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NIH Clinical Center

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)


Letting Sleeping Dogs Lie

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I got to let several sleeping dogs lie during NIH’s “Puppycam” event, which was recently livestreamed on social media. In addition to interacting with these adorable Labrador retriever pups, which will be trained to help people with physical disabilities, including military veterans, the event was a great opportunity to discuss stress reduction, mindfulness, and pet therapy. It was also my pleasure to join in the conversation. Puppycam, held on February 13, 2020 at the NIH Clinical Center, was hosted by NIH and Hero Dogs, Silver Spring, MD.

A New Year’s Moment at NIH Clinical Center

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A New Year's Moment at NIH Clinical Center
To mark the new year, I spent my lunch hour playing the piano for patients, their families, and staff in the atrium of the NIH Clinical Center on January 3, 2020. If you’d like to share in the moment, it ends with Auld Lang Syne. Photo: NIH


Meeting with Congressman Flores

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Representative Flores Visit
I enjoyed spending time with Congressman Bill Flores of Texas (left) during his tour of NIH on September 17, 2019. Here, we talk in the lobby of the NIH Clinical Center with Jim Gilman (right), chief executive officer of the NIH Clinical Center. Credit: NIH.

In Memory of Andrew Lee

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Andrew Lee Composite
Caption: Clockwise from left, Andrew Lee with his Nissan GT-R; Andrew Lee and me; Isaac Barchus with his parents, Steve and Kathe Barchus, and Andrew’s father Bruce Lee. Credits: Driven to Cure, Foundation for the NIH, The Children’s Inn at NIH

A lot of young people are driven—driven to get a good education, land a great job, find true love, or see the world. But, today, I want to honor the life of a young man who was driven by something even bigger. Andrew Lee was driven to cure kidney cancer—not only for himself, but for others as well.

I knew and loved Andrew. And so did the legion of doctors, nurses, researchers, and other team members who had the privilege of fighting cancer with him over four very challenging years. Andrew was 19, just finishing his freshman year of college, when he received a devastating diagnosis: stage 4 kidney cancer, a rare type called Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC). There is no known cure for HLRCC, and doctors estimated his survival at about a year at best.

Still, Andrew and his family weren’t about to go hide somewhere and wait for the end. They began a journey that led him to take part in at least seven clinical trials, including ones at Yale University, New Haven, CT; Georgetown University, Washington, DC; and the NIH Clinical Center, Bethesda, MD. Experimental treatments slowed down the cancer, but sometimes made him terribly sick. Yet, Andrew always remained optimistic and cheerful. If a trial didn’t help him, maybe it would help someone else.

Andrew’s generosity didn’t stop there. Inspired by his father’s gift of a totally awesome 2015 Liberty Walk Nissan GT-R, he founded the Driven To Cure (DTC) nonprofit and traveled the country in his orange sports car to raise funds for kidney cancer research. According to the National Cancer Institute, nearly 63,000 Americans are diagnosed with kidney and renal pelvis cancers each year.

Andrew figured out how to put the “fun” in fundraising, drawing crowds at car shows and raising more than $500,000 in donations in just three years. His efforts were recognized by the Foundation for the NIH’s Charlie Sanders Award, which I had the privilege of presenting to him last fall.

But I think it was Andrew’s humanity that touched us the most. He always had time to share his story, to encourage another child or adult struggling with a frightening diagnosis. He’d give thrills to kids at The Children’s Inn at NIH when he rumbled into the parking lot with his 700 horsepower GT-R. At car shows, throngs of people were drawn in by the turbocharged ride and then captivated by the young man with the bright smile and compelling story. Andrew wrote: “I realized that the vehicle of my dreams was also the vehicle which gave me the opportunity to make a difference; to do something bigger than myself.”

Still, on the personal level, kidney cancer proved relentless. Options for treatment eventually ran out. As the disease progressed, Andrew and his family had to make another difficult transition—choosing to celebrate life, even in the face of its approaching end. He needed a wheelchair, so family and friends came up with one, keeping in mind one of Andrew’s last wishes. When Andrew needed 24-hour care and pain control, he was admitted to the NIH Clinical Center Hospice Unit, where comfort could be provided and his loved ones could gather around. That even included getting government permission for a visit from his dog Milo! Surrounded by friends and family, he died peacefully on April 21.

Andrew made friends with everyone—especially kids at The Children’s Inn. One special buddy was Isaac Barchus, who has a rare autoinflammatory disease called CANDLE Syndrome. When he was back home in Omaha, NE, Isaac enjoyed challenging Andrew to long-distance video games, especially FIFA Soccer.

Although Isaac can walk, it can be very painful, so he sometimes turned to an old, beat-up wheelchair to cover long distances. But not anymore. When Isaac turned 15 on June 7, Andrew’s father Bruce Lee fulfilled his son’s wish for the future of his wheelchair. He presented Isaac with Andrew’s wheelchair, which had now been painted the same orange color as Andrew’s GT-R and emblazoned with the feisty slogan on Andrew’s personalized license plate—F CANCR. What a cool birthday gift!

During his final weeks and days, Andrew and his dad often listened to the Andy Grammer song, “Don’t Give Up on Me.” Andrew’s family never gave up on him, and he never gave up on them either. In fact, Andrew never gave up caring, loving, and believing. He wouldn’t want us to either, as his favorite song reminds us: “I will fight, I will fight for you; I always do until my heart is black and blue.”

Yes, Andrew, our hearts are black and blue from losing you. But we won’t give up on all you stood for in your short but inspiring life. Race In Peace, dear Andrew.

Links:

Remembering Andrew Lee (Foundation for the National Institutes of Health)

NIH Cancer Patient Receives Humanitarian Award (The NIH Record)

The Children’s Inn at NIH

Driven To Cure (Silver Spring, MD)

Video: Fighting Cancer With a 700-hp Nissan GT-R (The Drive)

Video: Andy Grammer—”Don’t Give Up On Me” [Official Lyric Video] from the film Five Feet Apart

Hereditary Leiomyomatosis and Renal Cell Cancer (National Library of Medicine/NIH)

Kidney (Renal Cell) Cancer (National Cancer Institute/NIH)

CANDLE Syndrome (Genetic and Rare Diseases Information Center/NIH)

Treating CANDLE Syndrome (National Institute of Allergy and Infectious Diseases/NIH)


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