SARS-CoV-2 Stays in GI Tract Long After It Clears the Lungs

Marcia Frellick

May 10, 2022

Editor's note: Find the latest COVID-19 news and guidance in Medscape's Coronavirus Resource Center.

New data present further evidence that SARS-CoV-2 infection can settle in the gastrointestinal (GI) tract and that it can persist long after the infection has cleared the lungs.

Infection of the GI tract may figure prominently in long COVID, the study authors suggest.

Led by Aravind Natarajan, PhD, with the Departments of Genetics and Medicine at Stanford University, they analyzed fecal RNA shedding up to 10 months after a COVID-19 diagnosis in 673 stool samples from 113 patients with mild to moderate disease.

They found that in the week after diagnosis, COVID RNA remnants were present in the stool of approximately one half (49.2%) of the patients. Seven months later, about 4% of them shed fecal viral RNA.

The authors note that there was no ongoing SARS-CoV-2 RNA shedding in respiratory samples of patients at the 4-month mark.

Using self-reported symptoms regularly collected by questionnaire, they also found a correlation of long-term fecal shedding of SARS-CoV-2 RNA with abdominal pain, nausea, and vomiting.

The findings were published online in Med.

Implications of Long-term Viral Shedding

Previous studies have found SARS-CoV-2 RNA in respiratory and fecal samples and have documented viral replication in lung and intestinal tissue.

But before the current study, little had been known about long-term shedding, especially in those who have mild COVID. Most studies of viral shedding have been with severe COVID cases.

The authors note that most studies of this kind are cross-sectional. The few other longitudinal studies have focused on early time points just after diagnosis.

Dr Ami Bhatt

Senior author Ami S. Bhatt, MD, associate professor in the Departments of Medicine and Hematology at Stanford University, told Medscape Medical News that though the viral genetic material in the feces lingers, on the basis of available evidence, it is highly unlikely to be contagious in most cases.

She said that understanding the dynamics of fecal shedding of SARS-CoV-2 genetic material will help interpret wastewater-based studies that are trying to determine population prevalence of the virus.

"While we don't know the exact clinical importance of the longer-term shedding of SARS-CoV-2 in individuals with COVID-19, some have speculated that those who have long-term shedding of SARS-CoV-2 may have ongoing infections that might benefit from treatment," she said.

"Our data support the idea that the long-term GI-related symptoms in some people might be the consequence of an ongoing infection in the GI tract, even after the respiratory infection has cleared," Bhatt said.

"Alternatively, the presence of ongoing viral genetic material in the gut might be a trigger for the immune system to continually be active against the virus, and our immune system reaction may be the reason for long-COVID type symptoms," she added. "This area is ripe for additional studies."

Bhatt and colleagues will continue studying viral shedding in fecal samples as part of the nationwide RECOVER Initiative.

Dr David Johnson

When reached for comment, David A. Johnson, MD, professor of medicine and chief of gastroenterology, Eastern Virginia Medical School in Norfolk, Virginia, told Medscape Medical News that previous studies have indicated that the virus may be detected in the stool for a month or more and for about 2 weeks on average. Whether the virus is infectious has been in question.

But it's not so much that the virus is infectious in the GI tract and causing symptoms, he said. Rather, there are biomic changes related to COVID, including a loss of diversity in the gut bacteria, which disrupts the balance.

"This may actually in some way predispose some patients to impaired clearance of their symptoms," Johnson explained. "There seems to be a growing recognition that this entity called long-haul COVID may be related to specific bacterial disruptions, and the more rapidly you can resolve these disruptions, the less likely you are to continue with long-haul symptoms."

He said that among people who have mild COVID, the virus typically clears and gut bacteria return to normal. With severe or persistent illness, gut dysbiosis persists, he said.

"People need to be aware that the GI tract is involved in a sizable percent of patients with COVID," Johnson said. "The GI-tract testing may reflect that the virus is there, but persistence of the detectable test positivity is very unlikely to reflect active virus."

The authors note in this study that they collected only six samples from the participants over the 10-month period.

"Follow-up studies with more frequent sampling, especially in the first 2 months after diagnosis, may help build a more nuanced model of decline of fecal viral RNA concentration over time," they write.

The study was supported by a Stanford ChemH-IMA grant, fellowships from the AACR and the National Science Foundation, and the National Institutes of Health. The authors and Johnson report no relevant financial relationships. Johnson is a regular contributor to Medscape.

Med. Published online April 12, 2022. Full text

Marcia Frellick is a freelance journalist based in Chicago. She has previously written for the Chicago Tribune, Science News, and Nurse.com, and was an editor at the Chicago Sun-Times, the Cincinnati Enquirer, and the St. Cloud (Minnesota) Times. Follow her on Twitter at @mfrellick.

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