People with COVID can eliminate viruses in their feces for up to seven months after diagnosis

As long as nasal or throat tests are still relied upon to obtain the discharge of COVID-19, research could show that it is not such a wise point.

A study by scientists at Stanford Medicine at the University of California, United States, found that infected people can eliminate viral genetic material in their feces for up to seven months after diagnosis. Those who do so often suffer from persistent gastrointestinal symptoms such as nausea, vomiting, and abdominal pain. The study, which has just been published in the specialized journal Cell, is the first to evaluate the presence of viral RNA in fecal samples of individuals with mild to moderate COVID-19 who are collected at several points after they got sick. This adds to the growing evidence that the SARS-CoV-2 virus actively infects the intestine.

“The findings do not imply that there is fecal-to-oral transmission of the virus that causes COVID-19,” the researchers warn in their report. But the results highlight a possible viral reservoir that could partly explain the puzzling constellation of symptoms that affect a minority of COVID-19 patients for months after their initial infection.

“Nobody really knows what causes prolonged COVID,” explained Ami Bhatt, associate professor of medicine and genetics at the entity in charge of the study. But our work shows that SARS-CoV-2 can hide in the intestine for months. Perhaps prolonged COVID, and the wide variety of symptoms it causes, is due to the immune system's response to viral proteins in hidden reservoirs throughout the body. People with mainly gastrointestinal symptoms may have a persistent viral infection in the intestines, for example. Others with mental confusion commonly called “mental fog” could have a persistent infection in their nervous system,” Bhatt speculated.

This specialist, who investigates how the microbiome, the vast universe of bacteria that line the lining of our intestines, affects human health, is eager to study whether an individual's bacterial “gut footprint” is affected if the virus is eliminated and, in that case, how and for how long. She and her colleagues continue their study of viral spread in fecal samples as part of the U.S. Recover Initiative sponsored by the United States National Institutes of Health.

The research team took advantage of an initial clinical trial launched in May 2020 on one possible treatment: interferon lambda for mild COVID-19 infection. The participants in the trial were monitored to monitor the evolution of their symptoms and the degree and location of viral excretion. Fecal samples were collected from participants at specific time points.

Researchers took advantage of the interferon lambda trial because participants were less ill than hospitalized patients who were the focus of many other investigations at that time. They wanted to keep track of what was going on in most patients, those with a mild illness.

Bhatt and his colleagues analyzed samples from 113 people at different points after infection. They found that about half with mild to moderate cases of COVID-19 were eliminating viral genetic material in their feces a week after testing positive for the SARS-CoV-2 virus.

About 13% of people were still clearing viral RNA four months later, after having cleared the virus from their airways, and nearly 4% had viral RNA in their feces seven months after the initial infection. Stool elimination was also correlated with ongoing gastrointestinal symptoms of the virus, including nausea, vomiting, and abdominal pain.

“It's not clear why some infected people have gastrointestinal symptoms,” Bhatt suggested. But other coronaviruses are known to infect the intestines of animals, so the idea of an ongoing infection is not unreasonable.”

Scientists were unable to isolate enough RNA to determine which viral variant infected participants, or to conclusively demonstrate that samples isolated from any individual at the early and later time points were from the same strain. But because the samples were collected relatively early in the pandemic, re-infection with a second strain or variant during the study was probably unlikely, specialists believe. The findings have implications for wastewater surveillance that scientists and governments are using to infer COVID-19 case counts in cities and counties across the country. “We are clearly seeing large and increasing amounts of the Omicron BA.2 subvariant in wastewater across the country,” Bhatt reported referring to the United States. At the same time, there have been reports that Omicron is more likely to cause gastrointestinal symptoms.

So is this increase in wastewater really proportional to the number of people infected? Or do more people eliminate the virus in their feces longer? Understanding the dynamics of viral infection and spread is critical to planning. It is difficult to interpret wastewater monitoring if we don't understand the biology that determines who is spilling, when and how much. At the beginning of the pandemic, many doctors decided that SARS-CoV-2 did not infect the intestine, and that was dangerous to our understanding,” he concluded.

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