• Gastrointestinal pathogens, which were largely kept at bay during the early days of the COVID pandemic, may be surging back.
• Research published in the Journal of Clinical Microbiology looked at GI illnesses caused by pathogens like rotavirus, norovirus, and Escherichia coli in a northern California community during and after lockdowns.
• There are several ways to help prevent GI illnesses, including washing hands thoroughly, keeping your distance from people who are sick, and properly preparing and storing foods.

Though stay-at-home orders and other COVID precautions largely kept gastrointestinal (GI) bugs at bay in the early months of the pandemic, research shows that those pathogens may be coming back with a vengeance.

The claim comes from a new study looking at cases of GI illnesses in one northern California community during and after COVID-19 lockdowns.

The research, published in the Journal of Clinical Microbiology, shows that many GI pathogens nearly vanished in the community during stay-at-home orders, and then surged back to pre-pandemic or even higher levels in 2022 after those orders were lifted.

Researchers believe that the collective immunity to GI pathogens waned while people isolated themselves from others, setting the stage for a robust comeback once social distancing rules relaxed.

“The pandemic, and our efforts to combat it, had dramatic and lasting effects on many aspects of our society, including the transmissible pathogens that make us sick with diarrhea,” study author Niaz Banaei, MD, the medical director of the Clinical Microbiology Laboratory at Stanford Health Care, told Health. 

Though the study focused on detection rates in northern California, Dr. Banaei thinks “the changes may have occurred in other regions that experienced similar social distancing measures.” It’s possible, however, that results would differ in states that had looser pandemic restrictions, such as Arizona and Florida.

Norovirus Outbreaks Have Increased to Pre-Pandemic Levels, CDC Data Show

From Decline to Explosion

Research has shown a similar bust and boom pattern of RSV and influenza cases between 2020 and 2022, but this new study is the first to examine the pandemic’s longer-term effect on gastroenteritis cases.

“The pandemic lockdown and shelter-in-place had created a natural experiment to investigate the transmission dynamics of pathogens causing gastroenteritis,” Dr. Banaei explained in a press release.

For their investigation, researchers tested kits from more than 18,000 people using Stanford’s syndromic FilmArray GI panel, which can detect 22 of the most common viruses, bacteria, and parasites that cause diarrhea. They analyzed kits collected at three different periods: before California’s stay-at-home orders were enacted, after their implementation in March 2020, and after the state lifted them in January 2021.

The team found positive test results declined during lockdown for pathogens such as adenovirus, rotavirus, norovirus, Escherichia coli, Shigella, Cyclospora cayetanensis, and Giardia lamblia.

Except for E. coli, C. cayetanensis, and G. lamblia, all other pathogens made a significant comeback in 2022, more than a year after stay-at-home orders had lifted.

Infections of the strain of adenovirus most frequently associated with gastroenteritis—adenovirus F40/41—jumped exceptionally high, according to Dr. Banaei, to twice pre-pandemic levels.

Previous research from the Centers for Disease Control and Prevention has also highlighted a jump in stomach illnesses following COVID restrictions. In a September 2022 study published in the CDC's Morbidity and Mortality Weekly Report, the agency noted that norovirus cases were back at pre-pandemic levels, due to the easing of COVID restrictions.

Stomach Flu vs. Food Poisoning: How To Tell the Difference

How the Immunity Gap Factors In

Typically, GI infections spread when particles of vomit or feces from an infected person enter someone else’s mouth. Touching a contaminated surface, for example, or eating food prepared by a sick person who didn’t wash their hands can lead to transmission. Infections can spread quickly in crowded spaces such as airplanes, cruise ships, schools, daycares, and restaurants.

When shelter-in-place rules went into effect, however, there weren’t as many opportunities for these pathogens to spread. Therefore, the researchers “speculate that social distancing led to reduced person-to-person transmission of these viruses,” said Dr. Banaei.

She explained that the decline likely created a so-called immunity gap that made people more vulnerable to disease, which then fueled the post-pandemic transmission surge. Given adenovirus’s robust rebound, the researchers suspect that immunity to this pathogen in particular may decrease faster than other GI pathogens.

“It is easy to think of viruses and infection as inevitable,” Benjamin Neuman, PhD, a professor of biology and chief virologist of the Global Health Research Complex at Texas A&M University, told Health. “But this shows how much control we actually have to prevent infection.”

In the press release, Dr. Banaei said that the study provides researchers with information that could help them come closer to curbing GI cases, particularly in developing countries where it remains a significant cause of death. The research, she said in the release, may also “help us prepare for future unforeseen pandemics.”

Signs and Symptoms of a Stomach Virus

How to Prevent GI Illnesses

There are several ways to help prevent GI infections, according to the Centers for Disease Control and Prevention (CDC). They include:

• Washing hands often, especially after going to the bathroom or changing a diaper
• Keeping your distance from people who are sick
• Cooking foods to safe temperatures and washing fruits and vegetables thoroughly
• Disinfecting surfaces with bleach
• Avoid touching your eyes, nose, or mouth with unwashed hands

There are vaccines available for rotavirus, poliovirus, Salmonella typhi, and Vibrio cholerae.

Even with solid precautions in place, however, it’s not always possible to prevent transmission. “Food and water can get contaminated, and travelers from areas with poor sanitation can bring viruses,” Bernadette Boden Albala, MPH, DrPH, the director and founding dean of the program in public health at University of California, Irvine, told Health.

If you develop severe diarrhea, vomiting, fever, or other gastrointestinal disease symptoms, consult a healthcare provider. There’s no antiviral treatment for GI viruses, but rest, over-the-counter pain medicines, and drinking lots of fluids can help. There are treatments for some bacterial and parasitic GI pathogens.