Infectious COVID-19 Can Persist in Gut for Weeks

Damian McNamara

September 11, 2020

For the first time, researchers detected active and prolonged infection of SARS-CoV-2 virus in the gastrointestinal (GI) tracts of people with confirmed COVID-19. Stool tests were positive among people with no GI symptoms, and in some cases up to 6 days after nasopharyngeal swabs yielded negative results.

The small pilot study suggests a quiescent but active infection in the gut. Stool testing revealed genomic evidence of active infection in seven of the 15 participants tested in one of two hospitals in Hong Kong.

Professors Paul Chan (left), Francis Chan, and Siew Ng of the Centre for Gut Microbiota Research at the Chinese University of Hong Kong.

"We found active and prolonged SARS-CoV-2 infection in the stool of patients with COVID-19, even after recovery, suggesting that coronavirus could remain in the gut of asymptomatic carriers," senior author Siew C. Ng, MBBS, PhD, told Medscape Medical News.

"Due to the potential threat of fecal-oral transmission, it is important to maintain long-term coronavirus and health surveillance," said Ng, Associate Director of the Centre for Gut Microbiota Research at the Chinese University of Hong Kong (CUHK).

"Discharged patients and their caretakers should remain vigilant and observe strict personal and toileting hygiene," she added.

The prospective, observational study was published online July 20 in Gut.

Ramping Up COVID-19 Testing

As a follow-up to these and other findings — including the testing of more than 2000 stool samples in children and the needy arriving at Hong Kong airports starting March 29 — the same investigators are establishing a CUHK Coronavirus Testing Center.

As of August 31, the detection rate in tested children was 0.28%. The Center plans to offer as many as 2000 COVID-19 tests daily going forward to help identify asymptomatic carriers, the investigators announced in a September 7 news release.

In contrast to nasopharyngeal sampling, stool specimens are "more convenient, safe and non-invasive to collect in the pediatric population," professor Paul Chan, chairman of the Department of Microbiology, CU Medicine, said in the release. "This makes the stool test a better option for COVID-19 screening in babies, young children and those whose respiratory samples are difficult to collect."

Even though previous researchers identified SARS-CoV-2 in the stool, the activity and infectivity of the virus in the gastrointestinal tract during and after COVID-19 respiratory positivity remained largely unknown.

Active Infection Detected in Stool

This prospective study involved 15 people hospitalized with COVID-19 in March and April. Participants were a median 55 years old (range, 22 years to 71 years) and all presented with respiratory symptoms. Only one patient had concurrent GI symptoms at admission. Median length of stay was 21 days.

Investigators collected fecal samples serially until discharge. They extracted viral DNA to test for transcriptional genetic evidence of active infection, which they detected in seven of 15 patients. The patient with GI symptoms was not in this positive group.

The findings suggest a "quiescent but active GI infection," the researchers note.

Three of the seven patients continued to test positive for active infection in their stool up to 6 days after respiratory clearance of SARS-CoV-2.

Microbiome Matters

The investigators also extracted, amplified, and sequenced DNA from the stool samples. Their "metagenomic" profile revealed the type and amounts of bacterial strains in each patient's gut microbiome.

Interestingly, bacterial strains differed between people with high SARS-CoV-2 infectivity vs participants with low to no evidence of active infection.

"Stool with high viral activity had higher abundance of pathogenic bacteria," Ng said. In contrast, people with low or no infectivity had more beneficial bacterial strains, including bacteria that play critical roles in boosting host immunity.

Each patient's microbiome composition changed during the course of the study. Whether the microbiome alters the course of COVID-19 or COVID-19 alters the composition of the microbiome requires further study, the authors note.

The US Food and Drug Administration and officials in other countries have contacted the Hong Kong investigators for more details on their stool testing strategy, professor Francis KL Chan, dean of the faculty of medicine and director of the Centre for Gut Microbiota Research at CUHK, stated in the news release.

Further research into revealing the infectivity and pathogenesis of SARS-CoV- 2 in the GI tract is warranted. The value of modulating the human gut microbiome in this patient population could be worthwhile to investigate as well, the researchers said.

Novel Finding

"Some of it is not-so-new news and some is new," David A. Johnson, MD, told Medscape Medical News when asked to comment on the study.

For example, previous researchers have detected SARS-CoV-2 virus in the stool. However, this study takes it a step further and shows that the virus present in stool can remain infectious on the basis of metagenomic signatures.

Dr David A. Johnson

Furthermore, the virus can remain infectious in the gut even after a patient tests negative for COVID-19 through nasopharyngeal sampling — in this report up to 6 days later, said Johnson, professor of medicine, chief of gastroenterology, Eastern Virginia Medical School in Norfolk, Virginia.

The study carries important implications for people who currently test negative following active COVID-19 infection, he added. Centers for Disease Control and Prevention criteria clear a person as negative after two nasopharyngeal swabs at least 24 hours apart.

People in this category could believe they are no longer infectious and might return to a setting where they could infect others, Johnson said.

One potential means for spreading SARS-CoV-2 from the gut is from a toilet plume, as Johnson previously highlighted in a video report for Medscape Medical News.

The study authors disclosed no relevant financial relationships. Johnson serves as an adviser to WebMD/Medscape.

Gut. Published online July 20 2020. Full text

Damian McNamara is a staff journalist based in Miami. He covers a wide range of medical specialties, including infectious diseases, gastroenterology, and neurology. Follow Damian on Twitter: @MedReporter.

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