Predicting the response of the dental pulp to SARS-CoV2 infection: a transcriptome-wide effect cross-analysis

Osteopontin interacts with dendritic cells and macrophages in pulp inflammation: Comprehensive transcriptomic analysis and laboratory investigations

AIM

To investigate novel diagnostic markers for pulpitis and validate by clinical samples from normal and inflamed pulp. To explore the relationship between diagnostic markers and immune cells or their phenotypes during pulp inflammation.

METHODOLOGY

Two microarray datasets, GSE77459 and GSE92681, and identified differential expression genes were integrated. To understand immune features, gene functions, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO) and ImmuneSigDB Gene Set Enrichment Analysis (GSEA) were analysed. For predictive purposes, machine learning techniques were applied to detect diagnostic markers. Immune infiltration in inflamed pulp was studied using CIBERSORT. The relationship between diagnostic markers and immune cells was investigated and validated their gene expression in clinical samples from the normal or inflamed pulp by qRT-PCR. Finally, the correlation between one marker, secreted phosphoprotein 1 (SPP1), encoding osteopontin (OPN), and dendritic cells (DCs)/macrophages was identified via HE staining and multiplex immunohistochemistry. An in vitro inflammatory dental pulp microenvironment model of THP-1 macrophages cocultured with dental pulp cells derived conditioned media (DPCs-CM) to investigate OPN production and macrophage phenotypes was established.

RESULTS

Analysis revealed unique immunologic features in inflamed pulp. Three diagnostic markers for pulpitis: endothelin-1 (EDN1), SPP1, and purine nucleoside phosphorylase (PNP), and validated them using qRT-PCR were predicted. Multiplex immunohistochemistry demonstrated OPN co-localized with activated DCs and M2 macrophages during pulp inflammation. In vitro experiments showed that THP-1 macrophages produced the highest levels of OPN when stimulated with DPCs-CM derived from the 20 μg/mL LPS pre-conditioned group, suggesting an M2b-like phenotype by increasing surface marker CD86 and expression of IL6, TNFα, IL10, and CCL1 but not CCL17 and MerTK. Levels of CCL1 and IL10 elevated significantly in the macrophages' supernatant from the 20 μg/mL LPS pre-conditioned CM group. OPN was proven co-localizing with CD86 in the inflamed pulp by immunofluorescence.

CONCLUSIONS

The current findings suggest that OPN can serve as a promising biomarker for pulpitis, correlated with DCs and macrophages. OPN+ macrophages in the inflamed pulp are associated with M2b-like phenotypes. These insights offer the potential for improved diagnosis and targeted therapy.

Dental radiographic changes in individuals with COVID-19: a controlled retrospective study

OBJECTIVE

The aim of this study is to compare the pre-COVID-19 and post-COVID-19 dental radiological findings of individuals with positive rRT-PCR test results and with healthy controls using the apical periodontitis grade scale (APGS), radiographic-based periodontal bone loss (R-PBL), and radiographic DMFT indices, and to investigate the relatively long-term dental effects of COVID-19.

METHODS

This study included people who had two panoramic radiographs taken between 2018 and 2022. There are 52 patients with positive rRT-PCR tests in the study group. The control group included 50 individuals. Study and control groups were compared using the apical periodontitis grade scale (APGS), radiographic-based periodontal bone loss (R-PBL), and radiographic DMFT indices.

RESULTS

Although results showed a significant difference in percentage R-PBL value and R-PBL types in the study group, there was no significant difference in percentage R-PBL value and R-PBL types in the control group. Also, both groups showed a significant difference in the DMFT index.

CONCLUSIONS

According to the results of this study, it can be said that COVID-19 increases the incidence of periodontitis, and it can be interpreted that the pandemic may adversely affect the general oral health of all people.

Herpesviruses and SARS-CoV-2: Viral Association with Oral Inflammatory Diseases

The oral cavity is a niche for diverse microbes, including viruses. Members of the Herpesviridae family, comprised of dsDNA viruses, as well as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an ssRNA virus, are among the most prevalent viruses infecting the oral cavity, and they exhibit clinical manifestations unique to oral tissues. Viral infection of oral mucosal epithelia triggers an immune response that results in prolonged inflammation. The clinical and systemic disease manifestations of HHV have been researched extensively, and several recent studies have illuminated the relationship between HHV and oral inflammatory diseases. Burgeoning evidence suggests the oral manifestation of SARS-CoV-2 infection includes xerostomia, dysgeusia, periodontal disease, mucositis, and opportunistic viral and bacterial infections, collectively described as oral post-acute sequelae of COVID-19 (PASC). These diverse sequelae could be a result of intensified immune responses initially due to the copious production of proinflammatory cytokines: the so-called "cytokine storm syndrome", facilitating widespread oral and non-oral tissue damage. This review explores the interplay between HHV, SARS-CoV-2, and oral inflammatory diseases such as periodontitis, endodontic disease, and peri-implantitis. Additionally, the review discusses proper diagnostic techniques for identifying viral infection and how viral diagnostics can lead to improved overall patient health.

COVID-19 on Oral Health: A New Bilateral Connection for the Pandemic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission are generally known to be produced by respiratory droplets and aerosols from the oral cavity (O.C.) of infected subjects, as stated by the World Health Organization. Saliva also retains the viral particles and aids in the spread of COVID-19. Angiotensin-converting enzyme Type 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) are two of the numerous factors that promote SARS-CoV-2 infection, expressed by O.C. structures, various mucosa types, and the epithelia of salivary glands. A systemic SARS-CoV-2 infection might result from viral replication in O.C. cells. On the other hand, cellular damage of different subtypes in the O.C. might be associated with various clinical signs and symptoms. Factors interfering with SARS-CoV-2 infection potential might represent fertile ground for possible local pharmacotherapeutic interventions, which may confine SARS-CoV-2 virus entry and transmission in the O.C., finally representing a way to reduce COVID-19 incidence and severity.

Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB

Mimicry of host proteins is a strategy employed by pathogens to hijack host functions. Domain and motif mimicry was explored in the experimental and predicted SARS-CoV-2-human interactome. The host first interactor proteins were also added to capture the continuum of the interactions. The domains and motifs of the proteins were annotated using NCBI CD Search and ScanProsite, respectively. Host and pathogen proteins with a common host interactor and similar domain/motif constitute a mimicry pair indicating global structural similarity (domain mimicry pair; DMP) or local sequence similarity (motif mimicry pair; MMP). 593 DMPs and 7,02,472 MMPs were determined. AAA, DEXDc and Macro domains were frequent among DMPs whereas glycosylation, myristoylation and RGD motifs were abundant among MMP. The proteins involved in mimicry were visualised as a SARS-CoV-2 mimicry interaction network. The host proteins were enriched in multiple CVD pathways indicating the role of mimicry in COVID-19 associated CVDs. Bridging nodes were identified as potential drug targets. Approved antihypertensive and anti-inflammatory drugs are proposed for repurposing against COVID-19 associated CVDs. The SARS-CoV-2 mimicry data has been updated in ImitateDB (http://imitatedb.sblab-nsit.net/SARSCoV2Mimicry). Determination of key mechanisms, proteins, pathways, drug targets and repurposing candidates is critical for developing therapeutics for SARS CoV-2 associated CVDs.

Strategies and Trends in COVID-19 Vaccination Delivery: What We Learn and What We May Use for the Future

Vaccination has been the most effective way to control the outbreak of the COVID-19 pandemic. The numbers and types of vaccines have reached considerable proportions, even if the question of vaccine procedures and frequency still needs to be resolved. We have come to learn the necessity of defining vaccination distribution strategies with regard to COVID-19 that could be used for any future pandemics of similar gravity. In fact, vaccine monitoring implies the existence of a strategy that should be measurable in terms of input and output, based on a mathematical model, including death rates, the spread of infections, symptoms, hospitalization, and so on. This paper addresses the issue of vaccine diffusion and strategies for monitoring the pandemic. It provides a description of the importance and take up of vaccines and the links between procedures and the containment of COVID-19 variants, as well as the long-term effects. Finally, the paper focuses on the global scenario in a world undergoing profound social and political change, with particular attention on current and future health provision. This contribution would represent an example of vaccination experiences, which can be useful in other pandemic or epidemiological contexts.

The Role of Cellular Metabolism in Maintaining the Function of the Dentine-Pulp Complex: A Narrative Review

The cellular metabolic processes ensure the physiological integrity of the dentine-pulp complex. Odontoblasts and odontoblast-like cells are responsible for the defence mechanisms in the form of tertiary dentine formation. In turn, the main defence reaction of the pulp is the development of inflammation, during which the metabolic and signalling pathways of the cells are significantly altered. The selected dental procedures, such as orthodontic treatment, resin infiltration, resin restorations or dental bleaching, can impact the cellular metabolism in the dental pulp. Among systemic metabolic diseases, diabetes mellitus causes the most consequences for the cellular metabolism of the dentine-pulp complex. Similarly, ageing processes present a proven effect on the metabolic functioning of the odontoblasts and the pulp cells. In the literature, several potential metabolic mediators demonstrating anti-inflammatory properties on inflamed dental pulp are mentioned. Moreover, the pulp stem cells exhibit the regenerative potential essential for maintaining the function of the dentine-pulp complex.

Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks

The structure of proteins impacts directly on the function they perform. Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 proteins have been extensively studied during the pandemic. This wide dataset, related to sequence and structure, has enabled joint sequence-structure analysis. In this work, we focus on the SARS-CoV-2 S (Spike) protein and the relations between sequence mutations and structure variations, in order to shed light on the structural changes stemming from the position of mutated amino acid residues in three different SARS-CoV-2 strains. We propose the use of protein contact network (PCN) formalism to: (i) obtain a global metric space and compare various molecular entities, (ii) give a structural explanation of the observed phenotype, and (iii) provide context dependent descriptors of single mutations. PCNs have been used to compare sequence and structure of the Alpha, Delta, and Omicron SARS-CoV-2 variants, and we found that omicron has a unique mutational pattern leading to different structural consequences from mutations of other strains. The non-random distribution of changes in network centrality along the chain has allowed to shed light on the structural (and functional) consequences of mutations.

The Oral Cavity Potentially Serving as a Reservoir for SARS-CoV-2 but Not Necessarily Facilitating the Spread of COVID-19 in Dental Practice

Intraoral tissues, secretions, and microenvironments may provide severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with the conditions necessary for viral cellular entry and inhabitation. The aim of the present study is to overview the oral cavity that potentially serves as a reservoir for SARS-CoV-2, and then discuss the possibility that such oral cavity facilitates the spread of coronavirus disease 2019 (COVID-19) in dental practice. Articles were retrieved from PubMed/Medline, LitCovid, ProQuest, Google Scholar, and preprint medRxiv databases. Results of the literature search indicated that SARS-CoV-2 host cell entry-relevant receptor and virus/cell membrane fusion mediators are expressed in major and minor salivary glands, tongue, taste bud, periodontal tissue, and dental pulp, which would be a target and reservoir for SARS-CoV-2. SARS-CoV-2 is present in saliva and gingival crevicular fluid of COVID-19 patients. These secretions would contaminate dental aerosol and droplet with SARS-CoV-2. SARS-CoV-2 inhabits periodontal pocket, gingival sulcus, and dental caries lesion, which could provide SARS-CoV-2 with a habitat. SARS-CoV-2 ribonucleic acid is preserved in dental calculus, which may inform of the previous infection with SARS-CoV-2. Despite involvement of the oral cavity in SARS-CoV-2 transmission and infection, to date, there have been no clusters of COVID-19 in dental practice. Dental settings are much less likely to facilitate the spread of COVID-19 compared with general medical settings, which may be explained by the situation of dentistry that the number of patients to visit dental offices/clinics was decreased during the COVID-19 pandemic, the characteristics of dentistry that dental professionals have maintained high awareness of viral infection prevention, adhered to a strict protocol for infection control, and been using personal protective equipment for a long time, the experimental results that dental devices generate only small amounts of aerosol responsible for the airborne viral transmission, irrigant from the dental unit contributes to the aerosol microbiota much rather than saliva, and the commonly used evacuation or suction system effectively reduces aerosol and droplet generation, and the possibility that human saliva exhibits the antiviral activity and the property to inhibit SARS-CoV-2 infection. It is considered that dental treatment and oral health care can be delivered safely in the COVID-19 era.

The Role of Oral Health in the Acquisition and Severity of SARS-CoV-2: A Retrospective Chart Review

Objective

Studies have shown that gingival crevices may be a significant route for SARS-CoV-2 entry. However, the role of oral health in the acquisition and severity of COVID-19 is not known.

Design

A retrospective analysis was performed using electronic health record data from a large urban academic medical center between 12/1/2019 and 8/24/2020. A total of 387 COVID-19 positive cases were identified and matched 1:1 by age, sex, and race to 387 controls without COVID-19 diagnoses. Demographics, number of missing teeth and alveolar crestal height were determined from radiographs and medical/dental charts. In a subgroup of 107 cases and controls, we also examined the rate of change in alveolar crestal height. A conditional logistic regression model was utilized to assess association between alveolar crestal height and missing teeth with COVID-19 status and with hospitalization status among COVID-19 cases.

Results

Increased alveolar bone loss, OR = 4.302 (2.510 - 7.376), fewer missing teeth, OR = 0.897 (0.835-0.965) and lack of smoking history distinguished COVID-19 cases from controls. After adjusting for time between examinations, cases with COVID-19 had greater alveolar bone loss compared to controls (0.641 ± 0.613 mm vs 0.260 ± 0.631 mm, p < 0.01.) Among cases with COVID-19, increased number of missing teeth OR = 2.1871 (1.146- 4.174) was significantly associated with hospitalization.

Conclusions

Alveolar bone loss and missing teeth are positively associated with the acquisition and severity of COVID-19 disease, respectively.

PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks

MOTIVATION

Protein Contact Network (PCN) is a powerful method for analysing the structure and function of proteins, with a specific focus on disclosing the molecular features of allosteric regulation through the discovery of modular substructures. The importance of PCN analysis has been shown in many contexts, such as the analysis of SARS-CoV-2 Spike protein and its complexes with the Angiotensin Converting Enzyme 2 (ACE2) human receptors. Even if there exist many software tools implementing such methods, there is a growing need for the introduction of tools integrating existing approaches.

RESULTS

We present PCN-Miner, a software tool implemented in the Python programming language, able to (i) import protein structures from the Protein Data Bank; (ii) generate the corresponding PCN; (iii) model, analyse and visualize PCNs and related protein structures by using a set of known algorithms and metrics. The PCN-Miner can cover a large set of applications: from clustering to embedding and subsequent analysis.

AVAILABILITY AND IMPLEMENTATION

The PCN-Miner tool is freely available at the following GitHub repository: https://github.com/hguzzi/ProteinContactNetworks. It is also available in the Python Package Index (PyPI) repository.

Changes in the global burden of untreated dental caries from 1990 to 2019: A systematic analysis for the Global Burden of Disease study

Objective

To investigate the burden of untreated dental caries in 204 countries and territories over 30 years.

Methods

Data of untreated dental caries from 1990 to 2019, including the incidence, prevalence, and years lived with disability, were extracted from the Global Burden of Disease 2019 database. Estimated annual percentage changes were calculated to assess the changes in the age-standardized incidence, prevalence, and years lived with disability rates.

Results

Globally, in 2019, there were 3.09 billion (95% uncertainty interval [UI]: 2.76–3.39 billion) new cases of untreated dental caries in permanent teeth (48.00% increase), 2.03 billion (1.77–2.33) prevalent cases (46.07% increase), and 2.00 million (0.93–3.88) YLDs (45.64% increase), all since 1990. From 1990 to 2019, the age-standardized incidence rate (ASIR) of untreated dental caries in permanent teeth showed an upward trend (estimated annual percentage changes [EAPC] = 0.01), but age-standardized prevalence rate (ASPR) (EAPC = −0.13) and age-standardized YLD rate (ASYR) (EAPC = −0.13) decreased. There were 1.15 billion (0.79–1.52) new cases of untreated dental caries in deciduous teeth (11.74% increase), 0.52 billion (0.41–0.63) prevalent cases (5.89% increase), and 0.20 million (0.09–0.43) YLDs (6.03% increase), all since 1990. From 1990 to 2019, the ASIR of untreated dental caries in permanent teeth showed a stable trend (EAPC = 0), but the ASPR (EAPC = −0.15) and ASYR (EAPC = −0.14) decreased. The incidence of untreated dental caries peaked at the ages of 5–9 and 20–24 years, and the prevalence and years lived with disability at 1–4, 20–24, and 60–64 years.

Conclusion

Untreated dental caries remains a major global public health challenge, but demographic, sex, and regional differences in trends remain. Proactive intervention strategies, at both administrative and academic levels, based on dynamic changes, are needed.

Effect of Sodium Hypochlorite in Dental Unit Waterline on Aerosolized Bacteria-Generated from Endodontic Procedures

INTRODUCTION

Aerosol generation in a dental setting is a critical concern and approaches that aim at decreasing bacterial load in aerosols is of high priority for dental professionals. The objectives of this study were to evaluate the relative effect of various endodontic procedures on the generation and dissemination of aerosols and the effect of 0.1% sodium hypochlorite (NaOCl) in dental unit waterlines (DUWLs) on the bacterial load in the generated aerosols in a clinical setting.

METHODS

The study was completed in two phases. The classical passive sampling technique using brain heart infusion agar plates was utilized. Agar plates were strategically placed throughout the operatory at pre-defined locations.

PHASE I

To evaluate the effect of different endodontic procedures on generation and dissemination of aerosols, we collected a total of 38 samples. Following baseline collection, test samples were collected during vital pulp therapy (VPT) full pulpotomy (n=10), non-surgical root canal therapy (NSRCT; n=10), surgical root canal therapy (SRCT; n=10), and incision and drainage (I&D; n=8) procedures. Bacterial growth was expressed as colony-forming units at 48 hours post-sample collection. Data were analyzed using 1-way analysis of variance with Tukey's multiple comparisons post-hoc test.

PHASE II

To evaluate the effect of 0.1% NaOCl in DUWL on the bacterial load in the generated aerosols, a total of 30 samples were collected. All procedures including VPT (n=10), NSRCT (n=10), and SRCT (n=10) were performed with 0.1% NaOCl in DUWL. Bacterial growth was expressed as colony-forming units at 48 hours post-sample collection. Data were analyzed using 2-way analysis of variance with Tukey's multiple comparisons post-hoc test.

RESULTS

All endodontic procedures generated aerosols at all tested locations except I&D. Aerosols were disseminated as far as 3m from the patient's head with no significant difference between various locations (p>0.05). VPT procedures generated the maximum number of aerosols compared to NSRCT and SRCT. Adding 0.1% NaOCl to DUWLs significantly reduced the bacterial load in the generated aerosols in all treatment groups compared to groups treated with untreated waterlines (p<0.05). No significant difference was noted in the bacterial load between all groups with treated waterlines (p>0.05).

CONCLUSIONS

All tested endodontic procedures led to the generation and dissemination of contaminated aerosols, and the addition of 0.1% NaOCl as a biocide to the DUWL led to a statistically significant reduction in the bacterial load.

Covid-19 and SARS-CoV-2 infection in periodontology: A narrative review

The present review examined the available evidence on possible involvement of gingival tissues in SARS‐CoV‐2 infection. Gingival tissue possess SARS‐CoV‐2 entry and transmission factors, among them ACE2 (angiotensin‐converting enzyme 2) and TMPRSS2 (transmembrane protease serine 2), which are the principal mediators of the virus cell invasion. Clinical observations reveal SARS‐CoV‐2 RNA in periodontal tissues and crevicular fluid, suggesting that the periodontium may act as an entry point for the virus and/or as a dissemination site. The preliminary observations prove infection potential of gingival crevicular fluid and shed epithelial cells from the periodontium. There are also findings on potential associations between periodontitis and Covid‐19 (coronavirus disease 2019). PubMed and Scopus databases were used to search for suitable keywords such as: SARS‐CoV‐2, Covid‐19, oral virus infection, gingival crevicular fluid, oral mucosa, periodontium, gingiva, ACE2, TMPRSS2, Furin, diagnosis, topical treatment, vaccine and the related words for relevant publications. Data extraction and quality valuation of articles were performed by the author. The review addressed seven major domains: periodontal structures as SARS‐CoV‐2 infection site, the periodontal changes under SARS‐CoV‐2 infection, potential associations between periodontitis and Covid‐19, periodontal oral care in Covid‐19, crevicular fluid as potential transmission factor and preventive measures. The search process in PubMed and Scopus was updated up to 31 March 2022. Finally 68 articles were retrieved for the final analysis, from the initial database searches. According to the inclusion criteria articles in English language without any date restriction were included. The included studies were mostly original articles, and published in 2020 and 2021 with the aim to describe Covid‐19 and SARS‐CoV‐2 infection in periodontology. As a conclusion it can be stated that gingival tissues may play a role in SARS‐CoV‐2 infection.

Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs

SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.

Disease spreading modeling and analysis: a survey

MOTIVATION

The control of the diffusion of diseases is a critical subject of a broad research area, which involves both clinical and political aspects. It makes wide use of computational tools, such as ordinary differential equations, stochastic simulation frameworks and graph theory, and interaction data, from molecular to social granularity levels, to model the ways diseases arise and spread. The coronavirus disease 2019 (COVID-19) is a perfect testbench example to show how these models may help avoid severe lockdown by suggesting, for instance, the best strategies of vaccine prioritization.

RESULTS

Here, we focus on and discuss some graph-based epidemiological models and show how their use may significantly improve the disease spreading control. We offer some examples related to the recent COVID-19 pandemic and discuss how to generalize them to other diseases.

Beyond COVID-19 Pandemic: Topology-aware optimization of vaccination strategy for minimizing virus spreading

•

Paper discusses the relevance of the adoption of ad-hoc vaccination strategies.

•

Paper shows how to evaluate the impact of different vaccination strategy by considering network-based models.

•

Tailored interventions, e.g., vaccination, applied on central nodes of these networks may efficiently stop the propagation of an infection.

•

The way node "centrality" is defined is the key to curb infection spreading.

The mitigation of an infectious disease spreading has recently gained considerable attention from the research community. It may be obtained by adopting sanitary measurements (e.g., vaccination, wearing masks), social rules (e.g., social distancing), together with an extensive vaccination campaign. Vaccination is currently the primary way for mitigating the Coronavirus Disease (COVID-19) outbreak without severe lockdown. Its effectiveness also depends on the number and timeliness of administrations and thus demands strict prioritization criteria. Almost all countries have prioritized similar classes of exposed workers: healthcare professionals and the elderly, obtaining to maximize the survival of patients and years of life saved. Nevertheless, the virus is currently spreading at high rates, and any prioritization criterion so far adopted did not account for the structural organization of the contact networks.

We reckon that a network where nodes are people while the edges represent their social contacts may efficiently model the virus’s spreading. It is known that tailored interventions (e.g., vaccination) on central nodes may efficiently stop the propagation, thereby eliminating the “bridge edges.” We then introduce such a model and consider both synthetic and real datasets. We present the benefits of a topology-aware versus an age-based vaccination strategy to mitigate the spreading of the virus. The code is available at https://github.com/mazzalab/playgrounds.

A German AWMF's S2e/realist synthesis and meta-narrative snapshot of craniomaxillofacial manifestations in COVID-19 patients: Rapid living update on 1 January 2021

PURPOSES

To execute a review answering the following question: "Among novel coronavirus disease (COVID19) patients, what are craniomaxillofacial (CMF) manifestations?" based on the RAMESES and the German Association of Scientific Medical Societies (AWMF)'s S2e guidelines.

METHODS

We performed a realist synthesis and meta-narrative review extracting data in English, French, German and Thai from PubMed/Medline, Embase, Biomed Central, Cochrane Library, and Thai Journals Online, until 1 January 2021. The primary outcome variable was CMF manifestations grouped into 5 categories: (1) mouth and throat, (2) nose, paranasal sinus, and skull base (3) ocular/orbital and periorbital tissue, (4) ear, and (5) craniofacial skin. Appropriate statistics was computed.

RESULTS

Thirty-seven original articles meeting the inclusion criteria were analysed; all were in English and indexed in PubMed/Medline. Hand searches of their references yielded a total of 101 articles for the review. Most data were in low level of evidence and focused on smell and taste disturbances and non-specific orofacial lesions. Iatrogenic complications may occur in this body region. Conservative measures remained effective and were usually enough for patient care.

CONCLUSION

Because SARS-CoV-2 infection is new and becomes the stringent worldwide pandemic within a short time period, most of the data on CMF symptoms are of low level evidence. Apart from taste and smell dysfunctions, non-specific CMF lesions can be found and treated conservatively. Treatment complications are possible. Dentists and CMF surgeons are privileged to examine the orofacial region and work closely with colleagues in other specialities to combat this pandemic.

Oral Pathology in COVID-19 and SARS-CoV-2 Infection-Molecular Aspects

This review article was designed to evaluate the existing evidence related to the molecular processes of SARS-CoV-2 infection in the oral cavity. The World Health Organization stated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission is produced by respiratory droplets and aerosols from the oral cavity of infected patients. The oral cavity structures, keratinized and non-keratinized mucosa, and salivary glands' epithelia express SARS-CoV-2 entry and transmission factors, especially angiotensin converting enzyme Type 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). Replication of the virus in cells leads to local and systemic infection spread, and cellular damage is associated with clinical signs and symptoms of the disease in the oral cavity. Saliva, both the cellular and acellular fractions, holds the virus particles and contributes to COVID-19 transmission. The review also presents information about the factors modifying SARS-CoV-2 infection potential and possible local pharmacotherapeutic interventions, which may confine SARS-CoV-2 virus entry and transmission in the oral cavity. The PubMed and Scopus databases were used to search for suitable keywords such as: SARS-CoV-2, COVID-19, oral virus infection, saliva, crevicular fluid, salivary gland, tongue, oral mucosa, periodontium, gingiva, dental pulp, ACE2, TMPRSS2, Furin, diagnosis, topical treatment, vaccine and related words in relevant publications up to 28 December 2021. Data extraction and quality evaluation of the articles were performed by two reviewers, and 63 articles were included in the final review.

Viruses of the oral cavity: Prevalence, pathobiology and association with oral diseases

The human oral cavity contains a plethora of habitats and tissue environments, such as teeth, tongue, and gingiva, which are home to a rich microbial flora including bacteria, fungi, and viruses. Given the exposed nature of the mouth, oral tissues constantly encounter infectious agents, forming a complex ecological community. In the past, the discussion of microbiological aspects of oral disease has traditionally focused on bacteria and fungi, but viruses are attracting increasing attention as pathogens in oral inflammatory diseases. Therefore, understanding viral prevalence, pathogenicity, and preference regarding oral tissues is critical to understanding the holistic effects of viruses on oral infections. Recent investigations have demonstrated the abundance of certain viruses in oral inflammatory diseases, suggesting an association between viruses and disease. Human herpesviruses are the most extensively studied viruses in different oral inflammatory diseases. However, challenges in viral detection and the lack of reproducible in vitro and in vivo infection models have limited our progress in understanding viruses and their contribution to oral diseases. This review presents a summary of major mammalian viruses and associated diseases in the human oral cavity. The emergence of a recent pathogen SARS-CoV-2 and its tropism for salivary and periodontal tissues further highlights the relevance of the oral cavity in host-pathogen interaction. Understanding how these different viruses present clinically and influence oral health will advance our understanding of multifactorial oral diseases and their association with viruses.

Estimating the viral loads of SARS-CoV-2 in the oral cavity when complicated with periapical lesions

Background

The oral cavity represents a main entrance of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE-2), neuropilin-1 (NRP-1), and transmembrane serine protease 2 (TMPRSS2) are essential for the entry of SARS-CoV-2 to the host cells. Both ACE-2 and NRP-1 receptors and TMPRSS2 have been identified in the oral cavity. However, there is limited knowledge about the impact of periapical lesions and their metabolites on the expression of these critical genes. This study aims to measure the impact of periapical lesions and their unique fatty acids (FAs) metabolites on the expression of the aforementioned genes, in addition to interleukin 6 (IL-6) gene and hence SARS-CoV-2 infection loads can be estimated.

Methods

Gene expression of ACE-2, NRP-1, TMPRSS2, and IL-6 was performed in periapical lesions in comparison to healthy oral cavity. Since FAs are important immunomodulators required for the lipid synthesis essential for receptors synthesis and viral replication, comparative FAs profiling was determined in oral lesions and healthy pulp tissues using gas chromatography–mass spectrometry (GC–MS). The effect of major identified and unique FAs was tested on mammalian cells known to express ACE-2, NRP-1, and TMPRSS2 genes.

Results

Gene expression analysis indicated that ACE-2, NRP-1, and TMPRSS2 were significantly upregulated in healthy clinical samples compared to oral lesions, while the reverse was true with IL-6 gene expression. Saturated and monounsaturated FAs were the major identified shared and unique FAs, respectively. Major shared FAs included palmitic, stearic and myristic acids with the highest percentage in the healthy oral cavity, while unique FAs included 17-octadecynoic acid in periapical abscess, petroselinic acid and l-lactic acid in periapical granuloma, and 1-nonadecene in the radicular cyst. Computational prediction showed that the binding affinity of identified FAs to ACE-2, TMPRSS2 and S protein were insignificant. Further, FA-treated mammalian cells showed significant overexpression of ACE-2, NRP-1 and TMPRSS2 genes except with l-lactic acid and oleic acid caused downregulation of NRP-1 gene, while 17-octadecynoic acid caused insignificant effect.

Conclusion

Collectively, a healthy oral cavity is more susceptible to viral infection when compared to that complicated with periapical lesions. FAs play important role in viral infection and their balance can affect the viral loads. Shifting the balance towards higher levels of palmitic, stearic and 1-nonadecene caused significant upregulation of the aforementioned genes and hence higher viral loads. On the other hand, there is a reverse correlation between inflammation and expression of SARS-CoV-2 receptors. Therefore, a mouth preparation that can reduce the levels of palmitic, stearic and 1-nonadecene, while maintaining an immunomodulatory effect can be employed as a future protection strategy against viral infection.

Covid-19 and oral diseases: Crosstalk, synergy or association?

The coronavirus disease 2019 (Covid-19) is a viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that clinically affects multiple organs of the human body. Cells in the oral cavity express viral entry receptor angiotensin-converting enzyme 2 that allows viral replication and may cause tissue inflammation and destruction. Recent studies have reported that Covid-19 patients present oral manifestations with multiple clinical aspects. In this review, we aim to summarise main signs and symptoms of Covid-19 in the oral cavity, its possible association with oral diseases, and the plausible underlying mechanisms of hyperinflammation reflecting crosstalk between Covid-19 and oral diseases. Ulcers, blisters, necrotising gingivitis, opportunistic coinfections, salivary gland alterations, white and erythematous plaques and gustatory dysfunction were the most reported clinical oral manifestations in patients with Covid-19. In general, the lesions appear concomitant with the loss of smell and taste. Multiple reports show evidences of necrotic/ulcerative gingiva, oral blisters and hypergrowth of opportunistic oral pathogens. SARS-CoV-2 exhibits tropism for endothelial cells and Covid-19-mediated endotheliitis can not only promote inflammation in oral tissues but can also facilitate virus spread. In addition, elevated levels of proinflammatory mediators in patients with Covid-19 and oral infectious disease can impair tissue homeostasis and cause delayed disease resolution. This suggests potential crosstalk of immune-mediated pathways underlying pathogenesis. Interestingly, few reports suggest recurrent herpetic lesions and higher bacterial growth in Covid-19 subjects, indicating SARS-CoV-2 and oral virus/bacteria interaction. Larger cohort studies comparing SARS-CoV-2 negative and positive subjects will reveal oral manifestation of the virus on oral health and its role in exacerbating oral infection.

COVID-19 and oral diseases: Assessing manifestations of a new pathogen in oral infections

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a recently identified virus responsible for life-threatening coronavirus disease 19 (COVID-19). The SARS-CoV-2 infected subjects can be asymptomatic or symptomatic; the later may present a wide spectrum of clinical manifestations. However, the impact of SARS-CoV-2 on oral diseases remain poorly studied. Detection of SARS-CoV-2 in saliva indicates existence of virus in the oral cavity. Recent studies demonstrating the expression of ACE-2, a SARS-CoV-2 entry receptor, in oral tissues further strengthens this observation. Cytokine storm in severe COVID-19 patients and copious secretion of pro-inflammatory cytokines (IL-6, IL-1β and TNF-α) in multiple symptomatic oral pathologies including periodontitis and periapical periodontitis suggests that inflammatory microenvironment is a hallmark of both COVID-19 and oral diseases. Hyperinflammation may provide conducive microenvironment for the growth of local oral pathogens or opportunistic microbes and exert detrimental impact on the oral tissue integrity. Multiple case reports have indicated uncharacterized oral lesions, symptomatic irreversible pulpitis, higher plaque index, necrotizing/desquamative gingivitis in COVID-19 patients suggesting that SARS-CoV-2 may worsen the manifestations of oral infections. However, the underlying factors and pathways remain elusive. Here we summarize current literature and suggest mechanisms for viral pathogenesis of oral dental pathology derived from oral microbiome and oral mucosa-dental tissue interactions. Longitudinal studies will reveal how the virus impairs disease progression and resolution post-therapy. Some relationships we suggest provide the basis for novel monitoring and treatment of oral viral disease in the era of SARS-CoV-2 pandemic, promoting evidence-based dentistry guidelines to diagnose virus-infected patients to improve oral health.

Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis

The development of therapeutic targets for COVID-19 relies on understanding the molecular mechanism of pathogenesis. Identifying genes or proteins involved in the infection mechanism is the key to shedding light on the complex molecular mechanisms. The combined effort of many laboratories distributed throughout the world has produced protein and genetic interactions. We integrated available results and obtained a host protein-protein interaction network composed of 1432 human proteins. Next, we performed network centrality analysis to identify critical proteins in the derived network. Finally, we performed a functional enrichment analysis of central proteins. We observed that the identified proteins are primarily associated with several crucial pathways, including cellular process, signaling transduction, neurodegenerative diseases. We focused on the proteins that are involved in human respiratory tract diseases. We highlighted many potential therapeutic targets, including RBX1, HSPA5, ITCH, RAB7A, RAB5A, RAB8A, PSMC5, CAPZB, CANX, IGF2R, and HSPA1A, which are central and also associated with multiple diseases.

Exploiting the molecular basis of age and gender differences in outcomes of SARS-CoV-2 infections

Motivation: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (coronavirus disease, 2019; COVID-19) is associated with adverse outcomes in patients. It has been observed that lethality seems to be related to the age of patients. While ageing has been extensively demonstrated to be accompanied by some modifications at the gene expression level, a possible link with COVID-19 manifestation still need to be investigated at the molecular level. Objectives: This study aims to shed out light on a possible link between the increased COVID-19 lethality and the molecular changes that occur in elderly people. Methods: We considered public datasets of ageing-related genes and their expression at the tissue level. We selected human proteins interacting with viral ones that are known to be related to the ageing process. Finally, we investigated changes in the expression level of coding genes at the tissue, gender and age level. Results: We observed a significant intersection between some SARS-CoV-2 interactors and ageing-related genes, suggesting that those genes are particularly affected by COVID-19 infection. Our analysis evidenced that virus infection particularly involves ageing molecular mechanisms centred around proteins EEF2, NPM1, HMGA1, HMGA2, APEX1, CHEK1, PRKDC, and GPX4. We found that HMGA1 and NPM1 have different expressions in the lung of males, while HMGA1, APEX1, CHEK1, EEF2, and NPM1 present changes in expression in males due to ageing effects. Conclusion: Our study generated a mechanistic framework to clarify the correlation between COVID-19 incidence in elderly patients and molecular mechanisms of ageing. We also provide testable hypotheses for future investigation and pharmacological solutions tailored to specific age ranges.

Presence of SARS-CoV-2 and Its Entry Factors in Oral Tissues and Cells: A Systematic Review

Background and Objectives: The aim of this systematic review is to summarize the current data about the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its entry factors in oral tissues and cells. Materials and Methods: This systematic review was carried out based on the Preferred Reporting Items for a Systematic Review and Meta-Analysis (PRISMA). Three databases were analyzed (Pubmed, Web of science and Scopus) by three independent researchers. From the 18 identified studies, 10 of them met the inclusion criteria. The presence of SARS-CoV-2 or its entry factors (angiotensin-converting enzyme II (ACE2), transmembrane serine proteases (TMPRSS), and furin) was analyzed in these 10 studies during the pandemic. Results: ACE2 expression was analyzed in 9 of the 10 studies. ACE2 is expressed mainly in the tongue, oral mucosa, salivary glands and epithelial cells. The expression of the TMPRSS2 gene or protein was analyzed in 6 studies. These studies reported that the expression of TMPRSS2 was mainly in the salivary glands, tongue, sulcular epithelium and oral mucosa; as well as in cells of the salivary glands (ductal, acinar and myoepithelial cells) and the tongue (the spinous-based cell layer, horny layer and the epithelial surface). Other TMPRSS were also reported. The expression of TMPRSS3, TMPRSS4, TMPRSS5, TMPRSS7 and TMPRSS11D was reported mainly in salivary glands and in epithelial-type cells. Furan expression was analyzed in three studies. The expression of furin was detected mainly in epithelial cells of the tongue. A variety of methods were used to carry out the detection of SARS-CoV-2 or its input molecules. Conclusions: These results show that SARS-CoV-2 can infect a wide variety of oral tissues and cells, and that together with the theories dedicated to explaining the oral symptoms present in SARS-CoV-2 positive patients, it provides us with a good scientific basis for understanding the virus infection in the oral cavity and its consequences.

Saliva: What Dental Practitioners Should Know about the Role of This Biofluid in the Transmission and Diagnostic of SARS-CoV-2

A novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak has become a global ongoing pandemic. This pandemic represents a great work risk for all health professionals, it includes dental professionals who are in constant contact with saliva, which represents one of the main routes of transmission of the disease. This is due to the fact that a wide variety of oral tissues and cells are susceptible to infection by SARS-CoV-2 and that they express the ACE2 receptor, which is the main route of entry of the virus into cells, as well as the proteins TMPRSS and furin that contributes to the binding of the virus to the host cells. According to recent studies, some of the oral cells most susceptible to infection by SARS-CoV-2 are the epithelial cells of the salivary glands. This explains the presence of the virus in the saliva of infected patients and provides scientific evidence that supports the use of saliva as a biofluid that offers the opportunity to develop new detection and diagnostic techniques. This is because saliva is much easier to collect compared to nasopharyngeal swab. However, the presence of the virus in saliva, also represents a great source of transmission, since the main form of infection is through microscopic drops that are generated when infected people cough or sneeze. Likewise, health professionals, such as dentists are exposed to contagion through saliva. The objective of this review article is to provide a perspective on the main cells and tissues that can be affected by the virus, the risk of contagion that the presence of the virus in saliva represents for dentists; and the new techniques developed from saliva samples for the diagnosis and surveillance of SARS-CoV-2 infection. This review is expected to contribute to the knowledge of oral health professionals about the risk of saliva in the spread of SARS-CoV-2, but also its advantages as a diagnostic tool for pandemic control. In conclusion, the authors can mention that information that provides more scientific evidence of the mechanisms of infection of the coronavirus in oral cells and tissues is being published continually. This also explains the presence of the virus in the saliva of infected people and the risk of contagion that this means. It also provides scientific evidence of the use of saliva as a biofluid for the detection, diagnosis, monitoring, and control of the spread of the virus.

Response by Endodontists to the SARS-CoV-2 (COVID−19) Pandemic: An International Survey

As SARS-CoV-2 continues to wreak havoc, health care workers are on the front lines to protect our communities. Dentists, particularly endodontists who manage dental emergencies, are engaged in high risk procedures that necessitate the modification of their treatment strategies in order to protect themselves, their staff and their patients from exposure to SARS-CoV-2. This study gathered international data from 448 endodontists to describe their awareness, their clinical care modifications, their strategies for re-opening and their reflection on the effects of the pandemic on their lives. Most endodontic practitioners (78%, n = 350) provided but limited their treatments to emergency care during the government-mandated shutdowns. They agreed with their local government's actions more than that of the national government, screened their patients for symptoms prior to treatment and changed their clinical care protocol to mitigate the spread of the virus. The pandemic has impacted their income, their ability to retain staff, and their financial and personal outlook in life.