Coronavirus Infection Persists in the Gut for Weeks

Scientists report finding COVID-19 in stool samples – even with a negative respiratory test result. Now, they suggest stool testing may be a better option for COVID-19 screening.

Researchers previously established a link between COVID-19 and the gut microbiome. Now, for the first time, they’ve found that people with COVID-19 can also have an active and prolonged infection of the SARS-CoV-2 virus in their gastrointestinal (GI) tracts.

Active Infection Detected in Stool

A research team in Hong Kong has found the first known signature of active gut viral infection in a subset (47%) of patients with COVID-19, even in the absence of GI symptoms. This suggests a potential inactive or ‘quiescent’ GI infection of SARS-CoV-2.

Notably, they found that stool samples with high SARS-CoV-2 infectivity had a higher abundance of certain pathogens, Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis and Morganella morganii. Meanwhile, faecal samples with a low-to-none signature had a higher abundance of short-chain fatty acid producing bacteria, such as Parabacteroides merdae, Bacteroides stercoris, Alistipes onderdonkii and Lachnospiraceae bacterium 1_1_57FAA.

Stool samples with high SARS-CoV-2 infectivity had a higher abundance of certain pathogens.

Stool tests were positive among people who had no GI symptoms and, in certain cases, even up to 6 days after nasopharyngeal swabs yielded negative results. Moreover, since this infection can even persist after recovery, it seems that coronavirus could be present in the guts of asymptomatic carriers. 

Still, this was a small pilot study that involved 15 people hospitalized with COVID-19 in March and April. Participants were aged between 22 to 71 years, and all presented with respiratory symptoms. More research is needed to draw further conclusions. 

Stool Testing for COVID-19

Compared 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. “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.” Furthermore, the team also emphasises the need for long-term coronavirus and health surveillance, given the potential threat for fecal-oral transmission. 

This makes the stool test a better option for COVID-19 screening.

Ultimately, given that diarrhea has been noted as a very common symptom of COVID-19, it seems that stool testing may become more of the norm when montoiring patients for COVID-19. In the meantime, remember to observe strict personal and toileting hygiene, and stay vigilant about any disruptions to your digestive habits.


  1. Zuo T, Liu Q, Zhang F, et al. Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19Gut Published Online First: 20 July 2020. DOI: 10.1136/gutjnl-2020-322294
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