Decoding the Alphaviruses

Illustration of a floating particle of the virus that causes Eastern Equine Encephalitis, the mosquito vector, and bird, horse, and human hosts

Illustration by Davide Bonazzi

The coronavirus pandemic was caused by a virus that made the leap from animals to humans. Responding quickly and effectively to such viruses requires some foreknowledge of how they enter human cells—often by using a receptor common to several species. Armed with fundamental information about the interaction of a virus with a human receptor, virologists can build vaccines. And they can devise treatments, from antivirals that target the pathogen’s ability to reproduce, to antibody treatments that block viral entry into cells. But scientists know very little about the receptors that most zoonotic viruses—even well-known ones—use to infect cells. Much more fundamental research needs to be done on such viruses, in order to be prepared to prevent the next pandemic.

It didn’t take the current outbreak to persuade assistant professor of microbiology Jonathan Abraham of the importance of such research: he was co-mentored during his doctoral studies by Michael Farzan ’82, Ph.D. ’97, and Hyeryun Choe, the husband-and-wife team who first identified ACE2 as the receptor that the first SARS virus used to enter human cells during an international outbreak in 2003. That discovery aided preliminary research into vaccines and treatments—later abandoned when the disease fizzled out. In 2018, two years before the COVID-19 pandemic, Abraham began studying a pathogen called Semliki Forest Virus (SFV), which causes a mosquito-transmitted disease found in parts of Africa and Asia. Abraham chose this virus for study not because it was the most pathogenic he could find, but because it “behaves well in the lab,” where it has been modified to deliver vaccines and gene therapy. The idea behind the research, he says, was to “increase our fundamental understanding of the biology of these critters.”

Abraham and his lab group first built a system that would let them safely study the disease. Then they used the CRISPR-Cas9 gene-editing tool to knock out receptors—thousands of them—in human cells to see whether those missing a certain receptor protein could then resist entry by the virus.

Key to how viruses and receptors interact is their structure, since they literally fit together, much like three-dimensional puzzle-pieces, or a lock and key. Shape thus restricts the compatibility of a virus to particular receptors. What Abraham’s team discovered was that the virus could enter human cells using not one but two different receptors. This provided the first clue that he might have stumbled on a family of receptors with shared characteristics—and perhaps related vulnerabilities.

Upon close study, the researchers found that the two different receptors were nearly identical structurally, explaining why the virus could use either one interchangeably to break into cells. The receptors are similar, Abraham says, because they evolved from a common ancestral protein, and have barely changed through time. In fact, he reports, one of them is essentially the same in roundworms (C. elegans) as in humans, species separated by more than 500 million years of evolution. And the same receptor is conserved in everything in between, from mosquitos (the disease vector) to horses. This explains why the virus can infect a vast range of hosts.

Abraham and his team discovered, further, that two other viruses in the same alphavirus family use the same two receptors to infect cells. One is especially lethal: Eastern Equine Encephalitis (EEE), a mosquito-borne disease which kills about one-third of the people who come down with it, and which causes lifelong debilitating neurological damage in about half those who survive. Even though the number of people infected with EEE in the United States is small—a large outbreak in 2019 infected 34 people in seven states—the human and economic impacts are large. Stryker and Johnston professor of global health Megan Murray recalls seeing several such patients each summer at Massachusetts General Hospital when she was a practicing infectious-disease doctor. “These were otherwise perfectly healthy young people who were abruptly non-verbal, non-ambulatory, severely brain-damaged—and presumably,” she says, “would remain in that state permanently, given the degree of damage detected on imaging. It really was horrifying….” When the late public-health entomologist Andrew Spielman and colleagues quantified the economic impacts in 1995, they found that the cost of caring for a single neurologically impaired survivor of an EEE outbreak that occurred in the 1980s would be about $6.5 million (adjusted to 2022 dollars) during her lifetime.

“With SARS CoV-2,” says Abraham, “what we learned was that you can throw the kitchen sink at it, but you really have to better understand the biology of the virus to be prepared.” Abraham’s work has advanced this understanding on several fronts. First, his team discovered that a human protein called RAP (receptor-associated protein) can block infection of some cells by all three viruses (EEE, SFV, and the Sindbis virus, common in northern Europe). This suggests that it might be possible to develop a prophylactic drug or antibody treatment to prevent the spread of such diseases during an outbreak. Abraham says he thinks about that possibility mainly as a containment measure or early-acting form of therapy, “because everything that we have learned about these emerging viruses tells us that if somebody is in an intensive care unit, it is usually too late to make a difference.” By then, it is the patient’s own hyperactive immune response that is doing much of the damage.

At least as significant is Abraham’s contribution to scientists’ basic understanding of how such viruses operate. The receptors for EEE, SFV, and Sindbis virus that he and his colleagues discovered are part of a large family of proteins that transport fat-like molecules across cell membranes; they have existed since multicellular life first arose. That may explain why so many pathogens (not just viruses), from Rift Valley Fever to Clostridium difficile bacteria, exploit this receptor family to enter cells. A Nature commentary on Abraham’s research pointed out that Hepatitis B virus, Trojan-horse-like, coats itself in lipids to trick surface receptors into transporting it into cells, where it hijacks the internal machinery in order to reproduce. But EEE and the other alphaviruses Abraham described don’t use that method to enter cells. Discovering that mechanism, the commenters write, “might aid the development of targeted therapeutics for alphaviruses, and potentially for other virus groups that use members of [that] receptor family for cellular entry.”

Read more articles by Jonathan Shaw

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