-19 to outline its research priorities. The plan provides more information about the challenges of tracking SARS-CoV-2, as well as about efforts to accelerate research into possible treatments and vaccines. Take a look!

References:

[1] Temporal dynamics in viral shedding and transmissibility of COVID-19. He X, Lau EHY, Wu P, Deng X, Wang J, Hao X, Lau YC, Wong JY, Guan Y, Tan X, Mo X, Chen Y, Liao B, Chen W, Hu F, Zhang Q, Zhong M, Wu Y, Zhao L, Zhang F, Cowling BJ, Li F, Leung GM. Nat Med. 2020 Apr 15. [Epub ahead of publication]

[2] Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. Li, Q. et al. N. Engl. J. Med. 2020 Mar 26;382, 1199–1207.

[3] Apple and Google partner on COVID-19 contact tracing technology. Apple news release, April 10, 2020.

[4] USC-LA County Study: Early Results of Antibody Testing Suggest Number of COVID-19 Infections Far Exceeds Number of Confirmed Cases in Los Angeles County. County of Los Angeles Public Health News Release, April 20, 2020.

[5] COVID-19 Antibody Seroprevalence in Santa Clara County, California. Bendavid E, Mulaney B, Sood N, Sjah S, Ling E, Bromley-Dulfano R, Lai C, Saavedra-Walker R, Tedrow J, Tversky D, Bogan A, Kupiec T, Eichner D, Gupta R, Ioannidis JP, Bhattacharya J. medRxiv, Preprint posted on April 14, 2020.

Links:

Coronavirus (COVID-19) (NIH)

COVID-19, MERS & SARS (NIAID)

NIAID Strategic Plan for COVID-19 Research, FY 2020-2024

NIH Support: National Institute of Allergy and Infectious Diseases