Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus

Global prevalence of Porcine Astrovirus: A systematic review and meta-analysis

Porcine astrovirus (PAstV) is a widespread enteric virus in pigs, often co-infecting with other enteric viruses and contributing to diarrhea, leading to significant economic losses in the global swine industry. This study aims to identify the factors influencing PAstV prevalence by conducting a statistical meta-analysis of global data and evaluating heterogeneity across various subgroups. A systematic literature search was performed across PubMed, Web of Science, CNKI, Wanfang, and VIP databases, covering studies from the inception of the databases up to December 2023. A random-effects model was employed to estimate the global pooled prevalence of PAstV infection, and subgroup analyses were performed to evaluate the impact of different continents, years, detection methods, and sample types on the prevalence. Publication bias was assessed using a funnel plot and Egger's test. A total of 45 studies from 10 countries across three continents, involving 376 articles, were included in the meta-analysis. The global pooled prevalence of PAstV infection was found to be 28.19 % (95 % CI, 21.94 %-34.89 %). Subgroup analysis indicated significant differences in PAstV prevalence across continents, with Asia at 26.25 % (95 % CI, 25.41 %-27.09 %), Europe at 36.19 % (95 % CI, 34.09 %-38.33 %), and North America at 63.24 %. The prevalence of PAstV was highest between 2012 and 2014 (49.86 %, 95 % CI, 47.21 %-52.51 %), followed by a decreasing trend that stabilized below 30 % from 2015 to 2023. The analysis showed no significant influence of detection methods on PAstV prevalence. However, the prevalence in non-fecal samples (43.09 %, 95 % CI: 41.05 %-45.15 %) was significantly higher than in fecal samples (22.92 %, 95 % CI: 21.87 %-23.99 %). Additionally, the prevalence of PAstV in asymptomatic pigs (36.71 %, 95 % CI, 34.97 %-38.48 %) exceeded that in diarrheic pigs (28.18 %, 95 % CI, 26.94 %-29.44 %). Among different age groups, nursery pigs(6-10 weeks) exhibited the highest infection rate (63.19 %, 95 % CI, 58.45 %-67.75 %), followed by weaning pigs(3-6 weeks) (60.00 %, 95 % CI, 56.48 %-63.45 %), finisher pigs(>10 weeks) (49.89 %, 95 % CI, 46.59 %-53.19 %), sows (35.33 %, 95 % CI, 31.45 %-39.37 %), with suckling pigs(0-3 weeks) showing the lowest rate (31.93 %, 95 % CI, 30.23 %-33.68 %). This study highlights the widespread nature of PAstV infection in pig populations globally, with notable variations in prevalence across regions, years, and sample types. The high prevalence of asymptomatic infections underscores the need for enhanced PAstV surveillance and control measures.

Preferential apical infection of Caco-2 intestinal cell monolayers by SARS-CoV-2 is associated with damage to cellular barrier integrity: Implications for the pathophysiology of COVID-19

SARS-CoV-2 can infect different organs, including the intestine. In an in vitro model of Caco-2 intestinal cell line, we previously found that SARS-CoV-2 modulates the ACE2 receptor expression and affects the expression of molecules involved in intercellular junctions. To further explore the possibility that the intestinal epithelium can serve as an alternative infection route for SARS-CoV-2, we used a model of polarized monolayers of Caco-2 cells (or co-cultures of two intestinal cell lines: Caco-2 and HT29) grown on the polycarbonate membrane of Transwell inserts, inoculated with the virus either in the upper or lower chamber of culture to determine the tropism of the virus for the apical or basolateral pole of these cells. In both polarized Caco-2 cell monolayers and co-culture Caco-2/HT29 cell monolayer, apical SARS-CoV-2 inoculation was found to be much more effective in establishing infection than basolateral inoculation. In addition, apical SARS-CoV-2 infection triggers monolayer degeneration, as shown by histological examination, measurement of trans-epithelial electrical resistance, and cell adhesion molecule expression. During apical infection, the infectious viruses reach the lower chamber, suggesting either a transcytosis mechanism from the apical side to the basolateral side of cells, a paracellular trafficking of the virus after damage to intercellular junctions in the epithelial barrier, or both. Taken together, these data indicate a preferential tropism of SARS-CoV-2 for the apical pole of the human intestinal tract and suggest that infection via the intestinal lumen leads to a systemic infection.

Advances in the Development and Application of Human Organoids: Techniques, Applications, and Future Perspectives

Organoids are three-dimensional (3D) cell cultures derived from human pluripotent stem cells or adult stem cells that recapitulate the cellular heterogeneity, structure, and function of human organs. These microstructures are invaluable for biomedical research due to their ability to closely mimic the complexity of native tissues while retaining human genetic material. This fidelity to native organ systems positions organoids as a powerful tool for advancing our understanding of human biology and for enhancing preclinical drug testing. Recent advancements have led to the successful development of a variety of organoid types, reflecting a broad range of human organs and tissues. This progress has expanded their application across several domains, including regenerative medicine, where organoids offer potential for tissue replacement and repair; disease modeling, which allows for the study of disease mechanisms and progression in a controlled environment; drug discovery and evaluation, where organoids provide a more accurate platform for testing drug efficacy and safety; and microecological research, where they contribute to understanding the interactions between microbes and host tissues. This review provides a comprehensive overview of the historical development of organoid technology, highlights the key achievements and ongoing challenges in the field, and discusses the current and emerging applications of organoids in both laboratory research and clinical practice.

Human respiratory organoids sustained reproducible propagation of human rhinovirus C and elucidation of virus-host interaction

The lack of a robust system to reproducibly propagate HRV-C, a family of viruses refractory to cultivation in standard cell lines, has substantially hindered our understanding of this common respiratory pathogen. We sought to develop an organoid-based system to reproducibly propagate HRV-C, and characterize virus-host interaction using respiratory organoids. We demonstrate that airway organoids sustain serial virus passage with the aid of CYT387-mediated immunosuppression, whereas nasal organoids that more closely simulate the upper airway achieve this without any intervention. Nasal organoids are more susceptible to HRV-C than airway organoids. Intriguingly, upon HRV-C infection, we observe an innate immune response that is stronger in airway organoids than in nasal organoids, which is reproduced in a Poly(I:C) stimulation assay. Treatment with α-CDHR3 and antivirals significantly reduces HRV-C viral growth in airway and nasal organoids. Additionally, an organoid-based immunofluorescence assay is established to titrate HRV-C infectious particles. Collectively, we develop an organoid-based system to reproducibly propagate the poorly cultivable HRV-C, followed by a comprehensive characterization of HRV-C infection and innate immunity in physiologically active respiratory organoids. The organoid-based HRV-C infection model can be extended for developing antiviral strategies. More importantly, our study has opened an avenue for propagating and studying other uncultivable human and animal viruses.

Curcuma sp. "Khamin Oi" extracts inhibit human coronavirus OC43 replication in HCT-8 colorectal cell line

Plants belonging to the genus Curcuma have shown promise in exerting antiviral activity. In this study, Curcuma sp. "Khamin Oi" (CKO), a traditional Thai medicinal herb listed in Thai herbal pharmacopoeia, was subjected to extraction using a variety of solvents. Consequently, LC-MS/MS and GC-MS/MS analyses were conducted to assess the phytochemical profiles of all the crude extracts and identify the compounds potentially responsible for their antiviral effects. The antiviral effects of these extracts against the human coronavirus OC43 (HCoV-OC43) were also investigated. An in-cell ELISA was used to investigate the anti-HCoV-OC43 replication activity of the crude rhizome extracts of CKO. Among the extracts, the crude hexane extract of CKO exhibited the lowest IC50 (3.62 μg/mL), with a high selectivity index (SI) of 31.90, despite having the lowest curcuminoid content. While the methanolic extract of Curcuma longa L., known for its high curcuminoid content among Curcuma species, showed an IC50 of 14.83 μg/mL with an SI of 2.80. Further in vitro and in vivo investigations of CKO crude extract are necessary to understand its potential anti-HCoV-OC43 properties.

Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19

Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.

Oro-faecal transmission of SARS-CoV-2: A systematic review of studies employing viral culture from gastrointestinal and other potential oro-faecal sources and evidence for transmission to humans

The extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established.We systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO COVID-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28 November 2023.We included 13 studies involving 229 COVID-19 subjects - providing 308 faecal or rectal swab SARS-CoV2 reverse transcription-polymerase chain reaction (RT-PCR)-positive samples tested with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (two cohorts and one case series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole-genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 308 faecal samples subjected to cell culture showed replication-competent virus. One study found replication-competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans.Our review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed using standardized cell culture methods, control groups, adequate follow-up, and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.

Proton Pump Inhibitors and Risk of COVID-19 Infection in Children

OBJECTIVE

To evaluate the influence of proton pump inhibitor (PPI) use on COVID-19 susceptibility and severity in children.

STUDY DESIGN

This retrospective, case-control study included all children ≤21 years undergoing COVID-19 polymerase chain reaction testing at a tertiary children's hospital between March 2020 and January 2023. The main exposure was PPI usage. The primary outcome was COVID-19 infection. The secondary outcome was COVID-19 hospitalization. Log-binomial regressions were used to examine associations between PPI use and these outcomes.

RESULTS

116 209 patients age 8.5 ± 6.2 years underwent 234 867 COVID-19 tests. Current PPI use was associated with a decreased risk of COVID-19 test positivity compared with PPI nonuse [RR 0.85 (95% CI 0.76, 0.94), P = .002]; however, there was a significant interaction with time of testing, and an effect of PPIs was no longer seen in the final months of the study following lessening of COVID-19 precautions [RR 1.04 (95% CI 0.0.80, 1.36), P = .77]. PPI use was not associated with risk of hospitalization in patients positive for COVID-19 after adjusting for other hospitalization risk factors [RR 0.85 (95% CI 0.64, 1.13), P = .26].

CONCLUSIONS

We did not find an association between PPI use and increased COVID-19 susceptibility or severity in this pediatric sample. These results provide reassuring evidence that PPIs may not worsen COVID-19 outcomes in children.

Proton pump inhibitors associated with severe COVID-19 among two-dose but not three-dose vaccine recipients

BACKGROUND AND AIM

Proton pump inhibitors (PPIs) may increase the risk of COVID-19 among non-vaccinated subjects via various mechanisms, including gut dysbiosis. We aimed to investigate whether PPIs also affect the clinical outcomes of COVID-19 among vaccine recipients.

METHODS

This was a territory-wide cohort study of 3 272 286 vaccine recipients (aged ≥ 18 years) of ≥ 2 doses of either BNT162b2 or CoronaVac. Exclusion criteria included prior gastrointestinal surgery, immunocompromised status, and prior COVID-19. The primary outcome was COVID-19, and secondary outcomes included COVID-19-related hospitalization and severe infection (composite of intensive care unit admission, ventilatory support, and/or death). Covariates include age, sex, the Charlson Comorbidity Index, comorbidities, and concomitant medication use. Subjects were followed from index date (first dose of vaccination) until outcome occurrence, death, additional dose of vaccination, or March 31, 2022. Exposure was pre-vaccination PPI use (any prescription within 90 days before the index date). Propensity score (PS) matching and a Poisson regression model were used to estimate the adjusted incidence rate ratio (aIRR) of outcomes with PPI use.

RESULTS

Among 439 154 PS-matched two-dose vaccine recipients (mean age: 65.3 years; male: 45.7%) with a median follow-up of 6.8 months (interquartile range: 2.6-7.9), PPI exposure was associated with a higher risk of COVID-19 (aIRR: 1.08; 95% confidence interval [95% CI]: 1.05-1.10), hospitalization (aIRR: 1.20; 95% CI: 1.08-1.33), and severe infection (aIRR: 1.57; 95% CI: 1.24-1.98). Among 188 360 PS-matched three-dose vaccine recipients (mean age: 62.5 years; male: 49.0%; median follow-up: 9.1 months [interquartile range: 8.0-10.9]), PPIs were associated with higher infection risk (aIRR: 1.11; 95% CI: 1.08-1.15) but not other outcomes.

CONCLUSIONS

Although PPI use was associated with a higher COVID-19 risk, severe infection was limited to two-dose but not three-dose vaccine recipients.

Global Literature Analysis of Organoid and Organ-on-Chip Research

Organoids and cells in organ-on-chip platforms replicate higher-level anatomical, physiological, or pathological states of tissues and organs. These technologies are widely regarded by academia, the pharmacological industry and regulators as key biomedical developments. To map advances in this emerging field, a literature analysis of 16,000 article metadata based on a quality-controlled text-mining algorithm is performed. The analysis covers titles, keywords, and abstracts of categorized academic publications in the literature and preprint databases published after 2010. The algorithm identifies and tracks 149 and 107 organs or organ substructures modeled as organoids and organ-on-chip, respectively, stem cell sources, as well as 130 diseases, and 16 groups of organisms other than human and mouse in which organoid/organ-on-chip technology is applied. The analysis illustrates changing diversity and focus in organoid/organ-on-chip research and captures its geographical distribution. The downloadable dataset provided is a robust framework for researchers to interrogate with their own questions.

Recent Advances in Graphene Oxide-Based on Organoid Culture as Disease Model and Cell Behavior - A Systematic Literature Review

Due to their ability to replicate the in vivo microenvironment through cell interaction and induce cells to stimulate cell function, three-dimensional cell culture models can overcome the limitations of two-dimensional models. Organoids are 3D models that demonstrate the ability to replicate the natural structure of an organ. In most organoid tissue cultures, matrigel made of a mouse tumor extracellular matrix protein mixture is an essential ingredient. However, its tumor-derived origin, batch-to-batch variation, high cost, and safety concerns have limited the usefulness of organoid drug development and regenerative medicine. Its clinical application has also been hindered by the fact that organoid generation is dependent on the use of poorly defined matrices. Therefore, matrix optimization is a crucial step in developing organoid culture that introduces alternatives as different materials. Recently, a variety of substitute materials has reportedly replaced matrigel. The purpose of this study is to review the significance of the latest advances in materials for cell culture applications and how they enhance build network systems by generating proper cell behavior. Excellence in cell behavior is evaluated from their cell characteristics, cell proliferation, cell differentiation, and even gene expression. As a result, graphene oxide as a matrix optimization demonstrated high potency in developing organoid models. Graphene oxide can promote good cell behavior and is well known for having good biocompatibility. Hence, advances in matrix optimization of graphene oxide provide opportunities for the future development of advanced organoid models.

The Aftermath of COVID-19: Exploring the Long-Term Effects on Organ Systems

BACKGROUND

Post-acute sequelae of SARS-CoV-2 infection (PASC) is a complicated disease that affects millions of people all over the world. Previous studies have shown that PASC impacts 10% of SARS-CoV-2 infected patients of which 50-70% are hospitalised. It has also been shown that 10-12% of those vaccinated against COVID-19 were affected by PASC and its complications. The severity and the later development of PASC symptoms are positively associated with the early intensity of the infection.

RESULTS

The generated health complications caused by PASC involve a vast variety of organ systems. Patients affected by PASC have been diagnosed with neuropsychiatric and neurological symptoms. The cardiovascular system also has been involved and several diseases such as myocarditis, pericarditis, and coronary artery diseases were reported. Chronic hematological problems such as thrombotic endothelialitis and hypercoagulability were described as conditions that could increase the risk of clotting disorders and coagulopathy in PASC patients. Chest pain, breathlessness, and cough in PASC patients were associated with the respiratory system in long-COVID causing respiratory distress syndrome. The observed immune complications were notable, involving several diseases. The renal system also was impacted, which resulted in raising the risk of diseases such as thrombotic issues, fibrosis, and sepsis. Endocrine gland malfunction can lead to diabetes, thyroiditis, and male infertility. Symptoms such as diarrhea, nausea, loss of appetite, and taste were also among reported observations due to several gastrointestinal disorders. Skin abnormalities might be an indication of infection and long-term implications such as persistent cutaneous complaints linked to PASC.

CONCLUSIONS

Long-COVID is a multidimensional syndrome with considerable public health implications, affecting several physiological systems and demanding thorough medical therapy, and more study to address its underlying causes and long-term effects is needed.

Pathophysiological, immunological, and inflammatory features of long COVID

The COVID-19 pandemic continues to cause severe global disruption, resulting in significant excess mortality, overwhelming healthcare systems, and imposing substantial social and economic burdens on nations. While most of the attention and therapeutic efforts have concentrated on the acute phase of the disease, a notable proportion of survivors experience persistent symptoms post-infection clearance. This diverse set of symptoms, loosely categorized as long COVID, presents a potential additional public health crisis. It is estimated that 1 in 5 COVID-19 survivors exhibit clinical manifestations consistent with long COVID. Despite this prevalence, the mechanisms and pathophysiology of long COVID remain poorly understood. Alarmingly, evidence suggests that a significant proportion of cases within this clinical condition develop debilitating or disabling symptoms. Hence, urgent priority should be given to further studies on this condition to equip global public health systems for its management. This review provides an overview of available information on this emerging clinical condition, focusing on the affected individuals' epidemiology, pathophysiological mechanisms, and immunological and inflammatory profiles.

Coronavirus Receptor Expression Profiles in Human Mast Cells, Basophils, and Eosinophils

A major problem in SARS-CoV-2-infected patients is the massive tissue inflammation in certain target organs, including the lungs. Mast cells (MC), basophils (BA), and eosinophils (EO) are key effector cells in inflammatory processes. These cells have recently been implicated in the pathogenesis of SARS-CoV-2 infections. We explored coronavirus receptor (CoV-R) expression profiles in primary human MC, BA, and EO, and in related cell lines (HMC-1, ROSA, MCPV-1, KU812, and EOL-1). As determined using flow cytometry, primary MC, BA, and EO, and their corresponding cell lines, displayed the CoV-R CD13 and CD147. Primary skin MC and BA, as well as EOL-1 cells, also displayed CD26, whereas primary EO and the MC and BA cell lines failed to express CD26. As assessed using qPCR, most cell lines expressed transcripts for CD13, CD147, and ABL2, whereas ACE2 mRNA was not detectable, and CD26 mRNA was only identified in EOL-1 cells. We also screened for drug effects on CoV-R expression. However, dexamethasone, vitamin D, and hydroxychloroquine did not exert substantial effects on the expression of CD13, CD26, or CD147 in the cells. Together, MC, BA, and EO express distinct CoV-R profiles. Whether these receptors mediate virus-cell interactions and thereby virus-induced inflammation remains unknown at present.

SARS-CoV-2-Virus structure and life cycle

This book chapter presents a concise overview of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. It explores viral classification based on morphology and nucleic acid composition with a focus on DNA and RNA viruses, the SARS-CoV-2 structure including the structural as well as nonstructural proteins in detail, and the viral replication mechanisms. The chapter then delves into the characteristics and diversity of coronaviruses, particularly SARS-CoV-2, highlighting its similarities with other beta-coronaviruses. The replication and transcription complex, RNA elongation, and capping, as well as the role of accessory proteins in viral replication and modulation of the host immune response is discussed extensively.

Climate Changes and COVID-19

Climatic change, which influences population growth and land usage, has been theorized to be linked to the emergence and spread of new viruses like the currently unfolding COVID-19 pandemic. In this chapter, we explain how climate change may have altered the beginning, transmission, and maybe even the sickness consequences of the COVID-19 pandemic. Where possible, we also provide mechanistic explanations for how this may have occurred. We have presented evidence that suggests climate change may have had a role in the establishment and transmission of SARS-CoV-2 infection, and most possibly even in some of its clinical effects. Human activities bringing people into closer contact with bats and animals like pangolins that potentially represent the intermediate hosts, and evidence that climate-induced changes in vegetation are the main reservoir source of coronaviruses for human infection, are among the explanations. Although there are still unsubstantiated indications that the first viral pathogen may have escaped from a laboratory, it is possible that this encounter took place in the field or in marketplaces in the instance of COVID-19. We also present the argument that climate change is working to enhance transmission between diseased and uninfected humans, and this is true regardless of the source of the original development of the disease. Changes in temperature and humidity make it easier for viruses to survive, and the impacts of industrial pollution induce people to cough and sneeze, which releases highly infectious aerosols into the air. These three factors combine to make this a more likely scenario than it would otherwise be. We suggest that changes in climate are contributing to create conditions that are favorable for the development of more severe symptoms of illness. It is more difficult to build the argument for this circumstance, and much of it is indirect. However, climate change has caused some communities to adjust their nutritional habits, both in terms of the quantity of food they eat and the quality of the foods they consume. The effects frequently become apparent as a result of alterations that are imposed on the microbiome of the gut, which, in turn, influence the types of immune responses that are produced. The incidence of comorbidities like diabetes and animal vectors like bats that transmit other illnesses that modify vulnerability to SARS-CoV-2 are also two examples of the factors that have been affected by climate change. In order to curb the development of infectious illnesses caused by new viruses, it is necessary to understand the connection between environmental dynamics and the emergence of new coronaviruses. This knowledge should lead to initiatives aimed at reducing global greenhouse gas emissions.

In vitro digestion of SARS-CoV-2 contaminated berries reveals high inactivation of infectious virus during gastrointestinal passage

IMPORTANCE

During the pandemic, news outlets occasionally reported on the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA on various foods, raising concerns over contaminated foods initiating infections. Coronavirus disease 2019 (COVID-19) patients often experience gastrointestinal symptoms and shed SARS-CoV-2 RNA in their feces. In addition, active virus replication in the gastrointestinal tract was shown; however, infectious viruses were rarely detected in feces. We previously showed that SARS-CoV-2 remained infectious on frozen berries for at least a month. Here, in vitro digestion models showed that SARS-CoV-2 on berries exhibits minimal inactivation at the oral phase and the virus may escape gastric inactivation early during feeding. However, high intestinal inactivation of the virus on berries suggested that SARS-CoV-2 was less likely to initiate infection in the small intestine. In contrast, the oral cavity is a potential site where infection might be initiated, providing more input for the gastrointestinal tract. High intestinal inactivation might explain the difficulty of detecting infectious SARS-CoV-2 in feces but not of virus RNA.

Development and management of gastrointestinal symptoms in long-term COVID-19

Background

Emerging evidence reveals that SARS-CoV-2 possesses the capability to disrupt the gastrointestinal (GI) homeostasis, resulting in the long-term symptoms such as loss of appetite, diarrhea, gastroesophageal reflux, and nausea. In the current review, we summarized recent reports regarding the long-term effects of COVID-19 (long COVID) on the gastrointestine.

Objective

To provide a narrative review of abundant clinical evidence regarding the development and management of long-term GI symptoms in COVID-19 patients.

Results

Long-term persistent digestive symptoms are exhibited in a majority of long-COVID patients. SARS-CoV-2 infection of intestinal epithelial cells, cytokine storm, gut dysbiosis, therapeutic drugs, psychological factors and exacerbation of primary underlying diseases lead to long-term GI symptoms in COVID-19 patients. Interventions like probiotics, prebiotics, fecal microbiota transplantation, and antibiotics are proved to be beneficial in preserving intestinal microecological homeostasis and alleviating GI symptoms.

Conclusion

Timely diagnosis and treatment of GI symptoms in long-COVID patients hold great significance as they may contribute to the mitigation of severe conditions and ultimately lead to the improvement of outcomes of the patients.

COVID-19 and Gastrointestinal Tract: From Pathophysiology to Clinical Manifestations

Background: Since its first report in Wuhan, China, in December 2019, COVID-19 has become a pandemic, affecting millions of people worldwide. Although the virus primarily affects the respiratory tract, gastrointestinal symptoms are also common. The aim of this narrative review is to provide an overview of the pathophysiology and clinical manifestations of gastrointestinal COVID-19. Methods: We conducted a systematic electronic search of English literature up to January 2023 using Medline, Scopus, and the Cochrane Library, focusing on papers that analyzed the role of SARS-CoV-2 in the gastrointestinal tract. Results: Our review highlights that SARS-CoV-2 directly infects the gastrointestinal tract and can cause symptoms such as diarrhea, nausea/vomiting, abdominal pain, anorexia, loss of taste, and increased liver enzymes. These symptoms result from mucosal barrier damage, inflammation, and changes in the microbiota composition. The exact mechanism of how the virus overcomes the acid gastric environment and leads to the intestinal damage is still being studied. Conclusions: Although vaccination has increased the prevalence of less severe symptoms, the long-term interaction with SARS-CoV-2 remains a concern. Understanding the interplay between SARS-CoV-2 and the gastrointestinal tract is essential for future management of the virus.

Enteric nervous system as a target and source of SARS-CoV-2 and other viral infections

Coronavirus disease 2019 (COVID-19) has been demonstrated to affect several systems of the human body, including the gastrointestinal and nervous systems. The enteric nervous system (ENS) is a division of the autonomic nervous system that extends throughout the gut, regulates gastrointestinal function, and is therefore involved in most gut dysfunctions, including those resulting from many viral infections. Growing evidence highlights enteric neural cells and microbiota as important players in gut inflammation and dysfunction. Furthermore, the ENS and gastrointestinal immune system work together establishing relevant neuroimmune interactions during both health and disease. In recent years, gut-driven processes have also been implicated as players in systemic inflammation and in the initiation and propagation of several central nervous system pathologies, which seem to be hallmarks of COVID-19. In this review, we aim to describe evidence of the gastrointestinal and ENS infection with a focus on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We discuss here viral-induced mechanisms, neuroplasticity, and neuroinflammation to call attention to the enteric neuroglial network as a nervous system with a sensitive and crucial position to be not only a target of the new coronavirus but also a way in and trigger of COVID-19-related symptoms.

Organoids as a novel tool in modelling infectious diseases

Infectious diseases worldwide affect human health and have important societal impacts. A better understanding of infectious diseases is urgently needed. In vitro and in vivo infection models have brought notable contributions to the current knowledge of these diseases. Organoids are multicellular culture systems resembling tissue architecture and function, recapitulating many characteristics of human disease and elucidating mechanisms of host-infectious agent interactions in the respiratory and gastrointestinal systems, the central nervous system and the skin. Here, we discuss the applicability of the organoid technology for modeling pathogenesis, host response and features, which can be explored for the development of preventive and therapeutic treatments.

Environmental Stability and Transmissibility of Enveloped Viruses at Varied Animate and Inanimate Interfaces

Enveloped viruses have been the leading causative agents of viral epidemics in the past decade, including the ongoing coronavirus disease 2019 outbreak. In epidemics caused by enveloped viruses, direct contact is a common route of infection, while indirect transmissions through the environment also contribute to the spread of the disease, although their significance remains controversial. Bridging the knowledge gap regarding the influence of interfacial interactions on the persistence of enveloped viruses in the environment reveals the transmission mechanisms when the virus undergoes mutations and prevents excessive disinfection during viral epidemics. Herein, from the perspective of the driving force, partition efficiency, and viral survivability at interfaces, we summarize the viral and environmental characteristics that affect the environmental transmission of viruses. We expect to provide insights for virus detection, environmental surveillance, and disinfection to limit the spread of severe acute respiratory syndrome coronavirus 2.

Gastrointestinal Manifestations of SARS-CoV-2: Transmission, Pathogenesis, Immunomodulation, Microflora Dysbiosis, and Clinical Implications

The clinical manifestation of COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in the respiratory system of humans is widely recognized. There is increasing evidence suggesting that SARS-CoV-2 possesses the capability to invade the gastrointestinal (GI) system, leading to the manifestation of symptoms such as vomiting, diarrhea, abdominal pain, and GI lesions. These symptoms subsequently contribute to the development of gastroenteritis and inflammatory bowel disease (IBD). Nevertheless, the pathophysiological mechanisms linking these GI symptoms to SARS-CoV-2 infection remain unelucidated. During infection, SARS-CoV-2 binds to angiotensin-converting enzyme 2 and other host proteases in the GI tract during the infection, possibly causing GI symptoms by damaging the intestinal barrier and stimulating inflammatory factor production, respectively. The symptoms of COVID-19-induced GI infection and IBD include intestinal inflammation, mucosal hyperpermeability, bacterial overgrowth, dysbiosis, and changes in blood and fecal metabolomics. Deciphering the pathogenesis of COVID-19 and understanding its exacerbation may provide insights into disease prognosis and pave the way for the discovery of potential novel targets for disease prevention or treatment. Besides the usual transmission routes, SARS-CoV-2 can also be transmitted via the feces of an infected person. Hence, it is crucial to implement preventive and control measures in order to mitigate the fecal-to-oral transmission of SARS-CoV-2. Within this context, the identification and diagnosis of GI tract symptoms during these infections assume significance as they facilitate early detection of the disease and the development of targeted therapeutics. The present review discusses the receptors, pathogenesis, and transmission of SARS-CoV-2, with a particular focus on the induction of gut immune responses, the influence of gut microbes, and potential therapeutic targets against COVID-19-induced GI infection and IBD.

Gastrointestinal disorders in post-COVID syndrome. Clinical guidelines

Summary Post- COVID syndrome refers to the long-term consequences of a new coronavirus infection COVID-19, which includes a set of symptoms that develop or persist after COVID-19. Symptoms of gastrointestinal disorders in post- COVID syndrome, due to chronic infl ammation, the consequences of organ damage, prolonged hospitalization, social isolation, and other causes, can be persistent and require a multidisciplinary approach. The presented clinical practice guidelines consider the main preventive and therapeutic and diagnostic approaches to the management of patients with gastroenterological manifestations of postCOVID syndrome. The Guidelines were approved by the 17th National Congress of Internal Medicine and the 25th Congress of Gastroenterological Scientifi c Society of Russia.

Liver transplantation from a SARS-COV-2-positive donor: A road ahead or not

The COVID-19 pandemic has had a remarkable impact on the field of liver transplantation. Increasing evidence demonstrates a minimal risk of transmission of SARS-CoV-2 from non-lung donors who test positive for SARS-CoV-2; however, the risks of donor-derived SARS-CoV-2 from liver donors are unknown. We present our experience with two cases in which a liver was transplanted successfully from a brain-dead donor with incidental SARS-CoV-2 infection. Both donors were asymptomatic SARS-CoV-2-positive with negative bronchoalveolar lavage polymerase chain reaction (BAL PCR) and mechanism of death unrelated to COVID-19. Both the recipients did well after transplant and went home with a well-functioning liver. One patient did get readmitted and was found to be SARS-CoV-2-positive; however, it was probably related to hospital exposure rather than donor-derived. SARS-CoV-2-positive donors in select cases may be used for organ donation and liver transplant is safe for recipients.

Gut distress and intervention via communications of SARS-CoV-2 with mucosal exposome

Acute coronavirus disease 2019 (COVID-19) has been associated with prevalent gastrointestinal distress, characterized by fecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA or persistent antigen presence in the gut. Using a meta-analysis, the present review addressed gastrointestinal symptoms, such as nausea, vomiting, abdominal pain, and diarrhea. Despite limited data on the gut-lung axis, viral transmission to the gut and its influence on gut mucosa and microbial community were found to be associated by means of various biochemical mechanisms. Notably, the prolonged presence of viral antigens and disrupted mucosal immunity may increase gut microbial and inflammatory risks, leading to acute pathological outcomes or post-acute COVID-19 symptoms. Patients with COVID-19 exhibit lower bacterial diversity and a higher relative abundance of opportunistic pathogens in their gut microbiota than healthy controls. Considering the dysbiotic changes during infection, remodeling or supplementation with beneficial microbial communities may counteract adverse outcomes in the gut and other organs in patients with COVID-19. Moreover, nutritional status, such as vitamin D deficiency, has been associated with disease severity in patients with COVID-19 via the regulation of the gut microbial community and host immunity. The nutritional and microbiological interventions improve the gut exposome including the host immunity, gut microbiota, and nutritional status, contributing to defense against acute or post-acute COVID-19 in the gut-lung axis.

Evaluation of 3D Human Intestinal Organoids as a Platform for EV-A71 Antiviral Drug Discovery

Enteroviruses are a leading cause of upper respiratory tract, gastrointestinal, and neurological infections. Management of enterovirus-related diseases has been hindered by the lack of specific antiviral treatment. The pre-clinical and clinical development of such antivirals has been challenging, calling for novel model systems and strategies to identify suitable pre-clinical candidates. Organoids represent a new and outstanding opportunity to test antiviral agents in a more physiologically relevant system. However, dedicated studies addressing the validation and direct comparison of organoids versus commonly used cell lines are lacking. Here, we described the use of human small intestinal organoids (HIOs) as a model to study antiviral treatment against human enterovirus 71 (EV-A71) infection and compared this model to EV-A71-infected RD cells. We used reference antiviral compounds such as enviroxime, rupintrivir, and 2'-C-methylcytidine (2'CMC) to assess their effects on cell viability, virus-induced cytopathic effect, and viral RNA yield in EV-A71-infected HIOs and cell line. The results indicated a difference in the activity of the tested compounds between the two models, with HIOs being more sensitive to infection and drug treatment. In conclusion, the outcome reveals the value added by using the organoid model in virus and antiviral studies.

A Significant Difference in Core PDZ Interactivity of SARS-CoV, SARS-CoV2 and MERS-CoV Protein E Peptide PDZ Motifs In Vitro

Small structural E protein of coronaviruses uses its C-terminal PDZ motif to compromise the cellular PDZ interactome. In this work we compared core PDZ interactivity of small (seven amino acids) peptide PDZ motifs, originating from the envelope proteins of recently transmitted coronaviruses SARS-CoV, SARS-CoV2, and MERS-CoV. As the interaction targets we used 23 domains of the largest PDZ proteins MUPP1/MPDZ and PATJ/INAD. Results revealed exceptional affinity and interaction promiscuity of MERS-CoV PDZ motif in vitro, suggesting an increased probability of potential PDZ targets in vivo. We hypothesize that together with its known ability to enter the cells from both apical and basolateral sites, this might further contribute to its elevated disruption of cellular PDZ pathways and higher virulence.

Current SARS-CoV-2 Protective Strategies for Healthcare Professionals

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the Coronavirus disease 2019 (COVID-19). COVID-19 was first reported in China in December 2019. SARS-CoV-2 is highly contagious and spread primarily via an airborne route. Hand hygiene, surgical masks, vaccinations and boosters, air filtration, environmental sanitization, instrument sterilization, mouth rinses, and social distancing are essential infection control measures against the transmission of SARS-CoV-2. This paper aims to provide healthcare professionals with evidence-based protective strategies.

Pleiotropic Functions of Nitric Oxide Produced by Ascorbate for the Prevention and Mitigation of COVID-19: A Revaluation of Pauling's Vitamin C Therapy

Linus Pauling, who was awarded the Nobel Prize in Chemistry, suggested that a high dose of vitamin C (l-ascorbic acid) might work as a prevention or treatment for the common cold. Vitamin C therapy was tested in clinical trials, but clear evidence was not found at that time. Although Pauling's proposal has been strongly criticized for a long time, vitamin C therapy has continued to be tested as a treatment for a variety of diseases, including coronavirus infectious disease 2019 (COVID-19). The pathogen of COVID-19, SARS-CoV-2, belongs to the β-coronavirus lineage, which includes human coronavirus, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). This review intends to shed new light on vitamin C antiviral activity that may prevent SARS-CoV-2 infection through the chemical production of nitric oxide (NO). NO is a gaseous free radical that is largely produced by the enzyme NO synthase (NOS) in cells. NO produced by upper epidermal cells contributes to the inactivation of viruses and bacteria contained in air or aerosols. In addition to enzymatic production, NO can be generated by the chemical reduction of inorganic nitrite (NO2-), an alternative mechanism for NO production in living organisms. Dietary vitamin C, largely contained in fruits and vegetables, can reduce the nitrite in saliva to produce NO in the oral cavity when chewing foods. In the stomach, salivary nitrite can also be reduced to NO by vitamin C secreted from the epidermal cells of the stomach. The strong acidic pH of gastric juice facilitates the chemical reduction of salivary nitrite to produce NO. Vitamin C contributes in multiple ways to the host innate immune system as a first-line defense mechanism against pathogens. Highlighting chemical NO production by vitamin C, we suggest that controversies on the therapeutic effects of vitamin C in previous clinical trials may partly be due to less appreciation of the pleiotropic functions of vitamin C as a universal bioreductant.

SARS-CoV-2 and Hypertension: Evidence Supporting Invasion into the Brain Via Baroreflex Circuitry and the Role of Imbalanced Renin-Angiotensin-Aldosterone-System

Hypertension is considered one of the most critical risk factors for COVID-19. Evidence suggests that SARS-CoV-2 infection produces intense effects on the cardiovascular system by weakening the wall of large vessels via vasa-vasorum. In this commentary, we propose that SARS-CoV-2 invades carotid and aortic baroreceptors, leading to infection of the nucleus tractus solitari (NTS) and paraventricular hypothalamic nucleus (PVN), and such dysregulation of NTS and PVN following infection causes blood pressure alteration at the central level. We additionally explored the hypothesis that SARS-CoV-2 favors the internalization of membrane ACE2 receptors generating an imbalance of the renin-angiotensin-aldosterone system (RAAS), increasing the activity of angiotensin II (ANG-II), disintegrin, and metalloproteinase 17 domain (ADAM17/TACE), eventually modulating the integration of afferents reaching the NTS from baroreceptors and promoting increased blood pressure. These mechanisms are related to the increased sympathetic activity, which leads to transient or permanent hypertension associated with SARS-CoV-2 invasion, contributing to the high number of deaths by cardiovascular implications.

Non-pulmonary involvement in COVID-19: A systemic disease rather than a pure respiratory infection

During the early phase of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), diagnosis was difficult due to the diversity in symptoms and imaging findings and the variability of disease presentation. Pulmonary manifestations are reportedly the main clinical presentations of COVID-19 patients. Scientists are working hard on a myriad of clinical, epidemiological, and biological aspects to better understand SARS-CoV-2 infection, aiming to mitigate the ongoing disaster. Many reports have documented the involvement of various body systems and organs apart from the respiratory tract including the gastrointestinal, liver, immune system, renal, and neurological systems. Such involvement will result in diverse presentations related to effects on these systems. Other presentations such as coagulation defects and cutaneous manifestation may also occur. Patients with specific comorbidities including obesity, diabetes, and hypertension have increased morbidity and mortality risks with COVID-19.

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.

Environmental challenges of COVID-19 pandemic: resilience and sustainability - A review

The emergence of novel respiratory disease (COVID-19) caused by SARS-CoV-2 has become a public health emergency worldwide and perturbed the global economy and ecosystem services. Many studies have reported the presence of SARS-CoV-2 in different environmental compartments, its transmission via environmental routes, and potential environmental challenges posed by the COVID-19 pandemic. None of these studies have comprehensively reviewed the bidirectional relationship between the COVID-19 pandemic and the environment. For the first time, we explored the relationship between the environment and the SARS-CoV-2 virus/COVID-19 and how they affect each other. Supporting evidence presented here clearly demonstrates the presence of SARS-CoV-2 in soil and water, denoting the role of the environment in the COVID-19 transmission process. However, most studies fail to determine if the viral genomes they have discovered are infectious, which could be affected by the environmental factors in which they are found.The potential environmental impact of the pandemic, including water pollution, chemical contamination, increased generation of non-biodegradable waste, and single-use plastics have received the most attention. For the most part, efficient measures have been used to address the current environmental challenges from COVID-19, including using environmentally friendly disinfection technologies and employing measures to reduce the production of plastic wastes, such as the reuse and recycling of plastics. Developing sustainable solutions to counter the environmental challenges posed by the COVID-19 pandemic should be included in national preparedness strategies. In conclusion, combating the pandemic and accomplishing public health goals should be balanced with environmentally sustainable measures, as the two are closely intertwined.

Analogous comparison unravels heightened antiviral defense and boosted viral infection upon immunosuppression in bat organoids

Horseshoe bats host numerous SARS-related coronaviruses without overt disease signs. Bat intestinal organoids, a unique model of bat intestinal epithelium, allow direct comparison with human intestinal organoids. We sought to unravel the cellular mechanism(s) underlying bat tolerance of coronaviruses by comparing the innate immunity in bat and human organoids. We optimized the culture medium, which enabled a consecutive passage of bat intestinal organoids for over one year. Basal expression levels of IFNs and IFN-stimulated genes were higher in bat organoids than in their human counterparts. Notably, bat organoids mounted a more rapid, robust and prolonged antiviral defense than human organoids upon Poly(I:C) stimulation. TLR3 and RLR might be the conserved pathways mediating antiviral response in bat and human intestinal organoids. The susceptibility of bat organoids to a bat coronavirus CoV-HKU4, but resistance to EV-71, an enterovirus of exclusive human origin, indicated that bat organoids adequately recapitulated the authentic susceptibility of bats to certain viruses. Importantly, TLR3/RLR inhibition in bat organoids significantly boosted viral growth in the early phase after SARS-CoV-2 or CoV-HKU4 infection. Collectively, the higher basal expression of antiviral genes, especially more rapid and robust induction of innate immune response, empowered bat cells to curtail virus propagation in the early phase of infection.

Particle exposure risk to a lavatory user after flushing a squat toilet

Squat toilets are widely used in developing countries due to local customs and low costs. The flushing of a squat toilet can entrain strong airflow and produce aerosols. This investigation constructed a lavatory mock-up with a squat toilet. The flushing-induced airflow was both visualized and quantitatively measured by particle image velocimetry. The maximum height of the impacted airflow was identified by an ultrasonic anemometer. For inference of the particle emission rate, the toilet bowl was covered by an enclosed box for particle concentration measurement. The risks from skin contact of the deposited particles on the flushing button and the door handle and the possible inhalation of the released aerosols were evaluated. The results revealed that flushing a squat toilet can drive toilet plume to rise up to 0.9 m above the toilet bowl. A single flushing process can produce 0.29 million particles with diameters greater than 0.3 μm, among which 90% of the particles are submicron-sized. The flushing may cause particles to deposit on the flushing button and lavatory door handle as well as inhalation exposure even remaining in the lavatory for half a minute after flushing, especially for those lavatory users whose respiratory zones are below 1.0 m.

Viral and non-viral gene therapy using 3D (bio)printing

The overall success in launching discovered drugs is tightly restricted to the high rate of late-stage failures, which ultimately inhibits the distribution of medicines in markets. As a result, it is imperative that methods reliably predict the effectiveness and, more critically, the toxicity of medicine early in the drug development process before clinical trials be continuously innovated. We must stay up to date with the fast appearance of new infections and diseases by rapidly developing the requisite vaccinations and medicines. Modern in vitro models of disease may be used as an alternative to traditional disease models, and advanced technology can be used for the creation of pharmaceuticals as well as cells, drugs, and gene delivery systems to expedite the drug discovery procedure. Furthermore, in vitro models that mimic the spatial and chemical characteristics of native tissues, such as a 3D bioprinting system or other technologies, have proven to be more effective for drug screening than traditional 2D models. Viral and non-viral gene delivery vectors are a hopeful tool for combinatorial gene therapy, suggesting a quick way of simultaneously deliver multiple genes. A 3D bioprinting system embraces an excellent potential for gene delivery into the different cells or tissues for different diseases, in tissue engineering and regeneration medicine, in which the precise nucleic acid is located in the 3D printed tissues and scaffolds. Non-viral nanocarriers, in combination with 3D printed scaffolds, are applied to their delivery of genes and controlled release properties. There remains, however, a big obstacle in reaching the full potential of 3D models because of a lack of in vitro manufacturing of live tissues. Bioprinting advancements have made it possible to create biomimetic constructions that may be used in various drug discovery research applications. 3D bioprinting also benefits vaccinations, medicines, and relevant delivery methods because of its flexibility and adaptability. This review discusses the potential of 3D bioprinting technologies for pharmaceutical studies.

Survival of human coronavirus 229E at different temperatures on various food-contact surfaces and food and under simulated digestive conditions

The COVID-19 pandemic caused by SARS-CoV-2 has had a major impact on human health and the global economy. Various transmission possibilities of SARS-CoV-2 have been proposed, such as the surface of food in the cold chain and food packaging, as well as the fecal-oral route, although person-to-person contact via droplets and aerosols has been confirmed as the main route of transmission. This study evaluated the survivability of HCoV-229E, a SARS-CoV-2 surrogate, in suspension, on food-contact surfaces and on food at various temperatures, and in simulated digestive fluids by TCID₅₀ assay. In suspension, HCoV-229E survived after 5 days at 20 °C with a 3.69 log reduction, after 28 days at 4 °C with a 3.07 log reduction, and after 12 weeks at -20 °C with a 1.18 log reduction. On food-contact surfaces, HCoV-229E was not detected on day 3 on stainless steel (SS), plastic (LDPE), and silicone rubber (SR) at 20 °C with a 3.28, 3.24 and 3.28 log reduction, respectively, and survived after 28 days on SS and LDPE at 4 °C with a 3.13 and 2.88 log reduction, respectively, and survived after 12 weeks on SS, LDPE, and SR at -20 °C with a 1.92, 1.32 and 1.99 log reduction, respectively. On food, HCoV-229E was not detected on day 3 on lettuce and day 4 on chicken breast and salmon at 20 °C with a 3.61, 3.26 and 3.08 log reduction, respectively, and on day 14 on lettuce and day 21 on chicken breast and salmon at 4 °C with a 3.88, 3.44 and 3.56 log reduction, respectively. The virus remained viable for 12 weeks in all foods at -20 °C with 2-2.47 log reduction. In addition, in simulated digestive fluid experiments, HCoV-229E was relatively resistant in simulated salivary fluid (SSF; pH 7, 5), fed state simulated gastric fluid (FeSSGF; pH 3, 5, 7), and fasted state simulated intestinal fluid (FaSSIF; pH 7). However, the virus was less tolerant in fasted state simulated gastric fluid (FaSSGF; pH 1.6) and fed state simulated intestinal fluid (FeSSIF; pH 5). Therefore, this study suggested that HCoV-229E remained infectious on various food-contact surfaces and foods; in particular, it survived longer at lower temperatures and survived depending on the pH of the simulated digestive fluid.

COVID-19 and inflammatory bowel disease crosstalk: From emerging association to clinical proposal

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause coronavirus disease 2019 (COVID-19), an acute respiratory inflammation that has emerged worldwide since December 2019, and it quickly became a global epidemic. Inflammatory bowel disease (IBD) is a group of chronic nonspecific intestinal inflammatory diseases whose etiology has not been elucidated. The two have many overlapping symptoms in clinical presentation, such as abdominal pain, diarrhea, pneumonia, etc. Imbalance of the autoimmune system in IBD patients and long-term use of immunosuppressive drugs may increase the risk of infection; and systemic symptoms caused by COVID-19 may also induce or exacerbate intestinal inflammation. It has been found that the SARS-CoV-2 receptor angiotensin converting enzyme 2, which is highly expressed in the lung and intestine, is an inflammatory protective factor, and is downregulated and upregulated in COVID-19 and IBD, respectively, suggesting that there may be a coregulatory pathway. In addition, the immune activation pattern of COVID-19 and the cytokine storm in the inflammatory response have similar roles in IBD, indicating that the two diseases may influence each other. Therefore, this review aimed to address the following research questions: whether SARS-CoV-2 infection leads to the progression of IBD; whether IBD increases the risk of COVID-19 infection and poor prognosis; possible common mechanisms and genetic cross-linking between the two diseases; new treatment and care strategies for IBD patients, and the feasibility and risk of vaccination in the context of the COVID-19 epidemic.

Wastewater-based epidemiological investigation of SARS-CoV-2 in Porto Alegre, Southern Brazil

Wastewater-based epidemiology (WBE) may be successfully used to comprehensively monitor and determine the scale and dynamics of some infections in the community. We monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in raw wastewater samples from Porto Alegre, Southern Brazil. The samples were collected and analyzed every week between May 2020 to May 2021. Meanwhile, different social restrictions were applied according to the number of hospitalized patients in the region. Weekly samples were obtained from two wastewater treatment plants (WWTP), named Navegantes and Serraria. To determine the SARS-CoV-2 RNA titers in wastewater, we performed RT-qPCR analysis targeting the N gene (N1). The highest titer of SARS-CoV-2 RNA was observed between epidemiological weeks (EWs) 33-37 (August), 42-43 (October), 45-46 (November), 49-51 (December) in 2020, and 1-3 (January), 7-13 (February to March) in 2021, with viral loads ranging from 1 × 106-3 × 106 genomic copies/Liter. An increase in positive confirmed cases followed such high viral loads. Depending on the sampling method used, positive cases increased in 6-7 days and 15 days after the rise of viral RNA titers in wastewater, with composite sampling methods showing a lower time lag and a higher resolution on the analyses. The results showed a direct relation between strict social restrictions and the loads of detected RNA reduction in wastewater, corroborating the number of confirmed cases. Differences in viral loads between different sampling points and methods were observed, as composite samples showed more stable results during the analyzed period. Besides, viral loads obtained from samples collected at Serraria WWTP were consistently higher than the ones obtained at Navegantes WWTP, indicating differences in local dynamics of SARS-CoV-2 spread in different regions of Porto Alegre. In conclusion, wastewater sampling to monitor SARS-CoV-2 is a robust tool to evaluate the viral loads contributing to hospitalized patients' data and confirmed cases. In addition, SARS-CoV-2 detection in sewage may inform and alert the government when there are asymptomatic or non-tested patients.

Rock1 is a novel host dependency factor of human enterovirus A71: Implication as a drug target

Human enterovirus A71 (EV-A71) is the major causative agent of hand-foot-and-mouth disease (HFMD) commonly associated with severe neurological diseases, particularly in children under 5 years of age. Several investigational therapeutic agents and vaccine candidates are being developed. However, no approved drug against EV-A71 infection is available, and no proven drug target has been identified. Since host kinases are key regulators of multiple signaling pathways in response to viral infections, here we screened a kinase inhibitor library and identified potent inhibitors against EV-A71 infection. Among the hits, GSK269962A, a Rho Associated Coiled-Coil Containing Protein Kinase (Rock) inhibitor with potent antiviral activity, was selected for further analysis. We found that this Rock inhibitor not only efficiently suppressed the replication of EV-A71 in RD cells, but also in human intestinal organoids, in a dose-dependent manner. Interestingly, small interfering RNA depletion of Rock1, but not Rock2, significantly restricted viral replication in RD cells, indicating that Rock1 is a novel host dependency factor for EV-A71 replication and can serve as a target for the development of anti-EV-A71 therapeutics.

Gut as an Alternative Entry Route for SARS-CoV-2: Current Evidence and Uncertainties of Productive Enteric Infection in COVID-19

The gut has been proposed as a potential alternative entry route for SARS-CoV-2. This was mainly based on the high levels of SARS-CoV-2 receptor expressed in the gastrointestinal (GI) tract, the observations of GI disorders (such as diarrhea) in some COVID-19 patients and the detection of SARS-CoV-2 RNA in feces. However, the underlying mechanisms remain poorly understood. It has been proposed that SARS-CoV-2 can productively infect enterocytes, damaging the intestinal barrier and contributing to inflammatory response, which might lead to GI manifestations, including diarrhea. Here, we report a methodological approach to assess the evidence supporting the sequence of events driving SARS-CoV-2 enteric infection up to gut adverse outcomes. Exploring evidence permits to highlight knowledge gaps and current inconsistencies in the literature and to guide further research. Based on the current insights on SARS-CoV-2 intestinal infection and transmission, we then discuss the potential implication on clinical practice, including on long COVID. A better understanding of the GI implication in COVID-19 is still needed to improve disease management and could help identify innovative therapies or preventive actions targeting the GI tract.

On the Origins of Omicron's Unique Spike Gene Insertion

The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which are shared with or distinctive from those of other SARS-CoV-2 variants. We compared the mutations of the initially circulating Omicron variant (now known as BA.1) with prior variants of concern (Alpha, Beta, Gamma, and Delta), variants of interest (Lambda, Mu, Eta, Iota, and Kappa), and ~1500 SARS-CoV-2 lineages constituting ~5.8 million SARS-CoV-2 genomes. Omicron's Spike protein harbors 26 amino acid mutations (23 substitutions, 2 deletions, and 1 insertion) that are distinct compared to other variants of concern. While the substitution and deletion mutations appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) was not previously observed in any other SARS-CoV-2 lineage. Here, we consider and discuss various mechanisms through which the nucleotide sequence encoding for ins214EPE could have been acquired, including local duplication, polymerase slippage, and template switching. Although we are not able to definitively determine the mechanism, we highlight the plausibility of template switching. Analysis of the homology of the inserted nucleotide sequence and flanking regions suggests that this template-switching event could have involved the genomes of SARS-CoV-2 variants (e.g., the B.1.1 strain), other human coronaviruses that infect the same host cells as SARS-CoV-2 (e.g., HCoV-OC43 or HCoV-229E), or a human transcript expressed in a host cell that was infected by the Omicron precursor.

Advances in 3D bioprinting of tissues/organs for regenerative medicine and in-vitro models

Tissue/organ shortage is a major medical challenge due to donor scarcity and patient immune rejections. Furthermore, it is difficult to predict or mimic the human disease condition in animal models during preclinical studies because disease phenotype differs between humans and animals. Three-dimensional bioprinting (3DBP) is evolving into an unparalleled multidisciplinary technology for engineering three-dimensional (3D) biological tissue with complex architecture and composition. The technology has emerged as a key driver by precise deposition and assembly of biomaterials with patient's/donor cells. This advancement has aided in the successful fabrication of in vitro models, preclinical implants, and tissue/organs-like structures. Here, we critically reviewed the current state of 3D-bioprinting strategies for regenerative therapy in eight organ systems, including nervous, cardiovascular, skeletal, integumentary, endocrine and exocrine, gastrointestinal, respiratory, and urinary systems. We also focus on the application of 3D bioprinting to fabricated in vitro models to study cancer, infection, drug testing, and safety assessment. The concept of in situ 3D bioprinting is discussed, which is the direct printing of tissues at the injury or defect site for reparative and regenerative therapy. Finally, issues such as scalability, immune response, and regulatory approval are discussed, as well as recently developed tools and technologies such as four-dimensional and convergence bioprinting. In addition, information about clinical trials using 3D printing has been included.

Differential susceptibility of SARS-CoV-2 in animals: Evidence of ACE2 host receptor distribution in companion animals, livestock and wildlife by immunohistochemical characterisation

Angiotensin converting enzyme 2 (ACE2) is a host cell membrane protein (receptor) that mediates the binding of coronavirus, most notably SARS coronaviruses in the respiratory and gastrointestinal tracts. Although SARS-CoV-2 infection is mainly confined to humans, there have been numerous incidents of spillback (reverse zoonoses) to domestic and captive animals. An absence of information on the spatial distribution of ACE2 in animal tissues limits our understanding of host species susceptibility. Here, we describe the distribution of ACE2 using immunohistochemistry (IHC) on histological sections derived from carnivores, ungulates, primates and chiroptera. Comparison of mink (Neovison vison) and ferret (Mustela putorius furo) respiratory tracts showed substantial differences, demonstrating that ACE2 is present in the lower respiratory tract of mink but not ferrets. The presence of ACE2 in the respiratory tract in some species was much more restricted as indicated by limited immunolabelling in the nasal turbinate, trachea and lungs of cats (Felis catus) and only the nasal turbinate in the golden Syrian hamster (Mesocricetus auratus). In the lungs of other species, ACE2 could be detected on the bronchiolar epithelium of the sheep (Ovis aries), cattle (Bos taurus), European badger (Meles meles), cheetah (Acinonyx jubatus), tiger and lion (Panthera spp.). In addition, ACE2 was present in the nasal mucosa epithelium of the serotine bat (Eptesicus serotinus) but not in pig (Sus scrofa domestica), cattle or sheep. In the intestine, ACE2 immunolabelling was seen on the microvillus of enterocytes (surface of intestine) across various taxa. These results provide anatomical evidence of ACE2 expression in a number of species which will enable further understanding of host susceptibility and tissue tropism of ACE2 receptor-mediated viral infection.

Visualizing a Field of Research for the Coronavirus Replication in Humans with Knowledge Mapping: Evidence from Web of Science

Background

The outbreak of COVID-19 sweeping the globe in 2020 has caused widespread fear and threatened global health security. Compared to SARS and MERS, COVID-19 also causes severe respiratory diseases and even fatal diseases but have many differences, such as the unidentified gene sequence and replication mechanism. From SARS to MERS, and then to COVID-19, coronaviruses have significant variations in host adaptation, virus evolution, infectivity, spread, and pathogenicity due to its unique replication mechanism.

Methods

A field of research for the coronavirus replication in humans was visualized with a database covering 9177 kinds of literature in Web of Science from 2002 through October 2021 to provide cognitive direction for the epidemic situation of virus infection. Knowledge Mapping by CiteSpace and Bibliometrix Package in R Software was drawn to depict the underlying features of viral replication and changing trends of studies, with these analyses including co-citation, density visualization, keyword clustering, and time zone.

Results

The keyword frequencies of "replication," ''infection," and ''spike protein" repeatedly appeared in published papers. Coronavirus can promote or inhibit apoptosis, depending on the balance between viral protein and apoptotic factors. When the living environment of cells is irreversibly damaged by the virus, cells have to start the apoptosis mechanism to prevent the replication, transmission, and spread of the virus. The replication, assembly and transmission of coronavirus can inhibit cells from entering the apoptosis prematurely with the fusion of spike protein and cell receptor in human.

Conclusion

Our results indicated that "viral infection," spike protein," and "mutation" might be future research hotspots on coronavirus replication in humans. The attention should be paid to the mutations of S protein and these mutants carrying mutations.

Graphical abstract

Protective Effect of Food Against Inactivation of Human Coronavirus OC43 by Gastrointestinal Fluids

The involvement of the gastrointestinal (GI) tract in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has been reported in multiple studies. Since it has been demonstrated that human intestinal epithelial cells support productive viral replication and that a substantial portion of infected individuals shed the virus in feces, the possibility of fecal-oral and fecal-respiratory modes of transmission have been proposed for SARS-CoV-2. In order to establish viral replication in the intestine, enteric viruses need to retain their infectivity in often low pH gastric fluids, and in intestinal fluids, which contain digestive enzymes and bile salts. In this study, we examined whether human coronaviruses OC43 (HCoV-OC43) can remain infectious in simulated GI fluids that models human fasting-state and fed-state, in the presence or absence of food. We demonstrated that except for fasting-state gastric fluid (pH 1.6), the virus can remain infectious in all other gastrointestinal fluids for 1 h. Furthermore, we demonstrated that presence of food could significantly improve viral survival in gastric fluids. Therefore, this study provides evidence that ingestion with food could protect the virus against inactivation by the GI fluids.

Potential intestinal infection and faecal-oral transmission of human coronaviruses

Human coronaviruses (HCoVs) were first described in 1960s for patients experiencing common cold. Since then, increasing number of HCoVs have been discovered, including those causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the circulating coronavirus disease 2019 (COVID‐19), which can cause fatal respiratory disease in humans on infection. HCoVs are believed to spread mainly through respiratory droplets and close contact. However, studies have shown that a large proportion of patients with HCoV infection develop gastrointestinal (GI) symptoms, and many patients with confirmed HCoV infection have shown detectable viral RNA in their faecal samples. Furthermore, multiple in vitro and in vivo animal studies have provided direct evidence of intestinal HCoV infection. These data highlight the nature of HCoV GI infection and its potential faecal‐oral transmission. Here, we summarise the current findings on GI manifestations of HCoVs. We also discuss how HCoV GI infection might occur and the current evidence to establish the occurrence of faecal‐oral transmission.

Taxonomical and functional changes in COVID-19 faecal microbiome could be related to SARS-CoV-2 faecal load

Since the beginning of the pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the gastro-intestinal (GI) tract has emerged as an important organ influencing the propensity to and potentially the severity of the related COVID-19 disease. However, the contribution of the SARS-CoV-2 intestinal infection on COVID-19 pathogenesis remains to be clarified. In this exploratory study, we highlighted a possible link between alterations in the composition of the gut microbiota and the levels of SARS-CoV-2 RNA in the gastrointestinal tract, which could be more important than the presence of SARS-CoV-2 in the respiratory tract, COVID-19 severity and GI symptoms. As established by metaproteomics, altered molecular functions in the microbiota profiles of high SARS-CoV-2 RNA level faeces highlight mechanisms such as inflammation-induced enterocyte damage, increased intestinal permeability and activation of immune response that may contribute to vicious cycles. Uncovering the role of this gut microbiota dysbiosis could drive the investigation of alternative therapeutic strategies to favour the clearance of the virus and potentially mitigate the effect of the SARS-CoV-2 infection. This article is protected by copyright. All rights reserved.