Searching for Ways to Defeat COVID-19

Researchers developing therapies and vaccines look to find the best paths forward with the help of a Cummings School veterinary pathologist

Extreme closeup of infected tissue. Researchers developing therapies and vaccines look to find the best paths forward against COVID-19 with the help of a Cummings School veterinary pathologist

As health-care workers and scientists scramble to figure out the best ways to treat and stop COVID-19, they face many unknowns about the deadly infection.

How does SARS CoV-2—the virus responsible for the infection—invade the body? How does the immune system respond? Which cells involved in the immune response do a good job of beating back the coronavirus? And which cells, triggered by the immune response, cause potentially life-threatening collateral damage in vital organs and tissue?

“Those are the types of questions that we can really only answer with an animal model,” said Cummings School assistant professor Amanda Martinot.

The problem is there’s currently no known animal model that reflects exactly what is happening in people infected with COVID-19.

To find one in time to help people during this pandemic, Martinot is collaborating with both Dan Barouch—a physician, immunologist, and director of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center and professor of medicine at Harvard Medical School—and Peter Sorger, a professor, systems biologist, and director of the Laboratory of Systems Pharmacology at Harvard Medical School.

Using a $250,000 award from Fast Grants, the researchers are evaluating how studies in primates, ferrets, and hamsters can reveal what the virus is doing in the body over the first seven days of infection with COVID-19.

In a new finding published in Science on May 20, the team showed that monkeys demonstrate key features of human disease, and that those infected with COVID-19 are later protected from re-infection when exposed to the virus again.

After receiving samples from animals that were infected—research that is not done at Cummings School—Martinot examined the organs and tissues, helping the team also investigate many other details about the progression of the disease and the immune system’s response.

Addressing Pressing Questions

Human tissue samples available to study COVID-19 typically can only show what’s happened in the body after a patient has been sick for a month and died from the disease, explained Martinot, a veterinarian-scientist and board-certified veterinary pathologist at Tufts.

“Unfortunately, that information is not really helpful in terms of figuring out what you could have done to help that person four weeks ago,” she said.

However, by analyzing tissue from research animals, scientists can see how the coronavirus attacks and spreads in the body very early in the course of the infection. “We can determine which types of cells are getting infected, and which types of cells are helping fight the infection,” said Martinot.

Researchers can also see how certain cells that are trying to attack the virus might be harming the lung, by producing inflammatory cytokines, she said. In this way, researchers can more quickly identify the human patients most susceptible to life-threatening complications from COVID-19, as well as provide clues for developing new drugs to keep those patients from getting seriously ill.

“My role in this project is to help ask and answer the questions, ‘What do we see in the animals? And does it match what is being described for the human disease?’” Amanda Martinot said.“My role in this project is to help ask and answer the questions, ‘What do we see in the animals? And does it match what is being described for the human disease?’” Amanda Martinot said.
The researchers are looking at animal tissues from two, four, and seven days post-infection. Their study showed that the “two-day time point is absolutely critical in terms of the development of the disease,” said Martinot. 

The research team also is exploring the effects that early viral infection has on different cell types and how cells respond.

The results may show that certain types of cytokines are beneficial “because we know that it can knock down the virus,” said Martinot, while showing that “other cell types that want to help fight the virus are actually causing a lot of inflammation that’s contributing to pathology down the road.”

If researchers can translate that into what is likely happening in humans, they can get information about which pathways they should be targeting to help patients, said Martinot.

The Right Lens

Determining how faithful animal models are to the human condition is Martinot’s job. “My role in this project is to help ask and answer the questions, ‘What do we see in the animals? And does it match what is being described for the human disease?’” she said.

For instance, “doctors are describing patients experiencing thrombosis—little clots that plug up different vessels across the body,” she said. “If you have a plug in your vessels, like what happens in a heart attack, it causes tissue damage that can lead to kidney, liver, or heart failure.”

Thrombosis has been a fatal complication for some COVID-19 patients. “So as I look at various tissues from different animal species, I am looking for evidence of even a very small thrombosis, as this could inform our clinical understanding of what’s happening in those cases,” said Martinot.

Another question the veterinary pathologist hopes to answer is where the virus multiplies in the body when an animal is first infected, and in what particular types of cells.

“Scientists want to know why COVID-19 is so contagious. It is very different than the coronaviruses responsible for SARS and MERS, which in general cause much more severe disease, but are not transmitted nearly as efficiently from person to person,” said Martinot.

“Scientists think COVID-19 must be more efficiently infecting or persisting in nasal passages or upper airway cells in order for people to spread this virus so easily, and I’m looking for evidence of this in the animal samples.”

A Cutting-Edge Approach

Once research samples arrive at Cummings School, Martinot must decide how best to search for the answers the team needs.

“I basically take these larger pieces of tissue and decide how I want to cut them in order to see anything that may be important under a microscope,” she said. “It's like taking a slice from a loaf of bread.”

After Cummings School’s histology lab stains all the samples, Martinot reviews the slides and sends the ones with interesting pathology off to Sorger’s lab at Harvard to be further analyzed using a cutting-edge imaging technique.

In a traditional immunology study, scientists use a process called flow cytometry to determine what cell types are present or absent in tissue under certain conditions. Researchers grind up tissue—be it from the lung, spleen, or gastrointestinal tract—to collect all the cells in the tissue. They then apply various fluorescent antibodies to the cells and determine whether these antibodies bind to cells using a “sorting” machine that examines each cell by flowing in past a set of laser beams.

“This allows the researchers to see what kind of immune cells are present, to determine if they’re responding to a vaccine, infection, or some type of therapeutic treatment,” said Martinot.

“But the problem is you can’t really see what those cells are truly doing in the context of the tissue itself,” she continued. “Because you destroy the structure of the tissue during the processing, you can’t tell which cells are in the airspaces or the blood vessels—or how close they are to cells infected with the virus. It’s like putting it a blender.”

However, cyclic immunofluorescence—the technology developed by Sorger and senior scientist Zoltan Maliga at Harvard—allows scientists to see where all the individual cells types are present and what state they are in. They use the same antibodies described above but instead of grinding the tissue up, they take a picture with a special type of fluorescent microscope.

The fluorescent images collected by Maliga and Sorger make it possible to identify precisely which cells are infected with virus, how the immune system’s first responders find these cells, and how this causes tissue damage.

“Instead of looking at one protein at a time—for example, choosing to look at the virus or the T cells—we can actually look at 30 different things in one tissue section,” Martinot explained. “We get all that information in the context of the tissue pathology via all these fluorescent colors.”

Martinot said although the team is using this technique to accelerate the development of much-needed animal models, their approach has caught the attention of those working with samples from human patients as well.

“Human samples are going to be very limited—and tons of scientists are going to want access to them,” she said. “Our process can be applied to those samples to help get the most information out of them for many studies.”

The Harvard Medical School team is now imaging specimens from multiple COVID-19 patients and using the knowledge obtained from monkeys to understand how disease progresses in humans and why it can be so serious.

“In the spirit of one medicine, experts in animal models and human disease are working very closely to understand the disease, improve patient outcomes, and ultimately develop vaccines and cures,” said Martinot.

Genevieve Rajewski can be reached at

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