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Hidden COVID virus found more than a year after infection

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By Yosi Yahoudai
Founder and Managing Partner

Pieces of the COVID virus can lurk in our blood and tissue for almost two years after the initial illness has vanished, a discovery that might offer clues to the mystery of lingering post-infection disability, according to new research from UC San Francisco.

Four years after the U.S. went into lockdown, the worst of the pandemic has passed. But for people with long COVID, the illness remains a daily misery.

The new research suggests why: The virus is not always fully cleared after the initial infection, so remains deeply embedded, even though people are no longer contagious.

It is not yet known if these small viral proteins, called antigens, are causing long COVID. But, based on the new discovery, the UCSF team is conducting clinical trials of potential therapies that could attack the hidden pathogen.

“This can be a persistent infection for some people,” said Dr. Timothy Henrich, professor of medicine at UCSF who co-authored the research, presented at last week’s Conference on Retroviruses and Opportunistic Infections. “We’re concerned that this could be leading to, at least in part, some of the long COVID symptoms that people have been experiencing.”

While COVID remains much more serious than the usual seasonal flu, safe and highly effective vaccines have caused a dramatic decline in infections and deaths.

There is a desperate need for a diagnostic test and treatment for long COVID, which affects an estimated 7% of American adults. Currently, doctors are only treating the symptoms, rather than offering a cure. Experts predict that the disorder will place continuing demands on our healthcare system.

“Long COVID patients deserve swift, accurate diagnosis and timely, effective treatment,” said Jaime Seltzer, scientific director at the nonprofit MEAction, which advocates for patients with long COVID and myalgic encephalomyelitis/chronic fatigue syndrome, or ME/CFS.

Is the clandestine virus constantly provoking the immune system, causing symptoms? That’s one leading theory. Another possibility is that COVID triggers an autoimmune response when the body mistakenly attacks itself. Or perhaps, long after it fends off infection, the immune system fails to turn off.

Using an ultra-sensitive test of blood from 171 people who had been infected with COVID, the UCSF scientists found pieces of the viral “spike” protein that persisted up to 14 months after infection.

The viral proteins were identified in 7% to 14% of the patients.

They discovered that the likelihood of detecting the protein was about twice as high in people who had been severely ill, requiring hospitalization, than those who were not. Detection was also higher in the blood of people who reported being very sick, but were not hospitalized.

In tissue samples, traces of the virus were found up to two years after infection. It was hidden in connective tissue where immune cells are located.

The work was conducted at UCSF’s Long COVID Tissue Bank, the world’s first tissue bank with samples donated by patients with long COVID.

Patients are not infectious because the virus is not living in the respiratory tract, where it could be spread by coughing or sneezing, said Henrick. Instead, “there seems to ‘seeding’ of deeper tissue after the initial infection, that may persist over a long period of time.”

“The UCSF team includes people who helped make HIV and AIDS a treatable disease,” according to Amy Proal, president of PolyBio, a research foundation focused on long COVID. “These researchers rapidly pivoted into long COVID research at the outset of the pandemic, leveraging years of experience performing similar research with patients with HIV and AIDS.”