1. Introduction

While COVID-19 is mainly considered a respiratory disease, gastrointestinal (GI) symptomatology in COVID-19 has been reported. GI disorders, and particularly diarrhea, are proposed to be a direct consequence of SARS-CoV-2 intestinal infection, as many patients have detectable SARS-CoV-2 RNA in feces [5]. In addition, recent studies showed that non-human primates infected with SARS-CoV-2 had transient diarrhea [6]. Studies from other viruses identified different mechanisms-inducing diarrhea such as malabsorption or inflammation secondary to enterocyte damage and death [8,9], the release of virulent toxins [8] and gut microbiota dysbiosis [10,11]. Elevated fecal and serum levels of the inflammatory marker calprotectin in COVID-19 were not consistent with GI symptoms [13]. In line, limited intestinal inflammation was observed in patients with acute COVID-19 despite diarrhea, fecal viral RNA and SARS-CoV-2-specific immunoglobulin A (IgA) [14]. Thus, summarizing the current lines of evidence and uncertainties supporting intestinal infection and understanding the impact of intestinal SARS-CoV-2 on the GI system (epithelium damage, inflammation) could improve disease management, help to identify therapies or effective preventive actions targeting the GI tract.

Based on existing data and available literature, the AOP approach seeks to pragmatically focus on essential biological key events (KE) at the different biological levels (molecular, cellular, tissue, organ, individual) up to an adverse outcome via a domino effect [15,16,17,18]. A KE describes a measurable and essential change in a biological system that can be quantified in experimental or clinical settings [19]. The confidence that each KER occurs within an AOP is postulated by the evaluation of the weight of evidence [20]. Information contained in the KEs, KERs and AOPs are stored in an open access platform (https://aopwiki.org/) where they are identified by assigned unique numbers. There, AOPs can be continuously updated as new information becomes available. This AOP approach highlights important inconsistencies and gaps in the evidence. This study was realized under the CIAO project which aims to make sense of the overwhelming flow of publications and data related to COVID-19 pathogenesis by using the AOP framework [21,22]. The project is based on the assumption that such mechanistic organization of the COVID-19 knowledge across the different biological levels will improve the interpretation and efficient application of the scientific understanding of COVID-19 [23].

2. Current Evidence and Uncertainties of an Active SARS-CoV-2 Enteric Infection

2.1. S Proteins Bind to ACE2 in Enterocytes and Mediates Viral Entry

Biological plausibility. Upon binding of SARS-CoV-2 to ACE2 (KE1739), the spike (S) proteins of the virus need to be activated through proteolytic cleavage to allow fusion between host and viral membranes, a key step in viral entry (KE1738), that releases viral RNA and proteins into host cells. Many proteases were identified as aiding in cell surface entry, such as TMPRSS2. Only three cell types showed co-expression of ACE2 and TMPRSS2, including enterocytes [26,27].

Evidence. Regarding ACE2 as the entry receptor for SARS-CoV-2, the level of ACE2 expression did not correlate with infectivity of cells in human intestinal organoids [30]. Both ACE2-positive and ACE2-negative SARS-CoV-2 infected cells in intestinal organoids were observed [31], potentially suggesting the existence of alternative entry receptors, ACE2 downregulation after infection, or reflecting expression levels under the detection limit. However, ACE2-knock-out (KO) intestinal organoids were fully resistant to SARS-CoV-2 infection [31], suggesting that ACE2 is the obligate entry receptor for SARS-CoV-2 in intestinal cells. Accordingly, in human gut-on-chip models composed of intestinal epithelial Caco-2 co-cultured with mucin-secreting HT-29 intestinal cells, the highest levels of ACE2 expression were found in the Caco-2 cells and after viral infection, Spike protein-positive Caco-2 cells were detected [32]. Similarly, higher ACE2 levels correlated with the maturity of enterocytes present in human differentiated enteroids and SARS-CoV-2 was able to infect ACE2+ mature enterocytes [33], therefore mature enterocytes are likely highly susceptible to infection.

Uncertainties, inconsistencies and gaps. As previously noted, study in ACE2-KO intestinal organoids indicated ACE2 as the entry receptor of SARS-CoV-2 in enterocytes in vitro facilitated by TMPRSS2 [31]. The authors proposed that the discrepancy with the study considering TMPRSS4 could be explained by the expression in the KO organoids of physiological levels of the proteases rather than overexpression [31]. No studies have specifically investigated the role of NRP-1 in SARS-CoV-2 entry in the gut. However, it is interesting to note that different variants display different affinities for NRP-1, with omicron displaying higher affinity than previous variants. Future studies should elucidate whether this increase in affinity constitutes a functional evolutionary adaptation of SARS-CoV-2 to humans [43], and confer an advantage for viral entry.

2.2. Viral Entry Leads to Antiviral Response

Biological plausibility. Following cellular entry, the primary translation of the SARS-CoV-2 open reading frame (ORF) 1a and ORF1b genomic RNA produces non-structural proteins (NSPs) [44]. The ORF1a produces polypeptide 1a (pp1a) that is cleaved into NSP-1 through NSP11. A -1 ribosomal frameshift occurs immediately upstream of the ORF1a stop codon to allow translation through ORF1b, yielding pp1ab, which is cleaved into 15 NSPs (duplications of NSP1-11 and five additional proteins, NSP12-16). Viral proteases NSP3 and NSP5 cleave the polypeptides through domains functioning as a papain-like protease and a 3C-like protease, respectively [44].

Evidence. The innate immunity activated by viral infections resulting in quick resolution of disease occurs in many instances of SARS-CoV-2 infection, such as in adults with no or mild symptoms [46], the young [47], and bats that harbor the virus without disease [48]. SARS-CoV-2 infection of human intestinal epithelial cells was associated with a robust innate immune response mediated by type III interferon, which inhibits SARS-CoV-2 replication and de novo virus production [49].

Uncertainties, inconsistencies and gaps. For SARS-CoV-2 infection, initial transcriptional analyses of infected cells have generated ambiguous results on the induction of type I/III IFNs and the subsequent expression of ISG and many studies associate better prognosis with increased innate immunity activation. However, the effectiveness of IFN treatment is still uncertain due to some studies evaluating IFN and other drugs [52]. There are uncertainties based on differing disease outcomes, mainly associated with the timing of administering IFN; administering late, in the inflammatory stage, led to long-lasting harm and worsened disease outcomes [52].

2.3. Antagonized Antiviral Response Leads to Coronavirus Production

Biological plausibility. The SARS-CoV-2 virus has evolved a repertoire of proteins that bind and block proteins in the IFN cascade so the host antiviral proteins are not expressed, and the virus is free to replicate [56]. Interactions between SARS-CoV-2 proteins and human RNAs have been demonstrated to thwart the IFN response: NSP1 binds to 40S ribosomal RNA in the mRNA entry channel of the ribosome to inhibit host mRNA translation. NSP6 binds TANK binding kinase 1 (TBK1) to suppress interferon regulatory factor 3 (IRF3) phosphorylation, and NSP13 binds and blocks TBK1 phosphorylation [56]. NSP14 induces lysosomal degradation of type 1 IFN-alpha receptor (IFNAR) to prevent STAT activation [57]. ORF6 blocks nuclear import of IRF3 and STAT proteins to silence IFN-I gene expression [58]. ORF7a suppresses STAT2 phosphorylation and ORF7b suppresses STAT1 and STAT2 phosphorylation to block interferon-stimulated gene factor 3 (ISGF 3) complex formation with IRF9 [58].

Evidence. In human intestinal organoids, following entry, gene expression analysis demonstrated that SARS-CoV-2 replicated with low induction of type I and III IFNs, though increased expression of ISG was observed [27]. Infection of Caco-2 cells leads to a weaker intrinsic immune response, associated with more de novo infectious virus production than T84 cells [49]. In ex vivo human intestinal tissues, SARS-CoV-2 replicated less efficiently (less viral genome copies produced, less infectious particles generated) but induced a more robust innate immune response than SARS-Co-V, including both type I and III IFNs while SARS-Co-V induced only IFNa expression [64]. Studies in human primary nasal epithelial cell cultures have shown that if exogenous IFN-I/III were administered intranasally prior to infection and at sufficient concentration, SARS-CoV-2 infection was inhibited [66]. In humans, SARS-CoV-2 could productively replicate in surgically removed intestinal tissue but not in kidney or liver tissues [64]. SARS-CoV-2 RNA has been found in stools of infected individuals consistently, although with different frequencies (ranging from 15.3% to 81.8% of infected people [7]. In a retrospective cohort in China, the median duration of viral RNA in stool was 22 days [70]. In some patients, the viral load in feces reached 107 copies/g suggesting an enteric infection not blunted by an interferon response [71]. Viral RNA and intracellular staining of viral nucleocapsid protein were detected in GI epithelium from one patient in China who tested positive for SARS-CoV-2 RNA in feces [73] and duodenal biopsies of 2 out of 5 moderate COVID-19 patients; however, the staining was weak and scattered [74].

Uncertainties, inconsistencies and gaps. Contrasting results between ex vivo lung and intestinal tissues prove a line of evidence that SARS-CoV-2 infectivity and antiviral response is different in the gut than in lungs. Studies in lung cells and tissues showed that IFN expression is delayed or reduced by SARS-CoV-2 compared to influenza [66,77,78,79]. Autoantibodies against IFN-α have been identified in patients with severe disease and have been shown to contribute to delayed viral clearance in lung cells [80]. While SARS-CoV-2 replication in human enterocytes in vitro is supported by strong evidence, evidence of SARS-CoV-2 infection in the digestive tract of animals showed mixed results. In the intranasally inoculated hACE2 transgenic mice, viral RNA was detected, but no infectious virus was isolated and no viral antigens were detected in the intestines [35]. In another stable mouse model generated by CRISPR-Cas9 knock-in technology [36], robust virus replication were demonstrated in lungs. The GI epithelium is potentially susceptible to infection by SARS-CoV-2 but to date, it remains unclear whether SARS-CoV-2 replicates in the human gut, and for how long it could persist in the gut. Even if difficult to obtain, further staining of COVID-19 patients GI epithelia, as well as omics analysis of intestinal biopsies notably regarding IFN response, are needed to confirm and quantify the proportion of patients with active replication in the gut.

3. Current Evidence and Uncertainties of SARS-CoV-2 Damaging Intestinal Barrier

Biological plausibility. Within the host cell, the new virions are assembled (KE1847) and to release viral particles, the virus promotes host lysis, leading to cell death and compromising the integrity of the epithelial monolayer. The intestinal barrier is ensured by the integrity of the monolayer epithelium (via cell integrity and tight junctions/adherens proteins), together with the chemical barrier, the mucosal layer and the cellular immune system located in the lamina propria (KE1931). Alternatively, TJs might be altered following SARS-CoV-2 infection enhancing paracellular permeability. In addition, the mucus layer and/or the cellular immune system might be perturbed.

Evidence. No extensive cell death was observed after SARS-CoV-2 infection in intestinal organoids, compared to MERS-CoV that killed most cells within 48 h of infection [31]. SARS-CoV-2 also replicated less efficiently than SARS-CoV and induced less cytopathology in ex vivo human intestinal epithelium [64]. In contrast, studies in vitro with gut derived organoids report observable organoid disintegration [86] also associated with markers of apoptosis, such as caspase 3 [54,86]. No substantial histopathological changes were observed in the intestines of hACE2 intranasally inoculated mice in which no virus was isolated, nor viral antigens detected [35]. In humans, no relation was noted between fecal calprotectin (FC) levels and fecal SARS-CoV-2 RNA in a cohort of 40 hospitalized patients with COVID-19 [1]. In another exploratory study, COVID-19 patients had elevated plasma levels of LPS-binding protein (a gut leakage marker) but not of intestinal FABP (a marker of enterocyte damage) [90]. These data suggest impaired gut barrier function without excessive enterocyte damage and highlight gaps to comprehensively understand under which experimental or clinical conditions, SARS-CoV-2 productively infects and kills enterocytes.

Uncertainties, inconsistencies and gaps. While the biological plausibility was high, currently, there is not enough evidence to support that enterocyte massive cell death following SARS-CoV-2 infection occurs systematically [93]. Number of cases showing histomorphologic changes due intestinal infection by SARS-CoV-2 is still limited. While not easy to obtain, more (post-mortem) intestinal biopsies of COVID-19 patients showing the presence of replicating SARS-CoV-2 along with cell death markers in epithelial cells of the small intestine would be needed to determine precisely if cell death occurs. A small body of evidence points toward a potential alteration of TJs upon SARS-CoV-2 infection. However, definitive evidence is still limited and warrants further research.

4. Current Evidence and Uncertainties of SARS-CoV-2 Enteric Infection Contributing to the Inflammatory Response

4.1. Viral Entry Induces Pro-Inflammatory Mediators Release

Biological plausibility. Viral infections induce a proinflammatory response including expression of cytokines and chemokines via signal transduction pathways activation, such as NF-kB [96], JAK-STAT [97] and NFAT [98].

Evidence. Infection of human intestinal organoids with SARS-CoV-2 elicited a broad signature of cytokines [54] mediated by NFkB/TNF [30]. Lamers et al. [54] showed that the infection of human intestinal organoids with SARS-CoV-2 can induce Il7 expression. Intestinal viral infections cause IL22 expression in T cells via IFNβ1-mediated IL7 production by epithelial cells and IL6 production in fibroblasts. In non-human primates infected with SARS-CoV-2, increased serum concentrations of interleukin (IL)-8, IL-1RA, C-C motif chemokine ligand (CCL)2, CCL11, and chemokine (C-X-C motif) ligand (CXCL)13 were observed [6,42,99,100]. Higher levels of the pro-inflammatory cytokine IL-8 and lower levels of the anti-inflammatory cytokine IL-10 were detected in the feces of COVID-19 patients when compared to uninfected controls [14].

Inconsistencies, uncertainties and gaps. Several components of inflammation exist but we have limited knowledge on the nature of inflammatory pathways triggered in the GI tract by SARS-CoV-2. Additional investigations in COVID-19 patients are still needed, such as analysis of in situ produced cytokines in gut biopsies from COVID-19 patients with distinct disease severity profiles.

4.2. Pro-Inflammatory Mediators Recruit Inflammatory Cells in the Gut

Biological plausibility. Pro-inflammatory signaling (KE1496) recruits’ pro-inflammatory cells, such as neutrophils, macrophages, and T cells to the site of infection (KE1497).

Evidence. When cytokines are released, immune cells, such as neutrophils, macrophages, and lymphocytes, are recruited to the gut environment and facilitates an adaptive immune response [101]. . Histological examination of human intestinal samples revealed that lymphocytes and inflammatory cells infiltrate the lamina propria [103]. Neutrophils recruitment has been demonstrated by gut calprotein (neutrophil-specific alarmin protein) presence in COVID-19 patients where elevated fecal calprotectin and systemic IL-6 response were identified [1] and associated to intestine inflammation, adding to the evidence that SARS-CoV-2 triggers an inflammatory response in the intestine [104].

Uncertainties. Whether direct or indirect modulation in the gut immune activation during SARS-CoV-2 infection is responsible for immune cell recruitment needs to be examined more thoroughly. Recently, in a non-human primate (rhesus monkey) model of SARS-CoV-2 infection, in vivo infection of GI tract increased apoptosis of intestinal epithelial and goblet cells along with intestinal inflammation by macrophages has been reported [41]. However, these results could not explain whe, ther immune modulation in the GI tract was due to direct infection of GI tract cells by the virus or due to changes in the GI tract integrity and microbiota under the influence of systemic cytokines and hypoxic conditions or a combination of all [104].

5. Current Insights, Research Needs and Potential Impact on Clinical Practices

5.1. Productive Enteric Infection

There are multiple outstanding questions regarding SARS-CoV-2 interaction with the human gut. First, it is not firmly established whether SARS-CoV-2 can actively replicate in human intestine. Further studies are clearly needed to determine the experimental and clinical conditions under the gut represents an alternative entry route for the virus into the body. Secondly, based on the current evidence, it remains unclear whether GI symptoms, and particularly diarrhea, are caused by direct infection of the GI tract by SARS-CoV-2 or whether they are a consequence of a local and systemic immune activation. Finally, the potential implication of the gut on long COVID possibly by acting as viral reservoir or due to alteration of gut microbiota requires and deserves significant further investment in research, treatment and care of the PACS patients.

Thus, while the human gut expresses high levels of ACE2, and SARS-CoV-2 infection of human enterocytes in vitro is supported by strong evidence, human healthy gut may not be systematically permeable to viral entry due to the GI fluids, antiviral response and/or the protective multi-layers of the intestinal barrier. However, evidence of intestinal infection of SARS-CoV-2 has been reported, suggesting that there are some conditions that may render people susceptible to SARS-CoV-2 infection in the gut or that may protect the virus from degradation. For example, individuals with altered intestinal barrier prior to infection, or under certain medication or comorbidities, might be more vulnerable to gastrointestinal SARS-CoV-2 infection [118]. An inflammatory environment, as seen in many other conditions such as diabetes, obesity, or resulting from the cytokine storm in severe COVID-19, disrupting the intestinal barrier, may render the GI entry of the SARS-CoV-2 significant [33]. Sex and diet-specific responses partially explaining the effects of obesity and diabetes on COVID-19 disease were observed [119]. Age, medication, metabolic syndrome, via high fat diet for example, could be incorporated into models to mimic human comorbidities in order to investigate this important question. In addition, the colonic mucus barrier is shaped by the composition of the gut microbiota [121].

In conclusion, further research is needed to acquire a comprehensive understanding of the conditions under which SARS-CoV-2 productively infects enterocytes in humans in vivo. Notably, it is important to understand if specific conditions, including age, comorbidities or medication are associated with release of infectious particles from feces by tracking and surveillance of several groups in the population. These studies could be complemented by in situ hybridization or staining of human tissues acquired from biopsies or post-mortem samples of gut retried from COVID-19 positive people.

5.2. Infectious Virus in the Feces

If SARS-CoV-2 can establish an intestinal infection, then it remains unknown whether infectious viral particles can tolerate GI fluids and be shed alive through feces with sufficient concentration and infectivity for subsequent transmission. Infectious viral particles may be retrieved from anecdotal cases, although studies indicate that the vast majority of individuals infected with SARS-CoV-2 do not release infectious particles from stools [125]. While high viral RNA concentrations were observed in stools in two different studies (9 and 10 patients, respectively), infectious virus was not recovered in those samples [33,125,126]. In contrast, replicating SARS-CoV-2 virus was detected in feces in [127] and viable SARS-CoV-2 particles in stool samples in [128]. Several aspects could complicate SARS-CoV-2 isolation from fecal material, such as the stability of the virus in the feces [129] and the potential presence of numerous other viruses. These aspects could also make viral activity assays technically challenging.

Finally, fecal shedding may have important epidemiological implications for community surveillance tools such as wastewater monitoring, which inform public health measures. Detection of SARS-CoV-2 RNA in untreated wastewater has been reported [134]. Detecting SARS-CoV-2 in wastewater might represent a way to better surveille the status of the population and detect peaks of infection and admissions to hospital up to one week ahead development of symptoms or detection in nasopharyngeal swabs [135]. Currently the majority of the longitudinal studies of fecal viral RNA shedding have been limited to hospitalized patients with severe COVID-19 and/or with co-morbidities [138]. Since wastewater viral RNA levels are being considered for use in guiding community level policies, it is critical to better understand how aerosol transmissibility of SARS-CoV-2 RNA are temporally related to fecal viral RNA shedding [136].

More evidence is required to demonstrate whether and in which conditions SARS-CoV-2 can establish a fecal–oral transmission route. This requires determining which people are susceptible to GI infection, and from this pool, in what conditions may people shed infectious virus particles in feces. Another important outstanding question to resolve is determining the minimum infectious dose of SARS-CoV-2, which may vary for the different SARS-CoV-2 variants.

5.3. Gut Implication in the Severity of the COVID-19 Outcomes

It is still unclear whether GI symptoms could be predictive of disease severity. An important body of evidence, however, supports the crucial implication of the gut in the excessive inflammatory response in COVID-19. Impaired intestinal barrier function enhances the translocation of gut bacteria and of bacterial toxins, such as peptidoglycans and lipopolysaccharides (LPS), from the gut lumen into the blood. Increased levels of LPS in the blood (endotoxemia) activate Toll-Like Receptors, leading to the production of numerous pro-inflammatory cytokines and, hence, low-grade systemic inflammation [151]. In severely ill patients, intestinal barrier disruption and associated bacterial translocation exacerbates systemic inflammation [152,153]. Bacteria translocation from the gut into the systemic circulation might result in secondary infections and aggravate pulmonary symptoms in COVID-19 patients [155,156].

Disruption of the intestinal barrier also induces a local inflammatory response. Increased intestinal permeability and chronic intestinal inflammation are hallmarks of inflammatory bowel diseases (IBD), such as Crohn’s disease (CD) [157]. Taking advantage of the genetic aspect in CD, several studies reported that increased permeability might precede CD onset as abnormal lactulose-to-mannitol ratios in asymptomatic first-degree relatives of CD patients was associated with a CD diagnosis during the follow up time [158,159,160]. In line, in the IL-10 gene-deficient IBD mouse model, increased intestinal permeability was observed early in life and then mice spontaneously developed colitis at 12 weeks age [161]. In addition, IL-10 deficient animals treated with AT-1001, a zonulin peptide inhibitor previously shown to reduce small intestinal permeability, developed less colitis later in life. Results from IBD mouse models suggest that investigation of intestinal permeability and inflammation in SARS-CoV-2 infected mice or cells treated with AT-1001 could be informative of the sequential process.

Finally yet importantly, associations between levels of inflammatory markers and gut microbiota composition in COVID-19 patients suggest that the gut microbiota might be involved in the magnitude of COVID-19 severity [122]. Significant alterations in fecal microbiomes of COVID-19 patients were reported at all times of hospitalization [122,164,165,166]. A body of evidence supports that intestinal and systemic inflammation, dysregulation of intestinal ACE2 or infection of intestinal bacteria can be interconnected pathways leading to gut dysbiosis as an adverse outcome following SARS-CoV-2 in the gut, but further laboratory research and large-scale population-based studies are needed to validate these pathways [167]. In addition, changes in the lung microbiome with increase of bacteria normally found in the GI tract were reported in COVID-19 patients [168].

5.4. Gut Implication in Long COVID

Finally, GI disorders described in patients appeared to precede, accompany or follow the respiratory symptoms [5,171,172]. Long-term sequelae of COVID-19, collectively termed the post-acute COVID-19 syndrome (PACS) or long COVID, are rapidly emerging across the globe and many studies following patients who have recovered from the respiratory effects of COVID-19 identified persistent GI sequelae [173,174,175]. In a study from China, around half of the patients (41 of 74) had fecal samples positive for SARS-CoV-2 RNA, which remained positive for longer than the respiratory samples [173]. A recent study detected fecal RNA in around half of participants (113 patients with mild to moderate COVID-19) within the first week after diagnosis and around 4% of the patients shed up viral RNA up to 7 months after diagnosis while respiratory samples were negative [136]. These studies support the possibility that a prolonged SARS-CoV-2 presence in the GI tract, after the respiratory infection is cleared, might represent long-term viral reservoirs contributing to long COVID. A potential bacteriophage-like behavior of SARS-CoV-2 might also offer a way to explain the intestinal/fecal long-term presence of SARS-CoV-2. However, the concept that viral antigen persistence instigates immune perturbation and post-acute COVID-19 still requires validation in controlled clinical trials [176]. Towards that end, the RECOVER initiative (https://recovercovid.org/about) aims to bring together patients, caregivers, clinicians and scientists to understand, prevent and treat Long COVID, notably by collecting biopsies from the lower intestines of some participants [180]. In addition, animal models such as humanized mice [181] or Syrian hamsters [182] will help to highlight molecular mechanism of long COVID and to explore future therapeutics

6. Conclusions

There are multiple outstanding questions regarding SARS-CoV-2 interaction with the human gut. First, it is not firmly established whether SARS-CoV-2 can actively replicate in human intestine. Further studies are clearly needed to determine the experimental and clinical conditions under the gut represents an alternative entry route for the virus into the body. Such conditions encompass comorbidities, age, medication, inflammatory status, dysbiosis, fasted-fed status or ingestion with food. Secondly, based on the current evidence, it remains unclear whether GI symptoms, and particularly diarrhea, are caused by direct infection of the GI tract by SARS-CoV-2 or whether they are a consequence of a local and systemic immune activation. Finally, the potential implication of the gut on long COVID possibly by acting as viral reservoir or due to alteration of gut microbiota requires and deserves significant further investment in research, treatment and care of the PACS patients. In conclusion, in addition to calling for further research and large-scale studies, the potential impacts of SARS-CoV-2 productive enteric infection recommends applying appropriate precautions and potential preventive actions.

This entry is adapted from the peer-reviewed paper 10.3390/jcm11195691