Discovering our way out

With cases of COVID-19 exploding at the beginning of 2020, scientists at Stanford Medicine and around the globe veered onto new research paths. Their purpose: to understand and stop the spread of SARS-CoV-2, the coronavirus that causes COVID-19. Hundreds of COVID-19-related projects have emerged across Stanford’s campus.

Between scientists harnessing their expertise — such as those in Stanford’s clinical virology laboratory who devised an early in-house diagnostic test for COVID-19 — and scientists developing new skills to help combat the virus, the research community is pulling out all the stops.

Lawrence “Rusty” Hofmann, for instance, is a radiologist by trade, but was dismayed by an epidemiological problem: Nationally, COVID-19 testing rates were too low to indicate the ebb and flow of the virus at the local level.

So he created a method of predicting hot spots of COVID-19 through a project called the National Daily Health Survey, which tracks responses from people throughout the country about their health and whether they have symptoms of the virus.

“In the time that I’ve been at Stanford, I don’t think I’ve ever seen such a large group of people come together with a singular purpose,” said Euan Ashley, MD, DPhil, associate dean of precision health. “It’s been an incredible effort to be part of.”

Alongside Stanford, philanthropies, including the Gates Foundation; the National Institutes of Health; and companies Illumina and Takeda are supporting some of these research projects — just an example of the multibillion-dollar pool of funds that have been allocated to COVID-19 research and relief across the country.

It’s not just labs that are switching course, either. A university effort called the Innovative Medicines Accelerator, intended to help researchers overcome obstacles in developing new therapeutic drugs, has shifted goals and is now boosting nascent COVID-19 projects.

Beyond bench research and epidemiology, Stanford physicians were among the first to participate in clinical trials for COVID-19 treatments, helping to establish the efficacy of remdesivir, a go-to therapeutic for treating the virus. Physicians and clinical scientists are also investigating whether other drugs, such as lambda interferon and favipiravir, expedite patient recovery and slow the disease’s spread.

Here’s a small sample of Stanford researchers’ many efforts targeting COVID-19.

CRISPR-based nasal spray or inhalational therapy to fight COVID-19

Researchers are using the CRISPR gene-editing system to inhibit the replication of the virus that causes COVID-19.

Why it matters: A single dose of a nasal spray could provide weeks of protection from acquiring COVID-19; in patients who already have COVID-19 pneumonia, an inhaled version could help treat the infection.Timeline: It’s in early development — a trial in humans is likely two or more years away.

Four bioengineers are laying the groundwork for a rather futuristic approach for preventing COVID-19 infection: a nasal spray that harnesses a form of CRISPR that can be programmed to target any virus. The technique aims to arm the body with the ability to stunt infection caused by a range of coronaviruses, including SARS-CoV-2, serving much the same purpose as a vaccine or as a treatment for pneumonia.

A typical vaccine works by priming the host’s immune system with molecules that recognize and attack a specific viral intruder. The CRISPR-based tactic turns that approach on its head, directly targeting the virus instead of revving up host immunity. The team is using a special CRISPR system that deploys a molecule called Cas13D that “digests” or cuts other RNA molecules.

It’s also equipped with something called a guide, which helps it target the exact molecules to snip. The idea is to use Cas13D as a first line of defense for the body. In essence, Cas13D would act like a vicious bouncer, stopping the virus from replicating in the host cells it enters by chopping it into tiny pieces.

For now, because tampering with SARS-CoV-2 in the lab requires special clearance, the team is establishing the validity of their approach using coronaviruses that cause common colds.

“The great thing is, coronaviruses across the board tend to interact with the host’s cells and immune system in a fairly predictable manner,” said David Lewis, MD, a professor of pediatrics, immunology and allergy who’s leading the project with Stanley Qi, PhD, assistant professor of bioengineering and of chemical and systems biology, and Marie LaRussa, PhD, a senior research scientist in the Qi laboratory.

“So if we can get this to effectively block the replication of coronaviruses that cause the common cold, for example, it will be a big step in developing this as a prophylactic or treatment for SARS-CoV-2.”

A new role for lambda interferon

Researchers are focusing drug development efforts on patients who are not severely ill in the hopes that these therapeutics will keep them out of the hospital.

Why it matters: Lambda interferon might help patients with mild-to-moderate disease recover more quickly and keep them out of the hospital.

Timeline: A clinical trial is underway.

It’s sensible that the majority of early drug-development efforts against COVID-19, such as studies of remdesivir, were geared toward severe infection. But Upinder Singh, MD, professor of medicine and of microbiology and immunology, and Prasanna Jagannathan, MD, assistant professor of medicine and of microbiology and immunology, are targeting the opposite end of the disease spectrum.

Through a clinical trial at Stanford’s COVID-19 clinical trials research unit, Singh and Jagannathan are studying the efficacy of a long-used hepatitis drug known as lambda interferon in patients with COVID-19 who have mild to moderate symptoms.

Many efforts have focused on hospitalized patients. “We of course need to help the critically ill patients, but if you think about COVID-19 infection, 80% are outpatients, and those patients are still suffering — and they’re continuing to shed the virus,” said Singh.

“So we wanted to focus on the 80% of people who get mild-to-moderate disease, with the goal of finding drugs that would help people feel better, help avoid hospitalization and limit spread.”

Lambda interferon, a molecule naturally produced by the body, has been safely used to treat thousands of patients with hepatitis infections. It’s a compound that’s naturally released when a virus enters the body, orchestrating other molecules and cells involved in immune function. Essentially, it helps the body gird itself against the intruder.

“It’s sort of like, if the virus is a burglar about to enter a home, lambda interferon is the one locking the doors, turning the lights on and getting the dog,” said Singh.

In Singh’s trial, researchers are testing what happens when the body is given an extra boost, with the goal of catching the infection early and containing it, thereby heading off what could turn into more severe illness and enabling the patient to recuperate at home.

The researchers aim to enroll 120 patients with early, mild-to-moderate COVID-19 infection in the study, which began in April. A randomly selected half of the patients will receive a single injection of lambda interferon, while the other half will receive a placebo — and neither patient nor doctor will know who’s received what.

“We’re going to have to live with this virus for some time and there really isn’t one golden solution,” said Singh. “In addition to vaccine development, social distancing, sheltering in place, masks and hand hygiene, I’m hopeful that this therapy can work in an outpatient setting and help us get back a semblance of normal life.”

Swabbing the Bay Area

Scientists have investigated new ways to test for COVID-19 in the hopes that less invasive do-it-yourself nasal swabs will expand testing.

Why it’s important: Expanded testing is critical and still needed.

Timeline: Scientists plan to launch a pilot project in the near future that will allow individuals to swab themselves for SARS-CoV-2 and send their samples in for testing.

Often, the test for a current COVID-19 infection is administered via a swab going deep into the nose, all the way to the back of the throat. Some describe the sensation as akin to “probing your brain.”

Yvonne Maldonado, MD, is more nonchalant. “I’ve had it done,” said Maldonado, professor of pediatric infectious diseases and of health research and policy. “It’s not pleasant but it’s not horrible either.”

This procedure, called a nasopharyngeal swab, and an alternative, an oropharyngeal swab, that reaches a similar area via the mouth, are generally performed by a health care worker. The cells they collect are then processed and tested for the presence of SARS-CoV-2.

Aside from the discomfort, said Maldonado, these methods of testing for SARS-CoV-2 have a few other problems: Deep probing can elicit big coughs or sneezes, potentially expelling droplets of the virus and exposing health care workers to infection; and the need for staff to conduct the test limits how many tests can be done. It’s also not clear that a deep sampling method is the most reliable way to detect this virus.

So Maldonado and her colleagues posed a new question: Could people take their own samples using a more shallow, less irritating swab of the nostril and get accurate results?

Such an approach, if as effective as deep swabs collected by health professionals, could open up new research avenues and lead to more abundant testing, something the United States still sorely needs, said Maldonado.

The team conducted a study, published June 12 in the Journal of the American Medical Association, comparing the accuracy of self-collected nostril swabs and health care worker-collected oropharyngeal swabs. For 29 of the 30 participants in the study, the accuracy of the shallow swab method was as trustworthy as that of the more invasive test. In theory, folks at home could effectively swab themselves while sparing the tender parts of their sinuses.

The win for self-swabbing has boosted an offshoot project of Maldonado’s dubbed CATCH, for community alliance to test coronavirus at home. The goal is to facilitate widespread testing in the San Francisco Bay Area through kits that can be ordered online and sent to individuals by mail.

“The initial goal is to have thousands of people in the Bay Area order and perform these tests, then send them to labs,” said Maldonado. “We’re starting with this pilot project, but the eventual goal is to have this running across the country.”

‘Mini lung’ organoid models boost scientists’ understanding of COVID-19

Using miniature, living models of the human lung, researchers are parsing the details of COVID-19 infection.

Why it matters: Researchers get a more accurate look into how the virus infects the lungs.

Timeline: The technique is in an early phase of development but researchers are already using it to investigate SARS-CoV-2.

There’s no better way to research the effects of a virus than to go directly to its breeding ground; for COVID-19 that means the lungs. And since opening the chest of those infected just to study the virus is not an option, scientists need a way to investigate the novel coronavirus as it exists “in the wild,” or at least close to it.

Enter the organoid — a lab-made, miniature replica of a human organ that closely recapitulates the organ’s biological function, including what happens when a virus compromises its health. Calvin Kuo, MD, PhD, professor of medicine, is an organoid guru. As good fortune would have it, when the COVID-19 pandemic erupted he and his team had just grown a successful lung organoid, something that’s proved finicky and challenging to scientists in the past.

“SARS-CoV-2 became the most pressing virus on the planet and we quickly realized that we had an opportunity, really an obligation, to create a model of COVID-19 lung infection in the lab to be able to better understand the virus,” said Kuo, the Maureen Lyles D’Ambrogio Professor of Medicine.

In collaboration with Catherine Blish, MD, PhD, associate professor of medicine, and Manuel Amieva, MD, professor of pediatrics and of microbiology and immunology, the trio of scientists have done just that.

By infecting the lung organoids, which Kuo fondly deems “mini lungs,” with SARS-CoV-2, the team is studying how the virus infiltrates and damages healthy lung tissue and is testing the efficacy of new drugs or preventive treatments.

The researchers have now successfully infected the cells lining the deepest tubes within the lungs, and the air sacs at the end of these tubes, with live SARS-CoV-2 virus. The team was able to see this phenomenon using a laboratory technique developed by Amieva’s group that literally flips the organoid model inside out, thereby exposing the tissue that’s most susceptible to infection. “Think of it like exposing the insides of a pair of tube socks,” said Kuo.

The researchers are still exploring the genetic pathways that are activated during infection, specifically as they relate to the immune system. In particular, they’re interested in a phenomenon called a “cytokine storm,” which occurs in some COVID-19 cases and can lead to death.

During this flurry of activity, a variety of immune molecules are unleashed, which may sound like extra protection, but instead overwhelms the body in an onslaught of molecular destruction.

Addressing an unequal burden of COVID-19

Scientists are creating new data hubs to track regional prevalence of COVID-19 and buttress communities disproportionately affected by the pandemic.

Why it matters: Under-resourced communities are at a higher risk for COVID-19, and deeper data analysis could help guide resource allocation and community-level responses.

Timeline: The tool is in early stages of development, estimated to be ready for launch later this year.

As the coronavirus continues to spread, it’s clear that some people, including those working in the service industry or living in lower-income and high-density neighborhoods and communities, are at a much higher risk for infection, in part because it’s difficult to separate themselves from other people. In addition, if they have limited access to health care and become ill, they have a higher risk of developing serious symptoms.

A team of researchers launched an effort — a “geospatial data ecosystem” — to identify the social and demographic factors in California counties that play into an elevated risk of SARS-CoV-2 infection, and to pinpoint and predict geographic hotspots of infection. The team is collaborating with Google Cloud to build the data platform, which will help them collect de-identified COVID-19 case data and rich census data at the neighborhood level — detailing the social, occupational, environmental and medical factors that contribute to greatest risk.

“More data leads to a clearer understanding of the social drivers of risk for this virus. We can use the insights gained to direct interventions in the neighborhoods that need it most,” said Lorene Nelson, PhD, associate professor of epidemiology and population health, who is co-leading the project with David Rehkopf, ScD, associate professor of medicine, and Melissa Bondy, PhD, professor and chair of the Department of Epidemiology and Population Health.

Their project is still in its early days, so potential interventions remain to be developed. But possibilities include structural or behavioral interventions, including physical distancing or mask-wearing, to reduce risk of infection in public settings, as well as working with community organizations to address the adverse psychosocial and economic impact on disproportionately affected communities.

“Ultimately, we see this platform as a versatile tool to gain near real-time insights to create a wide range of county-level resources, such as culturally sensitive engagement strategies to increase testing and reduce the barriers to vaccination once a COVID-19 vaccine becomes available,” Nelson said.

Safer, more accessible breathing-based diagnostics

Scientists are trying to see if a simple lung function test can identify those with COVID-19, determine severity of disease and protect healthcare workers from exhaled particles.

Why it’s necessary: A standard lung function test can be difficult for people with breathing problems to carry out and can lead people with COVID-19 to expel viral particles into the air, raising the risk of infection for others.

Timeline: The research is still early in its development — in a proof-of-principle phase.

As a pulmonary pediatrician, Carlos Milla, MD, spends a lot of time thinking about how to make breathing tests easier and faster for squirming kids with little lungs. Before the pandemic, Milla, professor of pediatrics, was working on a new lung function test for small children and babies who have trouble huffing and puffing for standard pulmonary tests. But safety concerns shut down his research as coronavirus cases exploded around the world.

“It occurred to me that our test could serve another purpose — potentially helping both patients and health care workers,” said Milla.

Normal pulmonary tests that evaluate lung function involve a deep and forceful inhalation and exhalation. That’s problematic for COVID-19 patients for two reasons. Forceful exhalation of viral particles into the air puts health care workers and staff at higher risk of infection, even when they’re using personal protective equipment. Also, sick patients with lung problems aren’t always strong enough to inhale and exhale the air necessary for an effective evaluation.

Milla’s new test would allow people to breathe normally, decreasing the risk of spreading the virus and increasing utility among all patients, even those with respiratory symptoms, such as shortness of breath.

The test works by measuring the force, duration and other characteristics of an individual’s normal breathing. COVID-19 infection changes these parameters in very specific ways, said Milla, allowing clinicians to detect certain breathing-associated details that indicate infection, such as lung tissue stiffness.

In a small pilot group of COVID-19 patients, Milla has shown that the passive breathing test can detect lung abnormalities, and it works for virtually any patient — even people with pulmonary symptoms so severe they require extra oxygen. What’s more, almost no extraneous viral particles are exhaled into the open air in the process.

It will take many more patients with varying levels of COVID-19 severity to validate the test and its utility, said Milla. And although a larger study is not yet planned, he hopes the test could be used to predict severity of disease in patients, and as a screening tool to initially detect COVID-19, even in people who have the virus but have no symptoms.

In addition, the team plans to study whether the passive breathing test can detect who is at a higher risk for severe infection, based on readouts of lung function such as a constricted airway or tissue stiffness.

Using genetic clues to understand COVID-19 disease severity

Using genetic information from people who’ve had COVID-19 and from the virus itself, researchers aim to understand the range of symptom severity in COVID-19, as well as who may be most at risk for the disease.

Why it matters: There is a huge range in disease severity in patients with COVID-19.

Timeline: The work is underway, with early findings published online in a preprint study.

Although Euan Ashley is a geneticist and cardiologist by trade, he and a team of researchers are taking on perhaps the biggest conundrum facing virology today.

“From the earliest days of the pandemic, we’ve seen this unexplained range of responses to SARS-CoV-2, regardless of age,” said Ashley, professor of cardiovascular medicine, of genetics and of biomedical data sciences. For some people, the disease is lethal; some patients experience nothing more than a slight cough; and still others don’t even know they’re infected. “It’s a mystery that needs to be solved.”

Understanding who might be at a greater risk for severe illness is critical for individuals making decisions about their own health and for hospitals preparing for an influx of patients.

In collaboration with Chan Zuckerberg Biohiub, Ashley, along with Carlos Bustamante, PhD, professor of biomedical data science and of genetics; Matthew Wheeler, MD, assistant professor of medicine; Manuel Rivas, PhD, assistant professor of biomedical data science; and Victoria Parikh, assistant professor of medicine, turned to what they know: genomic sequencing.

Their technique uses cells collected through a nasal swab from patients with COVID-19 and analyzes the DNA (from the human host) and RNA (from the virus). The goal is to provide a window into a few things: how patients’ bodies respond on a molecular level to the viral attack; what, if anything, about their genetics might predispose them to a particular response to SARS-CoV-2; and how the virus interacts with human cells to incite damage.

“Understanding how the virus works on a basic level is a big part of being able to work out solutions,” said Ashley.

Rethinking travel: COVID-free flights and quarantine

To jump-start the economy, researchers consider travel norms, starting with international flights.

Why it matters: Limiting air travel is a personal hardship for many individuals and a blow to the economy.

Timeline: This study is postponed until logistics are worked out between the United States and Taiwan.

Travel has taken a huge hit during the pandemic, as people tend to think of planes as 30,000 mile-high incubators for COVID-19.

Jason Wang, MD, PhD, associate professor of pediatrics, hopes there’s a way to bring back travel — particularly international flights — with minimal spread of disease. He and his colleagues are preparing to conduct a study that evaluates a number of parameters related to taking to the skies during a pandemic, including how long someone traveling from another country should quarantine after they arrive in a new place.

Standard guidelines suggest two weeks for individuals who may have been exposed to SARS-CoV-2 — but Wang wondered if there might be a way for the guidelines to be less stringent for people who have tested negative for the virus and have limited their exposure to potential sources of infection.

His vision — which he admits would require a few big policy changes and would depend on testing capacity — looks something like this: Within 72 hours before their flight, the passengers would be tested for the virus, and when given the all-clear, would board a COVID-19-free plane, still taking precautions such as wearing a mask. Upon landing, passengers would isolate in a sanctioned area for a certain number of days to ensure no symptoms develop.

This is where Wang’s experiment comes in. Instead of blindly choosing the two-week quarantine period, Wang hopes to use experimental data to reset the time frame for travelers who don’t have COVID-19. For now, Wang said, the experiment is on hold until testing and quarantine logistics are worked out in Taiwan.

“Recent data has shown that most people are infectious a few days before the symptoms set in, and then about five days after; however, some people harboring the virus have no symptoms and can still be infectious. In either case, we’re talking about a one-week period when people who do have the disease are most infectious,” said Wang.

He and his colleagues plan to conduct a study that flies individuals from San Francisco to Taiwan on COVID-19-negative flights. Once they land, the participants would be quarantined and tested every day for two weeks to better elucidate when symptoms crop up and the duration for which most people need to be secluded to ensure they’re not sick or infectious.

“Our goal is not to say, ‘Here’s the length of time that a country should quarantine new arrivals.’ Our goal is to provide the data upon which governments can make informed decisions about policy,” said Wang. “Maybe they still administer testing, or maybe they ask foreign travelers to report on their symptoms every day — it’s up to the individual country to decide how to handle travel policies.”