Excretion of SARS-CoV-2 through faecal specimens

Fecal-oral transmission of SARS-CoV-2: A systematic review of evidence from epidemiological and experimental studies

BACKGROUND

SARS-CoV-2 ribonucleic acid (RNA) has been detected in feces, but RNA is not infectious. This systematic review aims to answer if fecal SARS-CoV-2 is experimentally infectious and if evidence of human fecal-oral SARS-CoV-2 transmission exists.

METHODS

On September 19, 2022, we searched PubMed, Embase, Web of Science, medRxiv, and bioRxiv. Biomedical studies inoculating SARS-CoV-2 from feces, rectal, or anal swabs in cells, tissue, organoids, or animals were included. Epidemiological studies of groups differing in exposure to fecal SARS-CoV-2 were included. Risk of bias was assessed using standardized tools. Results were summarized by vote counting, tabulation, and a harvest plot. PROSPERO registration no. CRD42020221719.

RESULTS

A total of 4,874 studies were screened; 26 studies were included; and 13 out of 23 biomedical studies (56.5%) succeeded in infection. Two (66.7%) epidemiological studies found limited evidence suggesting fecal-oral transmission. All studies had concerns about the risk of bias.

CONCLUSIONS

It is possible to experimentally infect cell cultures, organoids, and animals with fecal SARS-CoV-2. No strong epidemiologic evidence was found to support human fecal-oral transmission. We advise future research to study fecal infectivity at different time points during infection, apply appropriate controls, use in vivo models, and study fecal exposure as a risk factor of transmission in human populations.

SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population

Background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral-fecal transmission was suspected as a possible route of infection. The objective of this study was to describe RNA shedding in nasopharyngeal and stool samples obtained from asymptomatic and symptomatic children and to investigate virus viability.

Methods

This study included 179 stool and 191 nasopharyngeal samples obtained from 71 children, which included symptomatic (n = 64) and asymptomatic (n = 7) ones. They were collected every 7 days from the onset of the infection until negativation. Viral RNA was detected by real-time RT-PCR, targeting the N and ORF1 genes. Whole-genome sequencing was performed for positive cases. Viral isolation was assessed on Vero cells, followed by molecular detection confirmation.

Results

All cases included in this study (n = 71) were positive in their nasopharyngeal samples. SARS-CoV-2 RNA was detected in 36 stool samples obtained from 15 out of 71 (21.1%) children; 13 were symptomatic and two were asymptomatic. Excretion periods varied from 7 to 21 days and 7 to 14 days in nasopharyngeal and fecal samples, respectively. Four variants were detected: Alpha (n = 3), B.1.160 (n = 3), Delta (n = 7), and Omicron (n = 1). Inoculation of stool samples on cell culture showed no specific cytopathic effect. All cell culture supernatants were negative for RT-qPCR.

Conclusion

Our study demonstrated nasopharyngeal and fecal shedding of SARS-CoV-2 RNA by children up to 21 and 14 days, respectively. Fecal shedding was recorded in symptomatic and asymptomatic children. Nevertheless, SARS-CoV-2 was not isolated from positive stool samples.

Relationship between anal swab PCR for SARS-CoV-2 with gastrointestinal clinical manifestations and severity of COVID-19 infection in Indonesia

Introduction: Coronavirus disease 2019 (COVID-19) cases caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia remain high. The virus can bind with ACE2 receptor which is not only found in the lungs, but also in the digestive tract. Thus, it allows SARS-CoV-2 infection in the gastrointestinal tract, gastrointestinal manifestations, and detection of viral RNA on anal swab using polymerase chain reaction (PCR). There hasn't been similar study about the role of anal swab in Indonesia yet. Therefore, this study aims to determine the relationship between SARS-COV-2 anal swab PCR with gastrointestinal clinical manifestations, and the severity of COVID-19 in Indonesia. Methods: This is an analytical study with cross-sectional design. Samples were obtained from hospitalized COVID-19 patients from July 2020 to January 2021. Demographic data, clinical manifestations, severity, and SARS-CoV-2 anal swabs PCR were collected using case report form. Results: A total of136 patients were analyzed. 52 patients (38.2%) had positive SARS-CoV-2 anal swabs PCR and 84 patients (61.8%) had negative results. The most common gastrointestinal clinical manifestations were nausea and vomiting in 69 patients (50.7%), anorexia in 62 patients (45.6%), and abdominal pain in 31 patients (22.8%). There were 114 patients (83,8%) classified as mild-moderate symptoms and 22 patients (16,2%) classified as severe-critical symptoms. There was a statistically significant relationship between the gastrointestinal tract SARS-CoV-2 infection and gastrointestinal clinical manifestations (P=0.031). There was no statistically significant relationship between the gastrointestinal SARS-CoV-2 infection and the severity of COVID-19 infection (P = 0.844). Conclusions: This study showed there is a significant relationship between SARS-CoV-2 anal swab PCR with gastrointestinal clinical manifestations. There is no significant relationship between anal swab PCR with the severity of COVID-19 infection.

COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.

Intestinal Shedding of SARS-CoV-2 in Children: No Evidence for Infectious Potential

The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal-oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated 247 stool specimens from 213 pediatric patients to assess the prevalence of intestinal SARS-CoV-2 shedding in hospitalized children without or with COVID-19 and determined the infectious capacity of stool-borne viruses. Upon RT-qPCR screening, the infectivity of virus-positive samples was tested in cell culture using the Vero-E6 permissive cell line. SARS-CoV-2 RNA was detected by RT-qPCR in 32 (13%) stool specimens, but the analysis of virus-positive samples in cell culture revealed no cytopathic effects attributable to SARS-CoV-2-related cell damage. Our findings do not support the notion of potential fecal-oral SARS-CoV-2 spreading, thus questioning the role of hygienic measures designed to prevent this mode of viral transmission.

SARS-CoV-2 RNA levels in Scotland’s wastewater

Nationwide, wastewater-based monitoring was newly established in Scotland to track the levels of SARS-CoV-2 viral RNA shed into the sewage network, during the COVID-19 pandemic. We present a curated, reference dataset produced by this national programme, from May 2020 to February 2022. Viral levels were analysed by RT-qPCR assays of the N1 gene, on RNA extracted from wastewater sampled at 162 locations. Locations were sampled up to four times per week, typically once or twice per week, and in response to local needs. We report sampling site locations with geographical coordinates, the total population in the catchment for each site, and the information necessary for data normalisation, such as the incoming wastewater flow values and ammonia concentration, when these were available. The methodology for viral quantification and data analysis is briefly described, with links to detailed protocols online. These wastewater data are contributing to estimates of disease prevalence and the viral reproduction number (R) in Scotland and in the UK.

Measurement(s)	RNA viral genome
Technology Type(s)	quantitative reverse transcription polymerase chain reaction assay
Factor Type(s)	Geographical coordinate - Lat • Geographical coordinate - Long • Flow rate • Human population • Ammonia concentration • Sample collection date
Sample Characteristic - Organism	SARS Coronavirus 2
Sample Characteristic - Environment	wastewater treatment plant • sewage
Sample Characteristic - Location	Scotland

Gastrointestinal tract lesion in children with COVID-19: from pathogenesis to clinical manifestations

Since the beginning of the pandemic, the new coronavirus infection has been regarded primarily as a respiratory disease. By now, it has become obvious that COVID-19 is a systemic infectious process with multiple organ damage. Having affinity for ACE-2 receptors, the virus can infect the cells of the respiratory tract, as well as the cells of the cardiovascular and nervous systems and smooth muscle structures of various organs. Expression of ACE-2 by enterocytes of the small intestine makes the gastrointestinal tract vulnerable in COVID-19 disease and leads to the manifestation of symptoms of gastrointestinal damage, which is often observed in clinical practice. Gastrointestinal symptoms usually include anorexia, nausea, vomiting, diarrhea, and abdominal pain, which can occur both at the onset and during the disease. Several mechanisms are described to explain these changes in COVID-19. 

Gendered Impact of Age, Toilet Facilities, and Cooking Fuels on the Occurrence of Acute Respiratory Infections in Toddlers in Indonesia and the Philippines

INTRODUCTION

The purpose of the study was to analyze the risk factors of acute respiratory infections (ARI) in children under five in Indonesia and the Philippines and to implement a primary review of the characteristics of toddlers and their households in both countries.

METHODS

Data were obtained from the 2017 Demographic and Health Survey (DHS) of Indonesia and the Philippines. The characteristics of children, mothers, and households were analyzed using bivariate and multivariate logistic regression to examine the significant correlations between variables.

RESULTS

The percentage of children under five with ARI symptoms in 2017 was 1.51% in the Philippines and 4.22% in Indonesia. In Indonesia, males aged under one year had significantly lower occurrences of ARI symptoms (OR 0.54, 95% CI 0.36-0.82). In the Philippines, dirty cooking fuels had a significant effect on increasing the likelihood of ARI in female toddlers (OR 4.01, 95% CI 1.02-15.83). In the Philippines, the unavailability of toilet facilities had a significant effect on increasing the likelihood of ARI in male toddlers (OR 2.67, 95% CI 1.15-6.16).

CONCLUSION

The comparison of risk factors between male and female toddlers revealed different results in some variables, as follows: children aged under one year, dirty cooking fuels, and unavailable toilet facilities. The role of parents is fundamental in taking care of female toddlers, since they are more exposed to ARI at the age of under one year and are more prone to indoor air pollution from solid cooking fuels.

Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication

Background

Little is known of possible selection and replication of SARS-CoV-2 in the intestines and if viral load in feces is associated with severity of disease. Therefore, sequence variations of the spike region in strains collected from feces and nasopharynx (NPH) from the same patients were compared. It was also investigated whether viral load in feces related to severity of COVID-19 in hospitalized patients.

Results

SARS-CoV-2 RNA was found in 88 (79%) fecal samples from 112 patients. The complete spike region could be sequenced in 15 fecal and 14 NPH samples. Fourteen Alpha-variants and one Beta-variant of SARS-CoV-2 were identified. The majority of the viral genetic variants (viral populations) in two fecal samples, but none in NPH, had a reversion of the H69/V70 amino acid deletion normally seen in the Alpha variants. Nine fecal samples contained up to nine minority variants, each which may constitute a separate viral population. Five NPH samples had one genetic variant each, and one NPH sample contained nine minority populations of SARS-CoV-2 spike genes.

Conclusions

The higher genomic diversity of SARS-CoV-2 in feces compared to NPH, and the reversion of the H69/V70 deletion in Alpha variants from feces indicate a selection of viral strains and replication of SARS-CoV-2 in the gastrointestinal tract.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-022-00509-w.

Occupational safety of janitors in Ethiopian University during COVID-19 pandemic: Results from observational study

Introduction

Janitors are at high risk of COVID-19 infection, as they are among the frontline workers for the prevention and control of COVID-19. Poor occupational safety practices could contribute to loss of lives of janitors and the general public. However, there are no detailed investigations on occupational safety practices of janitors involved in different settings, such as universities where there are crowds of people. In addition, although observation is recognized as a better tool to investigate occupational safety practices, previous studies mainly employed self-administered questionnaires and/or face-to-face interviews as data collection mechanisms. Therefore, this study aimed to assess occupational safety practices to prevent COVID-19 transmission and associated factors among Ethiopian University janitors using an observation tool and a self-administered questionnaire.

Methods

An institutional-based cross-sectional study was conducted among 410 janitors of Bule Hora University (Ethiopia) from November to December, 2021. A multivariable logistic regression model was used to identify the independent factors associated with occupational safety practices.

Results

Occupational safety practices for COVID-19 were good only among 53.9% of the janitors. Training on COVID-19 prevention measures (AOR = 2.62; 95% CI: 1.57–4.37), availability of policy and protocol in the work place (AOR = 5.46; 95% CI: 3.57–8.36), and availability of soap/bleach (AOR = 2.71; 95% CI: 1.64–4.46) were found to significantly increase the likelihood of occupational safety of the janitors.

Conclusion

A significant proportion of the janitors had poor occupational safety practices. Therefore, an adequate supply of PPE and regular training and awareness creation on COVID-19 should be strengthened. Close follow-up and regular supervision of safety procedures should also be conducted as controlling strategies.

Cross-species recognition and molecular basis of SARS-CoV-2 and SARS-CoV binding to ACE2s of marine animals

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has an extremely broad host range that includes hippopotami, which are phylogenetically closely related to whales. The cellular ACE2 receptor is one of the key determinants of the host range. Here, we found that ACE2s from several marine mammals and hippopotami could efficiently bind to the receptor-binding domain (RBD) of both SARS-CoV and SARS-CoV-2 and facilitate the transduction of SARS-CoV and SARS-CoV-2 pseudoviruses into ACE2-expressing cells. We further resolved the cryo-electron microscopy complex structures of the minke whale ACE2 and sea lion ACE2, respectively, bound to the RBDs, revealing that they have similar binding modes to human ACE2 when it comes to the SARS-CoV-2 RBD and SARS-CoV RBD. Our results indicate that marine mammals could potentially be new victims or virus carriers of SARS-CoV-2, which deserves further careful investigation and study. It will provide an early warning for the prospective monitoring of marine mammals.

Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection

Background

COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.^1, SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.2, 3, 4 Although much is known about early fecal RNA shedding, little is known about long-term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.⁵.

Methods

We analyzed the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlated shedding with disease symptoms.

Findings

Fecal SARS-CoV-2 RNA is detected in 49.2% [95% confidence interval, 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we found that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA.

Conclusions

The extended presence of viral RNA in feces, but not in respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract and that this infection can be prolonged in a subset of individuals with COVID-19.

Funding

This research was supported by a Stanford ChemH-IMA grant; fellowships from the AACR and NSF; and NIH R01-AI148623, R01-AI143757, and UL1TR003142.

Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Vitamin D3 and COVID-19 as Potential Therapeutic Targets

Purpose: The persistent pandemic of coronavirus disease 2019 (COVID-19), the discovery of gastrointestinal transmission routes and the possible susceptibility of cancer patients to COVID-19 have forced us to search for effective pathways against stomach adenocarcinoma (STAD)/COVID-19. Vitamin D3 (VD3) is a steroid hormone with antiviral, anti-inflammatory and immunomodulatory properties. This study aimed to evaluate the possible functional role and potential mechanisms of action of VD3 as an anti-COVID-19 and anti- STAD. Methods: Clinicopathological analysis, enrichment analysis and protein interaction analysis using bioinformatics and network pharmacology methods. Validate the binding activity of VD3 to core pharmacological targets and viral crystal structures using molecular docking. Results: We revealed the clinical characteristics of STAD/COVID-19 patients. We also demonstrated that VD3 may be anti- STAD/COVID-19 through antiviral, anti-inflammatory, and immunomodulatory pathways. Molecular docking results showed that VD3 binds well to the relevant targets of COVID-19, including the spike RBD/ACE2 complex and main protease (Mpro, also known as 3CLpro). We also identified five core pharmacological targets of VD3 in anti-STAD/COVID-19 and validated the binding activity of VD3 to PAI1 by molecular docking. Conclusion: This study reveals for the first time that VD3 may act on disease target gene SERPINE1 through inflammatory and viral related signaling pathways and biological functions for the therapy of STAD/COVID-19. This may provide a new idea for the use of VD3 in the treatment of STAD/COVID-19.

Prolonged Shedding of SARS-CoV-2 in Feces of COVID-19 Positive Patients: Trends in Genomic Variation in First and Second Wave

The main route of the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are through respiratory pathways and close contact of human-to-human. While information about other modes of transmission is comparatively less, some published literature supporting the likelihood of a fecal-oral mode of transmission has been accumulating. The diagnosis of SARS-COV-2 infected cases is based on the real-time reverse transcription-PCR (RT-PCR). The fecal excretion of SARS-COV-2 has been reported frequently, however, the role of fecal viral load with the severity of disease is not yet clear. Our study focused on the investigation of SARS-CoV-2 shedding in the fecal samples of patients with coronavirus disease 2019 (COVID-19). A total of 280 RT-PCR-positive patients were enrolled, among them 15.4% had gastrointestinal (GI) symptoms. It was shown that 62% of the patients were positive for SARS-CoV-2 RNA in fecal specimens. This positivity was not related to the presence of GI symptoms and the severity of disease. The next generation sequencing [NGS] of SARS-CoV-2 from fecal samples of patients was performed to analyze mutational variations. Findings from this study not only emphasized the potential presence of SARS-CoV-2 in feces, but also its continuing mutational changes and its possible role in fecal-oral transmission.

Maintaining safe office spaces to minimise risks of SARS-CoV-2 transmission

BACKGROUND

SARS-CoV-2 can be transmitted within offices. Traditional respiratory transmission modes have undergone reassessment and a new paradigm has emerged. This paradigm needs examining prior to identifying control measures to prevent office acquired infections (OAI).

METHODS

An ongoing assessment of the SARS-CoV-2 transmission literature, including international public health guidance, began 30/1/2020 and continued to submission 7/2/2022. The evidence for the established respiratory transmission paradigm (either droplet or aerosols) and that of a newly emerging paradigm (aerosol and/or droplets) were explored. Based on the new paradigm control measures needed to minimise OAI were produced.

RESULTS

The old paradigm of respiratory transmission of being either droplet or airborne cannot be evidenced. SARS-CoV-2 is emitted in virus laden particles that can be inhaled and/or sprayed on facial mucous membranes (Airborne being the dominant route). Office hygiene measures include: minimising the opportunities for the virus to enter the building. Reducing the susceptibility of people to the virus. Minimising exposure risks within offices, and optimising success in deployment.

CONCLUSION

Standard office hygiene precautions are needed to reduce OAI risks from SARS-CoV-2. Efforts should focus on enabling the smooth functioning of the office whilst minimising risks that the virus will transmit therein. This includes: local risk assessments as transmission risks vary based on building design, ventilation, capacity, and ways of working. Additionally, using experts to optimise ventilation systems.

Next-generation sequencing: insights to advance clinical investigations of the microbiome

Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.

[The hazards of SARS-COV-2 for aquatic ecosystems]

Introduction

The current COVID-19 pandemic is due to a new emerging coronavirus SARS-CoV-2, belonging to the Coronaviridae family and to the Orthocoronavirinae subfamily. This virus was first reported in December 2019 in China. Although reported by several countries in several animal species, COVID-19 is a disease transmitted from human to human. Moreover, SARS-CoV-2 virus and its RNA were detected in body excretions besides saliva, such as urine and fecal matter discharged into sewage.

Bibliographic review

Within this framework, this article aims to synthesize the bibliographical reviews on SARS-CoV-2 in aquatic environment. It will underline the generalities on SARS-CoV-2, the possible sources of potential contaminations of SARS-CoV-2 in water environment, the viability of SARS-CoV-2 in aquatic environment, the receptive species and the impacts of SARS-CoV-2 on the aquatic ecosystems.

Conclusion

We compile key information about SARS-CoV-2 that are considered important to remember and highlight the importance of further research in this area in order to assess the hazards of SARS-CoV-2 on aquatic ecosystems.

Efficacy of SARS-CoV-2 wastewater surveillance for detection of COVID-19 at a residential private college

Many colleges and universities utilized wastewater surveillance testing for SARS-CoV-2 RNA as a tool to help monitor and mitigate the COVID-19 pandemic on campuses across the United States during the 2020-2021 academic year. We sought to assess the efficacy of one such program by analyzing data on relative wastewater RNA levels from residential buildings in relation to SARS-CoV-2 cases identified through individual surveillance testing, conducted largely independent of wastewater results. Almost 80% of the cases on campus were associated with positive wastewater tests, resulting in an overall positive predictive value of 79% (Chi square 48.1, Df = 1, p < 0.001). However, half of the positive wastewater samples occurred in the two weeks following the return of a student to the residence hall following the 10-day isolation period, and therefore were not useful in predicting new infections. When these samples were excluded, the positive predictive value of a positive wastewater sample was 54%. Overall, we conclude that the continued shedding of viral RNA by patients past the time of potential transmission confounds the identification of new cases using wastewater surveillance, and decreases its effectiveness in managing SARS-CoV-2 infections on a residential college campus.

Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater

Detection and quantification of viruses supplies key information on their spread and allows risk assessment for public health. In wastewater, existing detection methods have been focusing on non‐enveloped enteric viruses due to enveloped virus transmission, such as coronaviruses, by the fecal‐oral route being less likely. Since the beginning of the SARS‐CoV‐2 pandemic, interest and importance of enveloped virus detection in wastewater has increased. Here, quantitative studies on SARS‐CoV‐2 occurrence in feces and raw wastewater and other enveloped viruses via quantitative real‐time reverse transcription polymerase chain reaction (RT‐qPCR) during the early stage of the pandemic until April 2021 are reviewed, including statistical evaluation of the positive detection rate and efficiency throughout the detection process involving concentration, extraction, and amplification stages. Optimized and aligned sampling protocols and concentration methods for enveloped viruses, along with SARS‐CoV‐2 surrogates, in wastewater environments may improve low and variable recovery rates providing increased detection efficiency and comparable data on viral load measured across different studies.

COVID-19: Gastrointestinal manifestations, liver injury and recommendations

Coronavirus disease 2019 (COVID-19) has caused a pandemic that affected all countries with nearly 270 million patients and 5 million deaths, as of as of December, 2021. The severe acute respiratory syndrome coronavirus 2 virus targets the receptor, angiotensin-converting enzyme 2, which is frequently found in human intestinal epithelial cells, bile duct epithelial cells, and liver cells, and all gastrointestinal system organs are affected by COVID-19 infection. The aim of this study is to review the gastrointestinal manifestations and liver damage of COVID-19 infection and investigate the severe COVID-19 infection risk in patients that have chronic gastrointestinal disease, along with current treatment guidelines. A literature search was conducted on electronic databases of PubMed, Scopus, and Cochran Library, consisting of COVID-19, liver injury, gastrointestinal system findings, and treatment. Liver and intestinal involvements are the most common manifestations. Diarrhea, anorexia, nausea/vomiting, abdominal pain are the most frequent symptoms seen in intestinal involvement. Mild hepatitis occurs with elevated levels of transaminases. Gastrointestinal involvement is associated with long hospital stay, severity of the disease, and intensive care unit necessity. Treatments and follow-up of patients with inflammatory bowel diseases, cirrhosis, hepatocellular carcinoma, or liver transplant have been negatively affected during the pandemic. Patients with cirrhosis, hepatocellular carcinoma, auto-immune diseases, or liver transplantation may have a greater risk for severe COVID-19. Diagnostic or therapeutic procedures should be restricted with specific conditions. Telemedicine should be used in non-urgent periodic patient follow up. COVID-19 treatment should not be delayed in patients at the risk group. COVID-19 vaccination should be prioritized in this group.

Prolonged SARS-CoV-2 nucleic acid conversion time in military personnel outbreaks with presence of specific IgG antibodies

Coronavirus disease 2019 (COVID-19) is transmitted person-to-person mainly by close contact or droplets from respiratory tract. However, the actual time of viral shedding is still uncertain as well as the different routes of transmission. We aimed to characterize RNA shedding from nasopharyngeal and rectal samples in prolonged cases of mild COVID-19 in young male soldiers. Seventy patients from three different military locations were monitored after recommending to follow more strict isolation measures to prevent the spread of the virus. Then, nasopharyngeal, rectal, and blood samples were taken. SARS-CoV-2 RNA was detected by RT-PCR and specific antibodies by chemiluminescent immunoassays. The median nucleic acid conversion time (NACT) was 60 days (IQR: 7-85 days). Rectal swabs were taken in 60 % of patients. Seven patients (10 %) were positive in nasopharyngeal and rectal swabs, and five (7.14 %) remained positive in rectal swabs, but negative in nasopharyngeal samples. Four patients (5.71 %) that had been discharged, were positive again after 15 days. No significant difference was found in nucleic acid conversion time between age groups nor clinical classification. Maintaining distancing among different positive patients is essential as a possible re-exposure to the virus could cause a longer nucleic acid conversion time in SARS-COV-2 infections.

Gastrointestinal viral shedding in children with SARS-CoV-2: a systematic review and meta-analysis

BACKGROUND

Coronavirus disease 2019 (COVID-19) has different manifestations in pediatric cases. It is assumed that they might present more gastrointestinal symptoms with a different viral shedding pattern in gastrointestinal samples. In this systematic review and meta-analysis, we aimed to evaluate the viral shedding pattern in gastrointestinal specimens of children with COVID-19.

METHODS

We searched all published studies in English language in PubMed, Web of Science, and Scopus, up to date as of October 2021. Our search included the term "severe acute respiratory syndrome coronavirus 2, COVID-19, SARS-CoV-2, novel coronavirus, or coronavirus; and shed, excrete, secret, or carriage; and stool or rectal; and children or pediatrics". We included studies evaluating SARS-CoV-2 shedding in gastrointestinal specimens, including rectal swabs and stool samples of children with COVID-19 infection. We excluded duplicated data, case reports, and studies without original data.

RESULTS

Twelve studies met the eligibility criteria for the qualitative synthesis, 10 of which were included in the meta-analysis. The pooled prevalence of gastrointestinal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in children with COVID-19 was 86% (95% confidence interval 73%-96%, I² = 62.28%). After respiratory specimen had become negative, 72% (43/60) had persistent shedding in gastrointestinal specimens. The gastrointestinal RNA had a positive test result for more than 70 days after symptoms onset.

CONCLUSIONS

Gastrointestinal shedding of SARS-CoV-2 might occur in a substantial portion of children and might persist long after negative respiratory testing. Further research is recommended to find the role of SARS-CoV-2 gastrointestinal shedding in transmission in children.

SARS-CoV-2 infection and replication in human gastric organoids

COVID-19 typically manifests as a respiratory illness, but several clinical reports have described gastrointestinal symptoms. This is particularly true in children in whom gastrointestinal symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. These observations raise the question of whether the virus can replicate within the stomach. Here we generate gastric organoids from fetal, pediatric, and adult biopsies as in vitro models of SARS-CoV-2 infection. To facilitate infection, we induce reverse polarity in the gastric organoids. We find that the pediatric and late fetal gastric organoids are susceptible to infection with SARS-CoV-2, while viral replication is significantly lower in undifferentiated organoids of early fetal and adult origin. We demonstrate that adult gastric organoids are more susceptible to infection following differentiation. We perform transcriptomic analysis to reveal a moderate innate antiviral response and a lack of differentially expressed genes belonging to the interferon family. Collectively, we show that the virus can efficiently infect the gastric epithelium, suggesting that the stomach might have an active role in fecal-oral SARS-CoV-2 transmission.

What is the risk of acquiring SARS-CoV-2 from the use of public toilets?

Public toilets and bathrooms may act as a contact hub point where community transmission of SARS-CoV-2 occurs between users. The mechanism of spread would arise through three mechanisms: inhalation of faecal and/or urinary aerosol from an individual shedding SARS-CoV-2; airborne transmission of respiratory aerosols between users face-to-face or during short periods after use; or from fomite transmission via frequent touch sites such as door handles, sink taps, lota or toilet roll dispenser. In this respect toilets could present a risk comparable with other high throughput enclosed spaces such as public transport and food retail outlets. They are often compact, inadequately ventilated, heavily used and subject to maintenance and cleaning issues. Factors such as these would compound the risks generated by toilet users incubating or symptomatic with SARS-CoV-2. Furthermore, toilets are important public infrastructure since they are vital for the maintenance of accessible, sustainable and comfortable urban spaces. Given the lack of studies on transmission through use of public toilets, comprehensive risk assessment relies upon the compilation of evidence gathered from parallel studies, including work performed in hospitals and prior work on related viruses. This narrative review examines the evidence suggestive of transmission risk through use of public toilets and concludes that such a risk cannot be lightly disregarded. A range of mitigating actions are suggested for both users of public toilets and those that are responsible for their design, maintenance and management.

Transmission of severe acute respiratory syndrome coronavirus 2 via fecal-oral: Current knowledge

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 93 million cases and 2 million deaths in the world. SARS-CoV-2 respiratory tract infection and its main clinical manifestations such as cough and shortness of breath are well known to the scientific community. However, a growing number of studies have reported SARS-CoV-2-related gastrointestinal involvement based on clinical manifestations, such as diarrhea, nausea, vomiting, and abdominal pain as well as on the pathophysiological mechanisms associated with coronavirus disease 2019. Furthermore, current evidence suggests SARS-CoV-2 transmission via the fecal-oral route and aerosol dissemination. Moreover, studies have shown a high risk of contamination through hospital surfaces and personal fomites. Indeed, viable SARS-CoV-2 specimens can be obtained from aerosols, which raises the possibility of transmission through aerosolized viral particles from feces. Therefore, the infection by SARS-CoV-2 via fecal-oral route or aerosolized particles should be considered. In addition, a possible viral spread to sources of drinking water, sewage, and rivers as well as the possible risk of viral transmission in shared toilets become a major public health concern, especially in the least developed countries. Since authors have emphasized the presence of viral RNA and even viable SARS-CoV-2 in human feces, studies on the possible fecal-oral coronavirus disease 2019 transmission become essential to understand better the dynamics of its transmission and, then, to reinforce preventive measures against this infection, leading to a more satisfactory control of the incidence of the infection.

Covid-19 and development of heart failure: mystery and truth

Coronavirus disease 2019 (Covid-19) is a novel worldwide pandemic caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). During Covid-19 pandemic, socioeconomic deprivation, social isolation, and reduced physical activities may induce heart failure (HF), destabilization, and cause more complications. HF appears as a potential hazard due to SARS-CoV-2 infection, chiefly in elderly patients with underlying comorbidities. In reality, the expression of cardiac ACE2 is implicated as a target point for SARS-CoV-2-induced acute cardiac injury. In SARS-CoV-2 infection, like other febrile illnesses, high blood viscosity, exaggerated pro-inflammatory response, multisystem inflammatory syndrome, and endothelial dysfunction-induced coagulation disorders may increase risk of HF development. Hypoxic respiratory failure, as in pulmonary edema, severe acute lung injury (ALI), and acute respiratory distress syndrome (ARDS) may affect heart hemodynamic stability due to the development of pulmonary hypertension. Indeed, Covid-19-induced HF could be through the development of cytokine storm, characterized by high proliferation pro-inflammatory cytokines. In cytokine storm-mediated cardiac dysfunction, there is a positive correlation between levels of pro-inflammatory cytokine and myocarditis-induced acute cardiac injury biomarkers. Therefore, Covid-19-induced HF is more complex and related from a molecular background in releasing pro-inflammatory cytokines to the neuro-metabolic derangements that together affect cardiomyocyte functions and development of HF. Anti-heart failure medications, mainly digoxin and carvedilol, have potent anti-SARS-CoV-2 and anti-inflammatory properties that may mitigate Covid-19 severity and development of HF. In conclusion, SARS-CoV-2 infection may lead to the development of HF due to direct acute cardiac injury or through the development of cytokine storms, which depress cardiomyocyte function and cardiac contractility. Anti-heart failure drugs, mainly digoxin and carvedilol, may attenuate severity of HF by reducing the infectivity of SARS-CoV-2 and prevent the development of cytokine storms in severely affected Covid-19 patients.

Is the Gut Microbiome a Target for Adjuvant Treatment of COVID-19?

High expression of the transmembrane protein angiotensin I converting enzyme 2 (ACE2), more than 100-times higher as in the lung, and transmembrane serine protease 2 (TMPRSS2) in the gastrointestinal tract leads to infection with SARS-CoV-2. According to meta-analysis data, 9.8–20% of COVID-19 patients experience gastrointestinal symptoms, where diarrhoea is the most frequent, and about 50% shed viruses with high titre through their faeces, where a first faecal transmission was reported. Furthermore, gut inflammation, intestinal damage, and weakening of the gut mucosal integrity that leads to increased permeability has been shown in different studies for COVID-19 patients. This can lead to increased inflammation and bacteraemia. Low mucosal integrity combined with low intestinal damage is a good predictor for disease progression and submission to the intensive care unit (ICU). Several pilot studies have shown that the gut microbiome of COVID-19 patients is changed, microbial richness and diversity were lower, and opportunistic pathogens that can cause bacteraemia were enriched compared to a healthy control group. In a large proportion of these patients, dysbiosis was not resolved at discharge from the hospital and one study showed dysbiosis is still present after 3 months post COVID-19. Consequently, there might be a link between dysbiosis of the gut microbiome in COVID-19 patients and chronic COVID-19 syndrome (CCS). Various clinical trials are investigating the benefit of probiotics for acute COVID-19 patients, the majority of which have not reported results yet. However, two clinical trials have shown that a certain combination of probiotics is beneficial and safe for acute COVID-19 patients. Mortality was 11% for the probiotic treatment group, and 22% for the control group. Furthermore, for the probiotic group, symptoms cleared faster, and an 8-fold decreased risk of developing a respiratory failure was calculated. In conclusion, evidence is arising that inflammation, increased permeability, and microbiome dysbiosis in the gut occur in COVID-19 patients and thus provide new targets for adjuvant treatments of acute and chronic COVID-19. More research in this area is needed.

An optimised protocol for detection of SARS-CoV-2 in stool

BACKGROUND

SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to nasopharyngeal swab samples, the complexity of the stool matrix poses a challenge in the detection of the virus that has not yet been solved. However, robust and reliable methods are needed to estimate the prevalence and persistence of SARS-CoV-2 in the gut and to ensure the safety of microbiome-based procedures such as faecal microbiota transplant (FMT). The aim of this study was to establish a sensitive and reliable method for detecting SARS-CoV-2 in stool samples.

RESULTS

Stool samples from individuals free of SARS-CoV-2 were homogenised in saline buffer and spiked with a known titre of inactivated virus ranging from 50 to 750 viral particles per 100 mg stool. Viral particles were concentrated by ultrafiltration, RNA was extracted, and SARS-CoV-2 was detected via real-time reverse-transcription polymerase chain reaction (RT-qPCR) using the CDC primers and probes. The RNA extraction procedure we used allowed for the detection of SARS-CoV-2 via RT-qPCR in most of the stool samples tested. We could detect as few as 50 viral particles per 100 mg of stool. However, high variability was observed across samples at low viral titres. The primer set targeting the N1 region provided more reliable and precise results and for this primer set our method had a limit of detection of 1 viral particle per mg of stool.

CONCLUSIONS

Here we describe a sensitive method for detecting SARS-CoV-2 in stool samples. This method can be used to establish the persistence of SARS-CoV-2 in stool and ensure the safety of clinical practices such as FMT.

Sewage Systems Surveillance for SARS-CoV-2: Identification of Knowledge Gaps, Emerging Threats, and Future Research Needs

The etiological agent for novel coronavirus (COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), not only affects the human respiratory system, but also the gastrointestinal tract resulting in gastrointestinal manifestations. The high rate of asymptomatic infected individuals has challenged the estimation of infection spread based on patients' surveillance, and thus alternative approaches such as wastewater-based epidemiology (WBE) have been proposed. Accordingly, the number of publications on this topic has increased substantially. The present systematic review thus aimed at providing state-of-the-knowledge on the occurrence and existing methods for sampling procedures, detection/quantification of SARS-CoV-2 in sewage samples, as well as anticipating challenges and providing future research direction to improve the current scientific knowledge. Articles were collected from three scientific databases. Only studies reporting measurements of virus in stool, urine, and wastewater samples were included. Results showed that improving the scientific community's understanding in these avenues is essential if we are to develop appropriate policy and management tools to address this pandemic pointing particularly towards WBE as a new paradigm in public health. It was also evident that standardized protocols are needed to ensure reproducibility and comparability of outcomes. Areas that require the most improvements are sampling procedures, concentration/enrichment, detection, and quantification of virus in wastewater, as well as positive controls. Results also showed that selecting the most accurate population estimation method for WBE studies is still a challenge. While the number of people infected in an area could be approximately estimated based on quantities of virus found in wastewater, these estimates should be cross-checked by other sources of information to draw a more comprehensive conclusion. Finally, wastewater surveillance can be useful as an early warning tool, a management tool, and/or a way for investigating vaccination efficacy and spread of new variants.

Sewage Systems Surveillance for SARS-CoV-2: Identification of Knowledge Gaps, Emerging Threats, and Future Research Needs

The etiological agent for novel coronavirus (COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), not only affects the human respiratory system, but also the gastrointestinal tract resulting in gastrointestinal manifestations. The high rate of asymptomatic infected individuals has challenged the estimation of infection spread based on patients' surveillance, and thus alternative approaches such as wastewater-based epidemiology (WBE) have been proposed. Accordingly, the number of publications on this topic has increased substantially. The present systematic review thus aimed at providing state-of-the-knowledge on the occurrence and existing methods for sampling procedures, detection/quantification of SARS-CoV-2 in sewage samples, as well as anticipating challenges and providing future research direction to improve the current scientific knowledge. Articles were collected from three scientific databases. Only studies reporting measurements of virus in stool, urine, and wastewater samples were included. Results showed that improving the scientific community's understanding in these avenues is essential if we are to develop appropriate policy and management tools to address this pandemic pointing particularly towards WBE as a new paradigm in public health. It was also evident that standardized protocols are needed to ensure reproducibility and comparability of outcomes. Areas that require the most improvements are sampling procedures, concentration/enrichment, detection, and quantification of virus in wastewater, as well as positive controls. Results also showed that selecting the most accurate population estimation method for WBE studies is still a challenge. While the number of people infected in an area could be approximately estimated based on quantities of virus found in wastewater, these estimates should be cross-checked by other sources of information to draw a more comprehensive conclusion. Finally, wastewater surveillance can be useful as an early warning tool, a management tool, and/or a way for investigating vaccination efficacy and spread of new variants.

Traditional Chinese Medicine Enema Therapy in a Patient With a Confirmed Negative SARS-CoV-2 Test in the Respiratory Tract but Positive in the Intestinal Tract: A Case Report

We report the case of a 43-year-old man who was infected with SARS-CoV-2 in February 2020 and actively cooperated with treatment in the hospital. During the course of treatment, we found that the respiratory SARS-CoV-2 nucleic acid became negative, but remained positive in the intestinal tract. As a result, we adjusted the treatment plan to include traditional Chinese medicine enema treatment. The patient had negative intestinal SARS-CoV-2 nucleic acid test within 4 days, and the subsequent repeated review of intestinal SARS-CoV-2 nucleic acid was negative, and the virus was undetectable. It is suggested that traditional Chinese medicine enema treatment may be helpful to remove the SARS-CoV-2 in the intestines of patients with COVID-19 infection, and may support the treatment of patients with respiratory SARS-CoV-2 nucleic acid negative and positive in the intestinal tract.

Impact of both socioeconomic level and occupation on antibody prevalence to SARS-CoV-2 in an Egyptian cohort: The first episode

We studied the impact of socioeconomic level on the anti-SARS-CoV-2-antibodies prevalence in an Egyptian cohort. The low socioeconomic standard group (LSS) included 51 humans, 30 females (F) and 21 males (M). The high socioeconomic standard group (HSS) included 55 subjects, 24 F and 31 M. Of the 30 LSSF, 6 were immunoglobulin M (IgM), 21 immunoglobulin G (IgG), and 6 double positive. Of the 21 LSSM, 5 were IgM, 12 IgG, and 5 double positive. Of the 24 HSSF, 6 were IgM, 11 IgG, and 5 double positive. Of the 31 HSSM, 6 were IgM, 14 IgG, and 4 double positive. Of the 51 LSS humans, 26 were symptomatic (S) and 25 asymptomatic (AS). Of the 26 S, 20 were IgG and 8 IgM/IgG double positive. Of the 25 AS, 13 were IgG and 3 IgM/IgG double positive. Of the 55 HSS humans, 38 were S and 17 AS. Of the 38S, 24 were IgG and 11 IgM positive of whom, 9 were double positive. Of the 17 AS, one was IgG and one IgM positive. The IgM prevalence was higher among the HSS humans. The IgG prevalence was significantly higher among the LSS humans. In the two different socioeconomic standards, the prevalence of either IgM or IgG was higher among F. An inverse correlation was observed between age and the anti-SARS-CoV-2-antibodies prevalence except for LSSF-IgG and LSSM-IgM. In conclusion, socioeconomic standard, gender, and age impact humoral responses to SARS-CoV-2 with a clear heterogeneity in individualized responses to the infection in terms of symptoms.

SARS-Cov-2 and COVID-19, Basic and Clinical Aspects of the Human Pandemic: A Review

In the last two decades, we have witnessed three major epidemics of the coronavirus human disease namely, severe acute respiratory syndrome (SARS), Middle Eastern respiratory syndrome, and more recently an ongoing global pandemic of coronavirus disease 2019 (COVID-19). Iran, a country of nearly 84 million, in the Middle East, severely involved with the COVID-19 disease. A documented multidimensional approach to COVID-19 disease is therefore mandatory to provide a well-balanced platform for the concerned medical community in our county and beyond. In this review, we highlight the disease status in Iran and attempt to provide a multilateral view of the fundamental and clinical aspects of the disease including the clinical features of the confirmed cases, virology, pathogenesis, epidemiology, and laboratory methods needed for diagnosis.

Analysis of viral load in different specimen types and serum antibody levels of COVID-19 patients

BACKGROUND

COVID-19 has caused a global pandemic and the death toll is increasing. However, there is no definitive information regarding the type of clinical specimens that is the best for SARS-CoV-2 detection, the antibody levels in patients with different duration of disease, and the relationship between antibody level and viral load.

METHODS

Nasopharyngeal swabs, anal swabs, saliva, blood, and urine specimens were collected from patients with a course of disease ranging from 7 to 69 days. Viral load in different specimen types was measured using droplet digital PCR (ddPCR). Meanwhile, anti-nucleocapsid protein (anti-N) IgM and IgG antibodies and anti-spike protein receptor-binding domain (anti-S-RBD) IgG antibody in all serum samples were tested using ELISA.

RESULTS

The positive detection rate in nasopharyngeal swab was the highest (54.05%), followed by anal swab (24.32%), and the positive detection rate in saliva, blood, and urine was 16.22%, 10.81%, and 5.41%, respectively. However, some patients with negative nasopharyngeal swabs had other specimens tested positive. There was no significant correlation between antibody level and days after symptoms onset or viral load.

CONCLUSIONS

Other specimens could be positive in patients with negative nasopharyngeal swabs, suggesting that for patients in the recovery period, specimens other than nasopharyngeal swabs should also be tested to avoid false negative results, and anal swabs are recommended. The antibody level had no correlation with days after symptoms onset or the viral load of nasopharyngeal swabs, suggesting that the antibody level may also be affected by other factors.

Management of environmental health to prevent an outbreak of COVID-19

The World Health Organization (WHO) has recently pronounced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a serious pandemic. It is, therefore, mandatory for public health authorities to have an environmental health management plan against COVID-19. This chapter summarizes articles and official reports related to environmental health management and prevention policies against COVID-19. Because medical sectors require comprehensive guidelines to follow in such pandemic situations, this chapter highlights the significant factors of COVID-19 transmission in our environment (e.g., air), waste management for COVID-19, and protection and disinfection policies against COVID-19. At present, scientists are still discovering more about COVID-19 and its effect on the environment and the health sector. As such, further research is required to increase knowledge about the structural and pathogenic features of COVID-19 and to find effective treatments to dominate this epidemic.