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Does fecal viral excretion provide insights into on GI symptoms of COVID-19?


The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that was first reported in 2019 in Wuhan, China. The rapid spread of SARS-CoV-2 throughout the world caused the coronavirus disease 2019 (COVID-19) pandemic. To date, SARS-CoV-2 has infected over 548 million individuals and claimed more than 6.3 million lives worldwide.


Previous studies have shown that SARS-CoV-2 is transmitted through droplets, direct contact, as well as aerosols and causes a wide range of pneumonia-like symptoms. Additionally, various gastrointestinal (GI) symptoms such as nausea, vomiting, diarrhea, anorexia, and abdominal pain have also been reported in COVID-19 patients. In fact, some patients report that their GI symptoms appeared before their respiratory symptoms.

The underlying mechanisms responsible for the GI symptoms reported in COVID-19 patients is not clearly understood. Some studies have reported the presence of intracytoplasmic nucleocapsid protein in digestive biopsies.

Previous studies have also indicated the presence of prolonged viable viral particle shedding in stool samples of COVID-19 patients. These findings imply that SARS-CoV-2 multiplies in the intestines, which enhances the risk of transmission through the fecal-oral route. To date, there remains limited evidence that establishes the relationship between SARS-CoV-2 fecal shedding and digestive disorders.

About the study

A new study published on the preprint server Research Square* while under consideration for publication at Scientific Reports discusses the physiopathological mechanisms associated with digestive symptoms associated with COVID-19. Herein, the researchers determined the effect of fecal viral shedding on digestive symptoms and propose a novel method to better understand the GI manifestations of acute COVID-19.

The current prospective study was conducted between March 1, 2020, and May 3, 2020, during the first COVID-19 wave in France. Both outpatients and hospitalized patients from Bichat-Claude Bernard hospital who had provided at least one stool sample for microbiological examination were included in the study. All patients underwent syndromic reverse transcription-polymerase chain reaction (RT-PCR) screening for COVID-19 and parasitological investigation for the presence of microsporidia and multiplex protozoa.

SARS-CoV-2 infection was detected by analyzing respiratory samples, frozen stool samples, and, in some cases, by serological methods. The authors also obtained clinical, biological, epidemiological, and radiological data and compared this information based on COVID-19 status, co-infection status, and fecal SARS-CoV-2 shedding.

The authors have categorized patients whose stool analysis showed the presence of SARS-CoV-2 ribonucleic acid (RNA) as the excretory group, while stool samples with undetectable fecal viral shedding were categorized as the non-excretory group.

Study findings

Previous studies have reported that patients who are at a high risk of developing severe COVID-19 are also susceptible to GI disorders. The current study reported the early onset of digestive disorders in COVID-19 patients; however, these symptoms persisted for a short period.

Although fecal shedding does not affect digestive presentation, the detection of SARS-CoV-2 RNA in stool samples indicates the risk of severe COVID-19. The researchers have also correlated the presence of SARS-CoV-2 RNA in stool samples with a high viral load in upper respiratory samples.

The study findings align with previous reports on the passive passage of SARS-CoV-2 from the upper respiratory tract to the GI tract through the ingestion of respiratory mucus. The authors, therefore, proposed that fecal shedding occurs as a result of a high respiratory viral load, rather than due to viral replication within the GI tract.

Taken together, 38% of stool samples in the current study were positive for SARS-CoV-2, 20% of which exhibited co-infection with GI pathogens that were identified through various microbiological analyses. A similar incidence of GI pathogens was observed in both the COVID-19 positive and healthy groups. This observation implies that COVID-19 patients were not overexposed to fecal-oral transmission as compared to the control group.

Some of the pathogens that were frequently detected in the study samples included enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), Clostridioides difficileBlastocystis spp., and Giardia duodenalis.

No GI co-infection was reported during the clinical course of COVID-19 and SARS-CoV-2 stool shedding. However, its influence on the intensity of digestive disorders or co-morbidities must be studied in the future.


One of the limitations of the present study is its monocentric design due to its small size. Small-sized study samples could bias the panel of enteric pathogens identified.

Additionally, as in most cases, only one stool sample was available, thus leading to a high possibility that the detected pathogens were underestimated.

The authors failed to standardize the clinical management and anti-infectious therapy, which added heterogeneity to clinical data. However, the researchers emphasized the importance of differential microbiological diagnosis for the detection of digestive disorders in COVID-19 patients, as the levels of pathogens were found to be similar in non-COVID-19 patients exhibiting enteric symptoms.

*Important notice

Research Square publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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