The perplexing question of trained immunity vs adaptive memory in COVID‐19

Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology

The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID-human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology.

Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control

COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.

Is the course of COVID-19 associated with tuberculin skin test diameter? A retrospective study

The pathogenesis of coronavirus disease 2019 (COVID‐19) is still not fully understood. As severe acute respiratory syndrome coronavirus 2 (SARS‐COV‐2) has a similar pathogenetic pathway to Mycobacterium tuberculosis, it has been reported that there may be a relationship between Bacille Calmette–Guérin (BCG) vaccination rate and COVID‐19 severity. This study investigated the relationship between tuberculin skin test (TST) induration diameter and the clinical course of COVID‐19. Of 1963 adult patients who underwent TST, 76 patients with SARS‐COV‐2 infection confirmed by RT‐PCR analysis of respiratory tract samples were included in the study. Relationships between COVID‐19 clinical severity and TST positivity, induration size, and other clinical parameters were analyzed. Of the 76 patients, TST results were negative for 53 patients (69.7%) and positive for 23 patients (30.3%). COVID‐19 severity was mild in 47 patients (61.8%), moderate in 22 patients (28.9%), and severe in seven patients (9.3%). All TST‐positive patients had mild disease. Patients with mild disease had a significantly higher TST positivity rate (p < 0.001) and larger induration diameter (p < 0.001). The area under the receiver operating characteristic (ROC) curve of TST induration size for the differentiation of mild with moderate and severe disease was 0.768 (p < 0.001). The maximum Youden J index value was 0.522 at an induration diameter of 6.5 mm, which had a sensitivity of 66.0% and specificity of 86.2%. COVID‐19 patients with positive TST showed a significantly higher rate of mild disease than those with negative TST. TST positivity is favorably associated with the course of COVID‐19.

TST induration diameters larger than 6.5 mm were highly specific in predicting a milder clinical presentation of COVID‐19.

Patients with positive tuberculin skin test (TST) had milder COVID‐19 symptoms.

TST induration diameter is favorably associated with the course of COVID‐19.

Immune response to SARS-CoV-2 in children: A review of the current knowledge

Host immune responses to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), especially in children, are still under investigation. Children with coronavirus disease 2019 (COVID‐19) constitute a significant study group of immune responses as they rarely present with severe clinical manifestations, require hospitalization, or develop complications such as multisystem inflammatory syndrome in children (MIS‐C) associated with SARS‐CoV‐2 infection. The deciphering of children’s immune responses during COVID‐19 infection will provide information about the protective mechanisms, while new potential targets for future therapies are likely to be revealed. Despite the limited immunological studies in children with COVID‐19, this review compares data between adults and children in terms of innate and adaptive immunity to SARS‐CoV‐2, discusses the possible reasons why children are mostly asymptomatic, and highlights unanswered or unclear immunological issues. Current evidence suggests that the activity of innate immunity seems to be crucial to the early phases of SARS‐CoV‐2 infection and adaptive memory immunity is vital to prevent reinfection.

Despite the limited immunological studies from children with COVID‐19, this review compares data between adults and children in terms of innate and adaptive immunity to SARS‐CoV‐2, discusses the possible reasons why children are mostly asymptomatic, and highlights unanswered or unclear immunological issues.

Long-Term Persistence of Anti-SARS-CoV-2 Antibodies in a Pediatric Population

Background: Antibody dynamics over time after SARS-CoV-2 infection are still unclear, and data regarding children are scarce. Methods: A prospective cohort study was performed including children infected by SARS-CoV-2 between March and May 2020. Patients were categorized into 3 groups: children admitted with COVID-19; outpatient children with mild COVID-19; and seropositive children participating in a seroprevalence study among cohabitants of infected healthcare workers (HCWs). Six months after the infection, a new serological control was performed. Results: A total of 58 children were included, 50% male (median age 8.3 [IQR 2.8–13.5] years). The median time between the two serological studies was 186 (IQR 176–192) days, and 86% (48/56) of the children maintained positive IgG six months after the infection. This percentage was 100% in admitted patients and 78% among the rest of the included children (p = 0.022). The diagnoses of lower respiratory tract infection and multisystemic inflammatory syndrome were associated with persistence of IgG (p = 0.035). The children of HCWs in the seroprevalence study lost antibodies more often (p = 0.017). Initial IgG titers of the children who remained positive six months after the infection were significantly higher (p = 0.008). Conclusions: Most children infected by SARS-CoV-2 maintain a positive serological response six months after the infection. Those children who lost their IgG titer were more frequently asymptomatic or mildly symptomatic, presenting with low antibody titers after the infection.

High Rates of SARS-CoV-2 Family Transmission in Children of Healthcare Workers During the First Pandemic Wave in Madrid, Spain: Serologic Study

BACKGROUND

Data on SARS-CoV-2 transmission among children living with healthcare workers (HCWs) are scarce.

METHODS

A cross-sectional study was performed at a tertiary Hospital in Madrid, including children of HCW who suffered from SARS-CoV-2 infection between March and May 2020. Children underwent enzyme-linked immunosorbent serological study for detecting SARS-CoV-2 antibodies: VIRCELL IgG assay.

RESULTS

One hundred thirteen children from 69 HCWs with confirmed SARS-CoV-2 infection were recruited: 47 children had positive IgG (41.6%). Children secondary attack rate was 43.7% (25% if both parents have had asymptomatic infection; 39.5% if one parent was symptomatic; and 47% when both parents had symptoms). Having a positive sibling was associated with a positive IgG result (odds ratio = 12.2; 95% confidence interval: 4.4-33.7, P < 0.001). Median age was higher in IgG positive children (P = 0.022). Children who referred anosmia presented higher IgG titles (P < 0.04).

CONCLUSIONS

We observed a very high SARS-CoV-2 transmission in children of HCW during the first pandemic wave, especially when both parents were symptomatic. Having a positive sibling was associated with seroconversion, supporting the important role of family clusters in the transmission of SARS-CoV-2.

Coronavirus Disease 19 and Future Ecological Crises: Hopes from Epigenomics and Unraveling Genome Regulation in Humans and Infectious Agents

With coronavirus disease 19 (COVID-19), we have witnessed a shift from public health to planetary health and a growing recognition of the importance of systems science in developing effective solutions against pandemics in the 21st century. COVID-19 and the history of frequent infectious outbreaks in the last two decades suggest that COVID-19 is likely a dry run for future ecological crises. Now is the right time to plan ahead and deploy the armamentarium of systems science scholarship for planetary health. The science of epigenomics, which investigates both genetic and nongenetic traits regarding heritable phenotypic alterations, and new approaches to understanding genome regulation in humans and pathogens offer veritable prospects to boost the global scientific capacities to innovate therapeutics and diagnostics against novel and existing infectious agents. Several reversible epigenetic alterations, such as chromatin remodeling and histone methylation, control and influence gene expression. COVID-19 lethality is linked, in part, to the cytokine storm, age, and status of the immune system in a given person. Additionally, due to reduced human mobility and daily activities, effects of the pandemic on the environment have been both positive and negative. For example, reduction in environmental pollution and lesser extraction from nature have potential positive corollaries on water and air quality. Negative effects include pollution as plastics and other materials were disposed in unconventional places and spaces in the course of the pandemic. I discuss the opportunities and challenges associated with the science of epigenomics, specifically with an eye to inform and prevent future ecological crises and pandemics that are looming on the horizon in the 21st century. In particular, this article underscores that epigenetics of both viruses and the host may influence virus infectivity and severity of attendant disease.

The epigenetic implication in coronavirus infection and therapy

Epigenetics is a relatively new field of science that studies the genetic and non-genetic aspects related to heritable phenotypic changes, frequently caused by environmental and metabolic factors. In the host, the epigenetic machinery can regulate gene expression through a series of reversible epigenetic modifications, such as histone methylation and acetylation, DNA/RNA methylation, chromatin remodeling, and non-coding RNAs. The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China, and spread worldwide, causes it. COVID-19 severity and consequences largely depend on patient age and health status. In this review, we will summarize and comparatively analyze how viruses regulate the host epigenome. Mainly, we will be focusing on highly pathogenic respiratory RNA virus infections such as coronaviruses. In this context, epigenetic alterations might play an essential role in the onset of coronavirus disease complications. Although many therapeutic approaches are under study, more research is urgently needed to identify effective vaccine or safer chemotherapeutic drugs, including epigenetic drugs, to cope with this viral outbreak and to develop pre- and post-exposure prophylaxis against COVID-19.

BCG vaccine may generate cross-reactive T cells against SARS-CoV-2: In silico analyses and a hypothesis

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BCG contains similar 9-amino acid sequences with SARS-CoV-2.

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The peptides have moderate to high binding affinity to common HLA class I molecules.

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Cross-reactive T cells against SARS-CoV-2 could be generated by BCG vaccination.

The world is facing the rising emergency of SARS-CoV-2. The outbreak of COVID-19 has caused a global public health and economic crisis. Recent epidemiological studies have shown that a possible association of BCG vaccination program with decreased COVID-19-related risks, suggesting that BCG may provide protection against COVID-19. Non-specific protection against viral infections is considered as a main mechanism of BCG and clinical trials to determine whether BCG vaccine can protect healthcare workers from the COVID-19 are currently underway. We hypothesized that BCG may carry similar T cell epitopes with SARS-CoV-2 and evaluated the hypothesis by utilizing publicly available database and computer algorithms predicting human leukocyte antigen (HLA) class I‐binding peptides. We found that BCG contains similar 9-amino acid sequences with SARS-CoV-2. These closely-related peptides had moderate to high binding affinity for multiple common HLA class I molecules, suggesting that cross-reactive T cells against SARS-CoV-2 could be generated by BCG vaccination.