Higher Risk of Stomach Issues with Omicron, BA.2? Decoding COVID & Gut Link

GI symptoms from Omicron Variant? Experts weigh in on how and why COVID impacts your gut health.

5 min read

With the list of COVID variants growing longer, so have the number of symptoms associated with COVID gone up. From fever and cough to heart conditions, diabetes and even osteoporosis, at this point, if you have it, chances are, it could be COVID.

The newest COVID variant taking the world by storm is Omicron's stealthy sub-variant BA.2, and it seems to have brought on a new barrage of gastrointestinal symptoms with it.

Many COVID patients across the world are now complaining of mostly gastrointestinal symptoms, with hardly any pulmonary symptoms.

So how exactly did a respiratory virus turn into a stomach bug? How does COVID impact gut health?

FIT speaks to Dr Lovkesh Anand, Consultant-Medical Gastroenterology & Hepatology, Manipal Hospital, Dwarka, and Dr Ashwini Setya, a leading gastroenterologist in New Delhi.


Omicron & GI Symptoms

Speaking to FIT, Dr Lovkesh Anand, says that he has, in fact, seen an influx in cases of GI symptoms in COVID patients in the last few weeks.

"In confirmed COVID positive patients, in the third wave, we were seeing a large number of patients who were having only GI symptoms, or along with fever and cough they were also having bloating and some pain, and loss of appetite."
Dr Lovkesh Anand, Consultant- Medical Gastroenterology & Hepatology, Manipal Hospital, Delhi

These included patients who had difference levels of illness, from mild to severe.

Dr Anand lists the common GI symptoms in these patients as being,

  • Malaise

  • Body ache

  • Abdominal pain

  • Severe bloating

  • Severe belching

"It troubled them a lot, but the symptoms were largely not severe," he adds.

"But lately, in the last few weeks," he says, "there is a surge in stomach ailments like, what we locally call food poisoning in which people are complaining of loose stools, pain in the abdomen and nausea."

"Even now, I have no less than 10 patients with these same complains," he says.

This time of the year is known for flu which can include GI symptoms which makes it harder to figure out if its COVID or just seasonal flu.

To make things worse, many of the patients being tested now are not testing positive, so it's difficult to say how many of these cases are really caused by COVID.

"Actually, there is an overlap between these symptoms and the flu like symptoms that we often have during a change of season.The problem is, as this virus is being called the 'stealth' omicron variant, it can evade, and there can be a false negative report."
Dr Lovkesh Anand, Consultant- Medical Gastroenterology & Hepatology, Manipal Hospital, Delhi

Really, It’s Not Just Omicron

Dr Ashwini Setya, However, says GI symptoms are not exclusive to the Omicron variant, and that they have always been symptoms of COVID.

"In my own practice (gastroenterology), I have seen people come in with various symptoms after COVID. It doesn't make much difference whether it is Delta (or Omicron)."
Dr Ashwini Setya, Gastroenterologist

They're just getting more attention now because with Omicron, other symptoms are generally milder, he adds.

“The most common symptom that I’m coming across is bloating. Diarrhoea was very profuse in patients in the first wave. And in the Delta wave, these GI symptoms took a backseat. They were there but other symptoms were so severe that nobody bothered about them,” he says.

"In the Delta wave, there was so much mortality, and so many people were dying because of mainly pulmonary symptoms. Nobody died of, say, GI haemorrhage."
Dr Ashwini Setya, Gastroenterologist

Why the Gut?

Experts have been reiterating that COVID is a multi-organ illness and we're only beginning to understand the extent of its impact on the body.

So, it only makes sense that the gut wouldn't be spared either. Several recent studies have found more solid evidence of a higher risk of GI issues in people infected with COVID.


A study by King's College London published last month, for instance, found that COVID-19 severely damages the small intestines, and disrupts the gut microbiome.

Sometimes these symptoms can manifest long after the patient has recovered from COVID.

"Many patients are coming three months and four months down the line after COVID and they are still complaining of similar symptoms."
Dr Lovkesh Anand, Consultant- Medical Gastroenterology & Hepatology, Manipal Hospital, Delhi

“It (post COVID) is a combination of so many different symptoms and GI symptoms are ones that draw the attention of the patient to go to the doctor and get checked (as opposed to fatigue, or brain fog that people generally tend to choose to ride out on their own)," says Dr Setya.

How exactly COVID impacts the gut is unknown. But there are theories and hypotheses.

"In a line, the answer would be, we don’t know the exact reason,' says Dr Setya.

One such hypothesis that Dr Anand presents is that "whenever there is a new variant, there are some mutations. Because of these genetic differences, maybe the receptors and the virus interactions differs and it probably has more tropism (attraction) for the gut mucosa, which is why its mainly causing gastro intestinal issues."

"Right now, the severe GI illness linked to COVID has been pancreatitis," says Dr Setya.

"This has also been because of a similar mechanism where the blood supply to that organ is curtailed, therefore leading to necrosis or degeneration of the organ and the problems start."
Dr Ashwini Setya

"So when the blood supply goes, everything goes for a toss. Although the body starts to compensate, that is the most severe issue of the GI tract that we noticed from COVID," he adds.

Both Dr Anand and Dr Setya agree that more research is needed to unravel the details of how and why this is happening exactly.

COVID Anxiety Could Be to Blame

According to Dr Setya, "the mechanism of how COVID impacts the gut are just conjectures. The problem with the GI thing is that the gut response can be related to the mental state as well."

"The response of the gut to stress and anxiety can be varied. Some people develop abdominal pain, others will experience bloating, diarrhoea etc."

How is it treated?

Like all other COVID variants and symptoms, GI symptoms are also treated with largely conservative treatment, says Dr Anand. "There is not specific treatment, or a specific antidote. it is mainly symptomatic treatment," he says.

One reason for this, Dr Setya explains is that we just don't know the exact root cause of these symptoms.

Some tips that Dr Anand gives to deal with and avoid GI symptoms are,

  • Avoid high carb diets

  • Avoid junk food, especially greasy food

  • Avoid eating out if you can

  • Have lots of fluids and fibre

"Drinking lots of water is very essential. This is true for all viral infections. Hydrate yourself very well so it flushes out the toxins and removes the virus from your body and helps you recover that much faster."
Dr Lovkesh Anand, Consultant- Medical Gastroenterology & Hepatology, Manipal Hospital, Delhi

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