The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity

Association analysis framework of genetic and exposure risks for COVID-19 in middle-aged and elderly adults

Coronavirus disease 2019 (COVID-19) is a current pandemic, and studies reported that older people have higher rates of infection and more severe cases. Recently, studies have revealed the involvement of both genetic and exposure factors in the susceptibility of COVID-19. However, the correlation between them is still unclear. Thus, we aimed to investigate the correlation between genetic and exposure factors associated with COVID-19. We retrieved the information of 7362 participants with COVID-19 testing results from the UK Biobank. We identified genetic factors for COVID-19 by genome-wide association studies (GWAS) summary analysis. In this study, 21 single-nucleotide polymorphisms (SNPs) and 15 exposure factors [smoking, alcohol intake, daytime dozing, body mass index (BMI), triglyceride, High Density Lipoprotein (HDL), diabetes, chronic kidney disease, chronic liver disease, dementia, atmosphere NO2 concentration, socioeconomic status, education qualification, ethnicity, and income] were found to be potential risk factors of COVID-19. Then, a gene-exposure (G × E) association network was built based on the correlation among and between these genetic factors and exposure factors. rs140092351, a SNP on microRNA miR1202, not only had the most significant association with COVID-19, but also interacted with multiple exposure factors. Dementia, alcohol consumption, daytime dozing, BMI, HDL, and atmosphere NO₂ concentration were among most significant G × E interactions with COVID-19 infection (P = 0.001).

Host Genetics at the Intersection of Autoimmunity and COVID-19: A Potential Key for Heterogeneous COVID-19 Severity

COVID-19 presentation is very heterogeneous across cases, and host factors are at the forefront for the variables affecting the disease manifestation. The immune system has emerged as a key determinant in shaping the outcome of SARS-CoV-2 infection. It is mainly the deleterious unconstrained immune response, rather than the virus itself, which leads to severe cases of COVID-19 and the associated mortality. Genetic susceptibility to dysregulated immune response is highly likely to be among the host factors for adverse disease outcome. Given that such genetic susceptibility has also been observed in autoimmune diseases (ADs), a number of critical questions remain unanswered; whether individuals with ADs have a significantly different risk for COVID-19-related complications compared to the general population, and whether studies on the genetics of ADs can shed some light on the host factors in COVID-19. In this perspective, we discuss the host genetic factors, which have been under investigation in association with COVID-19 severity. We touch upon the intricate link between autoimmunity and COVID-19 pathophysiology. We put forth a number of autoimmune susceptibility genes, which have the potential to be additional host genetic factors for modifying the severity of COVID-19 presentation. In summary, host genetics at the intersection of ADs and COVID-19 may serve as a source for understanding the heterogeneity of COVID-19 severity, and hence, potentially holds a key in achieving effective strategies in risk group identification, as well as effective treatments.

Interplay Between Air Travel, Genome Integrity, and COVID-19 Risk vis-a-vis Flight Crew

During air travel, flight crew (flight attendants, pilots) can be exposed to numerous flight-related environmental DNA damaging agents that may be at the root of an excess risk of cancer and other diseases. This already complex mix of exposures is now joined by SARS-CoV-2, the virus that causes COVID-19. The complex exposures experienced during air travel present a challenge to public health research, but also provide an opportunity to consider new strategies for understanding and countering their health effects. In this article, we focus on threats to genomic integrity that occur during air travel and discuss how these threats and our ability to respond to them may influence the risk of SARS-CoV-2 infection and the development of range of severity of the symptoms. We also discuss how the virus itself may lead to compromised genome integrity. We argue that dauntingly complex public health problems, such as the challenge of protecting flight crews from COVID-19, must be met with interdisciplinary research teams that include epidemiologists, engineers, and mechanistic biologists.

COVID-19-associated acute respiratory distress syndrome (CARDS): Current knowledge on pathophysiology and ICU treatment - A narrative review

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces coronavirus-19 disease (COVID-19) and is a major health concern. Following two SARS-CoV-2 pandemic “waves,” intensive care unit (ICU) specialists are treating a large number of COVID19-associated acute respiratory distress syndrome (ARDS) patients. From a pathophysiological perspective, prominent mechanisms of COVID19-associated ARDS (CARDS) include severe pulmonary infiltration/edema and inflammation leading to impaired alveolar homeostasis, alteration of pulmonary physiology resulting in pulmonary fibrosis, endothelial inflammation (endotheliitis), vascular thrombosis, and immune cell activation.

Although the syndrome ARDS serves as an umbrella term, distinct, i.e., CARDS-specific pathomechanisms and comorbidities can be noted (e.g., virus-induced endotheliitis associated with thromboembolism) and some aspects of CARDS can be considered ARDS “atypical.” Importantly, specific evidence-based medical interventions for CARDS (with the potential exception of corticosteroid use) are currently unavailable, limiting treatment efforts to mostly supportive ICU care.

In this article, we will discuss the underlying pulmonary pathophysiology and the clinical management of CARDS. In addition, we will outline current and potential future treatment approaches.

No impact of cancer and plague-relevant FPR1 polymorphisms on COVID-19

Formyl peptide receptor 1 (FPR1) is a pattern-recognition receptor that detects bacterial as well as endogenous danger-associated molecular patterns to trigger innate immune responses by myeloid cells. A single nucleotide polymorphism, rs867228 (allelic frequency 19–20%), in the gene coding for FPR1 accelerates the manifestation of multiple carcinomas, likely due to reduced anticancer immunosurveillance secondary to a defect in antigen presentation by dendritic cells. Another polymorphism in FPR1, rs5030880 (allelic frequency 12–13%), has been involved in the resistance to plague, correlating with the fact that FPR1 is the receptor for Yersinia pestis. Driven by the reported preclinical effects of FPR1 on lung inflammation and fibrosis, we investigated whether rs867228 or rs5030880 would affect the severity of coronavirus disease-19 (COVID-19). Data obtained on patients from two different hospitals in Paris refute the hypothesis that rs867228 or rs5030880 would affect the severity of COVID-19.

Germline immunoglobulin genes: Disease susceptibility genes hidden in plain sight?

Immunoglobulin genes are rarely considered as disease susceptibility genes despite their obvious and central contributions to immune function. This appears to be a consequence of historical views on antibody repertoire formation that no longer stand, and of difficulties that until recently surrounded the documentation of the suite of antibody genes in any individual. If these important genes are to be accessible to GWAS studies, allelic variation within the human population needs to be better documented, and a curated set of genomic variations associated with antibody genes needs to be formulated. Repertoire studies arising from the COVID-19 pandemic provide an opportunity to meet these needs, and may provide insights into the profound variability that is seen in outcomes to this infection.

The Intersection between COVID-19, the Gene Family of ACE2 and Alzheimer's Disease

We reviewed factors that might influence COVID-19 outcomes (eg, neurological symptoms), including the link to Alzheimer's disease. Since the virus triggers COVID-19 infection through binding to ACE2, we focused on the ACE2 gene family, including ACE. Both ACE2 and ACE are involved in the renin-angiotensin system (RAS). In general, ACE causes inflammation and vasoconstriction, while ACE2 leads to anti-inflammation activity and vasodilation. The disturbed balance between these counter-regulatory pathways could influence susceptibility to COVID-19. Notably, dysregulation of the RAS-equilibrium contributes to Alzheimer's disease. Differences in the incidence and symptoms of COVID-19 in diverse populations could be attributed to variability in the human genome. For example, ACE and ACE2 variations could modify the outcome of COVID-19 in different populations. It would be important to conduct genome-wide studies to detect variants influencing COVID-19 presentation, with a special focus on variants affecting immune-related pathways and expression of RAS-related genes.

Retrospective in silico HLA predictions from COVID-19 patients reveal alleles associated with disease prognosis

BACKGROUND

The Human Leukocyte Antigen (HLA) gene locus plays a fundamental role in human immunity, and it is established that certain HLA alleles are disease determinants.

METHODS

By combining the predictive power of multiple in silico HLA predictors, we have previously identified prevalent HLA class I and class II alleles, including DPA1*02:02, in two small cohorts at the COVID-19 pandemic onset. Since then, newer and larger patient cohorts with controls and associated demographic and clinical data have been deposited in public repositories. Here, we report on HLA-I and HLA-II alleles, along with their associated risk significance in one such cohort of 126 patients, including COVID-19 positive (n=100) and negative patients (n=26).

RESULTS

We recapitulate an enrichment of DPA1*02:02 in the COVID-19 positive cohort (29%) when compared to the COVID-negative control group (Fisher's exact test [FET] p=0.0174). Having this allele, however, does not appear to put this cohort's patients at an increased risk of hospitalization. Inspection of COVID-19 disease severity outcomes reveal nominally significant risk associations with A*11:01 (FET p=0.0078), C*04:01 (FET p=0.0087) and DQA1*01:02 (FET p=0.0121).

CONCLUSIONS

While enrichment of these alleles falls below statistical significance after Bonferroni correction, COVID-19 patients with the latter three alleles tend to fare worse overall. This is especially evident for patients with C*04:01, where disease prognosis measured by mechanical ventilation-free days was statistically significant after multiple hypothesis correction (Bonferroni p = 0.0023), and may hold potential clinical value.

COVID-19: A Great Mime or a Trigger Event of Autoimmune Manifestations?

Viruses can induce autoimmune diseases, in addition to genetic predisposition and environmental factors. Particularly, coronaviruses are mentioned among the viruses implicated in autoimmunity. Today, the world's greatest threat derives from the pandemic of a new human coronavirus, called "severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the responsible agent of coronavirus disease 2019 (COVID-19). First case of COVID-19 was identified in Wuhan, the capital of Hubei, China, in December 2019 and quickly spread around the world. This review focuses on autoimmune manifestations described during COVID-19, including pro-thrombotic state associated with antiphospholipid antibodies (aPL), acute interstitial pneumonia, macrophage activation syndrome, lymphocytopenia, systemic vasculitis, and autoimmune skin lesions. This offers the opportunity to highlight the pathogenetic mechanisms common to COVID-19 and several autoimmune diseases in order to identify new therapeutic targets. In a supposed preliminary pathogenetic model, SARS-CoV-2 plays a direct role in triggering widespread microthrombosis and microvascular inflammation, because it is able to induce transient aPL, endothelial damage and complement activation at the same time. Hence, endothelium might represent the common pathway in which autoimmunity and infection converge. In addition, autoimmune phenomena in COVID-19 can be explained by regulatory T cells impairment and cytokines cascade.

A "Window of Therapeutic Opportunity" for Anti-Cytokine Therapy in Patients With Coronavirus Disease 2019

The effects of cytokine inhibition in the different phases of the severe coronavirus disease 2019 (COVID-19) are currently at the center of intense debate, and preliminary results from observational studies and case reports offer conflicting results thus far. The identification of the correct timing of administration of anti-cytokine therapies and other immunosuppressants in COVID-19 should take into account the intricate relationship between the viral burden, the hyperactivation of the innate immune system and the adaptive immune dysfunction. The main challenge for effective administration of anti-cytokine therapy in COVID-19 will be therefore to better define a precise "window of therapeutic opportunity." Only considering a more specific set of criteria able to integrate information on direct viral damage, the cytokine burden, and the patient's immune vulnerability, it will be possible to decide, carefully balancing both benefits and risks, the appropriateness of using immunosuppressive drugs even in patients affected primarily by an infectious disease.

HOW GENETICISTS CONTRIBUTE TO UNDERSTANDING OF COVID-19 DISEASE PATHOGENICITY

Human populations are faced to the COVID-19 pandemic due to the emerging SARS-CoV-2 coronavirus originating from Wuhan (China) and with dramatic Public Health consequences. Despite periods of panic, the scientific community demonstrated an incredible innovation potential and energy ending up in one year with new vaccines to be used in population. Researchers are interrogating on how individual genetic differences contribute to the diversity of clinical manifestations or ethnic and geographic disparities of COVID-19. While efforts were spent to understand mechanistically the infectious potential of the virus, recent progresses in molecular genetics and bioinformatics allowed the characterization of viral sequence and construction of phylogeographical maps of viral dispersion worldwide. These data will help understanding epidemiological disparities among continents and ethnic populations. Much effort was also spent in analyzing host genetics by studying individual genes involved in innate and immune responses or explaining pathogenesis of comorbidities that complicate the fate of elderly patients. Several international consortia launched already Genome wide Association Studies (GWAS) and whole genome sequencing strategies to identify genetic markers with immediate application in patients at risk of respiratory failure. These new genetic data are important not only for understanding susceptibility factors for COVID-19 but they also contain an important message of hope for mankind warranting our survival and health.

The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity

This article provides a review of studies evaluating the role of host (and viral) genetics (including variation in HLA genes) in the immune response to coronaviruses, as well as the clinical outcome of coronavirus-mediated disease. The initial sections focus on seasonal coronaviruses, SARS-CoV, and MERS-CoV. We then examine the state of the knowledge regarding genetic polymorphisms and SARS-CoV-2 and COVID-19. The article concludes by discussing research areas with current knowledge gaps and proposes several avenues for future scientific exploration in order to develop new insights into the immunology of SARS-CoV-2.

Impact of COVID-19 Pandemic on Pediatrics and Pediatric Transplantation Programs

COVID-19 has dramatically altered the health care landscape and disrupted global health and world economics in ways that are still being measured. Its impact on children with chronic conditions or those undergoing transplantation is evolving. The organ specific manifestations in children will be reviewed and treatment strategies outlined. The impact on pediatric transplantation in the United States over the initial 6 months of the pandemic has shown significant regional variation and lags persist in resumption of normal transplant activity, particularly for living related transplantation. Finally, guidelines regarding return to school will be discussed.

COVID-19 and the liver: What do we know after six months of the pandemic?

Despite liver injury in patients infected with severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 (SARS-CoV-2) is associated with prolonged hospitalization, and liver dysfunction is mainly described in patients with severe viral disease. How liver abnormalities may affect virus infection is still unknown. Improved understanding of host genetics, lifestyle, underlying comorbidities and adequate follow-up of patients with liver damage are critical in the new scenario of the pandemic virus.