How COVID-19 Messes Up Your Gut Health

When you reach for a COVID-19 test, it’s probably because you’ve got a scratchy throat, runny nose, or cough. But those are far from the only symptoms that make Dr. Rohit Jain, an internal medicine doctor at PennState Health, suspect the virus.

These days, when someone complains of nausea, diarrhea, or vomiting, “I always get a COVID test on that patient,” Jain says.

Why? Despite its reputation as a respiratory virus, SARS-CoV-2 can also have a profound impact on the gut. Although most people don’t realize it, “COVID-19 really is a GI-tract disease” as well as a respiratory illness, says Dr. Mark Rupp, chief of infectious diseases at the University of Nebraska Medical Center.

Here’s what to know about the gastrointestinal symptoms of COVID-19.

What are the GI symptoms of COVID-19?

While some people experience no gastrointestinal symptoms or mild ones, a subset of COVID-19 patients have experienced significant digestive symptoms since the early days of the pandemic.

Loss of appetite, nausea, vomiting, diarrhea, and stomach pain are common GI symptoms of COVID-19, according to Jain’s research. Some people experience these issues as their first signs of infection, he says, while others initially experience cold-like symptoms and develop gastrointestinal issues as their illness progresses.

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It’s not entirely clear why the same virus can affect people so differently, but it’s good to be aware that SARS-CoV-2 can result in a wide range of symptoms, Rupp says.

How long do GI symptoms of COVID-19 last?

Some patients recover in a matter of days, Jain says, while others may suffer from diarrhea and other symptoms for weeks. 

Still others may be sick for even longer. Gastrointestinal problems are a common manifestation of Long COVID, the name for chronic symptoms that follow a case of COVID-19 and can last indefinitely.

One recent study in Clinical Gastroenterology and Hepatology found that, among a small group of adults who were hospitalized when they had acute COVID-19, more than 40% who originally experienced GI problems such as stomach pain, nausea, vomiting, or diarrhea still had at least one a year or more later. Overall, whether they were hospitalized or not, adults who have had COVID-19 are about 36% more likely than uninfected people to develop gastrointestinal disorders including ulcers, pancreatitis, IBS, and acid reflux, according to a 2023 study published in NatureCommunications.

GI problems are also common among kids with Long COVID. Stomach pain, nausea, and vomiting are telltale signs of the condition among children younger than 12, according to 2024 research published in JAMA.

Why a respiratory virus affects the gut

How can the same virus cause both a runny nose and the runs? 

Once SARS-CoV-2 gets into your body, it infects cells by binding to a protein called ACE2, which is found throughout the body. ACE2 is prevalent in the lungs, which helps explain COVID-19’s respiratory symptoms—but it’s also found in high concentrations in the gastrointestinal tract, “so it makes sense that the GI tract would be a target for the virus,” Rupp says. It’s in part because SARS-CoV-2 collects in the gut that wastewater surveillance is a useful tool for tracking the virus’ spread, Rupp adds.

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Studies have shown that the virus can hide out in the “nooks and crannies” of the digestive system for months or even years, says Ziyad Al-Aly, a clinical epidemiologist at the Washington University School of Medicine in St. Louis who co-authored the Nature Communications study on chronic post-COVID GI symptoms. This may explain why gut-related symptoms can long outlast an acute infection, Al-Aly says—but there are many potential hypotheses in play, and researchers don’t know for sure which one or ones are correct.

For example, many researchers also think the virus is capable of causing widespread and sometimes long-lasting inflammation, potentially affecting organs throughout the body. This inflammatory response may have trickle-down effects on the gut microbiome, the colony of bacteria and other microbes that live in the GI tract, Rupp says. “We’re just scratching the surface as to what happens there,” Rupp says, but studies have already shown that SARS-CoV-2 can change the composition of the gut microbiome both during an acute infection and chronically.

There’s also a complex relationship between the gut and the brain, adds Dr. Badih Joseph Elmunzer, a gastroenterologist at the Medical University of South Carolina and co-author of the Clinical Gastroenterology and Hepatology study on prolonged post-COVID GI symptoms. His research suggests people are particularly likely to suffer long-term GI problems if they also have signs of PTSD from their acute illness or hospitalization.

That’s not to say GI symptoms are all in patients’ heads; on the contrary, Elmunzer says, they are very real. But, he says, there’s a lot left to learn about the microbiome, the gut, and the myriad ways they interact with other bodily systems.