Systematic Review With Meta-analysis

SARS-CoV-2 Stool Testing and the Potential for Faecal-oral Transmission

Amarylle S. van Doorn; Berrie Meijer; Chris M. A. Frampton; Murray L. Barclay; Nanne K. H. de Boer


Aliment Pharmacol Ther. 2020;52(8):1276-1288. 

In This Article


In this study, we performed a systematic review of the rapidly expanding body of literature to assess the performance and accuracy of testing stool samples or anal swabs and investigate the potential faecal-oral transmission of SARS-CoV-2. We conclude that the gastrointestinal tract is a potential shedding route of SARS-CoV-2 as all but four of the 95 studies with GI specimens testing found positive results of SARS-CoV-2 RNA by RT-PCR in at least one of the patients. A pooled proportion of 51.4% of all included patients tested positive in GI specimens.

Viral RNA can be detected in GI specimens up to 70 days after onset of symptoms or after the first positive SARS-CoV-2 test in any specimen. After respiratory tests turned negative, GI samples stayed persistently positive up to a maximum of 33 days, implying that the virus may be actively replicating in the patient's gastrointestinal tract and that faecal–oral transmission might occur after viral clearance in the respiratory tract. Although we observed a relation of patients with gastrointestinal symptoms to be more likely to test positive for SARS-CoV-2, the absence of gastrointestinal symptoms is not a firm indicator for negative GI specimen tests.

While SARS-CoV-2 may be shedding through stool in a notable subset of patients, the detection of viral genetic material in stool does not necessarily imply that viable infectious virions are present in GI specimens or that the virus can or has spread through faecal transmission. Live SARS-CoV-2 was found in 6/17 (35%) of the patients in which this was specifically investigated. Isolation of live SARS-CoV-2 in cultured GI specimens underlines the possibility of faecal-oral transmission through infected faeces.

Similar patterns of faecal-oral transmission and the relevance of stool testing of other coronaviridae have been witnessed over the years.[50,51] The initial SARS-CoV outbreak in the Amoy Gardens was primarily attributed to an airborne spread via inefficient sanitation and toilet ventilation systems.[52,53] Infection of the GI tract with the previous coronaviridae is proposed to be mediated via Angiotensin Converting Enzyme (ACE)-2 receptors. ACE-2 has also been identified as the host receptor that interacts with the viral spike protein to facilitate entry of SARS-CoV-2 into the host cell.[50] ACE-2 receptors are highly expressed in the small intestine and the binding affinity of ACE-2 receptors determine infectivity. As ACE-2 modulates intestinal inflammation, SARS-CoV-2 may disrupt ACE-2 function and result in GI shedding and symptoms, such as diarrhoea, vomiting and abdominal pain.

Furthermore, wastewater surveillance and wastewater-based epidemiology are considered a complementary approach to estimate the presence and even the prevalence of COVID-19 in communities, detecting SARS-CoV-2 in wastewater from households with infection.[54] Additionally, a recent study observed prolonged gut microbiome dysbiosis in COVID-19 patients and its association with faecal SARS-CoV-2 virus shedding and disease severity, suggesting that SARS-CoV-2 infection may be associated with a more long-lasting effect on the gut microbiome.[55]

Besides the fact that the genome of both SARS-CoV viridea and thus the shedding routes are very similar, SARS-CoV-2 also falls under the same shell disorder category as SARS-CoV, and SARS-CoV-2 has the hardest outer shell within the entire corona family. The hardness of the outer shell could provide SARS-CoV-2 with greater resilience to conditions outside the body and in bodily fluid, as the harder shell will provide better protection. Chances of infection via indirect contact and airborne virus from faeces and bodily fluids are therefore higher and faecal-oral transmission more likely.[56]

The results of this study may have various consequences for the diagnosis, prognosis and spread of COVID-19. First and foremost, worldwide the decision to isolate or discharge a patient is primarily based on relevant clinical symptoms, focusing on the respiratory tract, and (sequential) negative test results on respiratory specimens collected more than 24 hours apart.[57] We observed that in 64% of patients who tested positive for SARS-CoV-2 in GI specimens, their GI specimens remained positive for a mean of 12.5 days after respiratory samples became negative. As a result, a number of patients were discharged up to a month before the absence of SARS-CoV-2 in GI specimens could be guaranteed. The (additional) use of GI specimen testing may provide a more appropriate rationale for isolation and discharge.

A major concern could be continuing person-to-person transmission by the faecal-oral route, which argues for closer attention to hand and sanitation hygiene. This should be considered when determining diagnosis and isolation policies.

In general the risk to health care professionals from patient exposure is well known, specifically in high aerosol-generating procedures. Currently, medical management protocols include measures to mitigate the aerosol transmission risks from procedures related to respiratory tract.[8] Our analysis suggests that faecal-oral transmission risk from gastrointestinal procedures such as colonoscopies or physical examination, should also be taken into account.

Determining whether a virus is viable using RNA detection by RT-PCR is challenging. Limited studies have observed viable virus in stool and further research is needed to determine whether the irrefutable faecal shedding and the high and long-lasting detection rate of viral RNA in GI specimens really indicates the likelihood of faecal-oral transmission. Studies using fresh stool samples at later time points in patients with extended duration of GI specimen positivity are required to define transmission potential. Nevertheless, the importance of GI specimen tests for detection of SARS-CoV-2 in general, and even more in the longer term surveillance of infected patients, has been confirmed in our systematic review.

All included studies were observational case studies without control groups, based on a relatively small number of heterogeneous patients (I2 approximately 90%), and the timing of specimen collection has been largely inconsistent and unstandardised. In particular, evidence for viable virions in GI specimens is based on a small number of patients whose specimens were collected at different times over the course of illness or convalescence. This is not surprising, as most included studies are case reports or small case series of patients treated on the frontlines during the pandemic, in which adhering to standard research protocols is difficult. This generates the risk of bias in these kinds of studies, especially publication bias.

As a result, our analyses were based on relatively small patient groups (median 9; range 1–401 patients) and inconsistent methods, parameters, sample timing, sample frequencies and study endpoints differing widely between the included studies, impeding comparisons and robust conclusions. In the early response to the emerging COVID-19 outbreak, only respiratory specimens were required for the detection of SARS-CoV-2 according to initial clinical guidelines. A lot of studies, therefore, refrained from obtaining GI specimens from the patients during their first few days of hospitalisation or observation and could not determine whether respiratory and GI specimens were positive on RT-PCR analysis simultaneously. Furthermore, the phenomenon that viral RNA of SARS-CoV-2 can remain positive in GI specimens after respiratory samples became negative was not identified in all studies. This resulted in inadequate (follow-up) information, potentially causing a (outcome) measurement bias.

The sole four studies that reported no positive tests in GI specimens were all based on small sample size (1–4 patients) and the testing was performed at an early stage of the disease course. Our review demonstrated that there seems a tendency for SARS-CoV-2 to be more detectable in the respiratory tract at an early stage of the disease and later on, more likely to be detected in GI specimens, which could explain the early negative testing.

Our review confirms that SARS-Cov-2 is commonly present in stool samples or anal swabs in which the virus can persist long after respiratory testing has become negative and that the virus may be viable. This suggests the possibility of faecal-oral transmission and that stool sample or anal swab testing should be (re)considered in relation to decisions for isolating or discharging a patient.