Genomewide Association Study of Severe Covid-19 with Respiratory Failure

Human-genetic variants associated with susceptibility to SARS-CoV-2 infection

SARS-CoV-2, the third major coronavirus of the 21st century, causing COVID-19 disease, profoundly impacts public health and workforces worldwide. Identifying individuals at heightened risk of SARS-CoV-2 infection is crucial for targeted interventions and preparedness. This study investigated 35 SNVs within viral infection-associated genes in SARS-CoV-2 patients and uninfected controls from the Basque Country (March 2020-July 2021). Its primary aim was to uncover genetic markers indicative of SARS-CoV-2 susceptibility and explore genetic predispositions to infection. Association analyses revealed previously unreported associations between SNVs and susceptibility. Haplotype analyses uncovered novel links between haplotypes and susceptibility, surpassing individual SNV associations. Descriptive modelling identified key susceptibility factors, with rs11246068-CC (IFITM3), rs5742933-GG (ORMDL1), rs35337543-CG (IFIH1), and GGGCT (rs2070788, rs2298659, rs17854725, rs12329760, rs3787950) variation in TMPRSS2 emerging as main infection-susceptibility indicators for a COVID-19 pandemic situation. These findings underscore the importance of integrated SNV and haplotype analyses in delineating susceptibility to SARS-CoV-2 and informing proactive prevention strategies. The genetic markers profiled in this study offer valuable insights for future pandemic preparedness.

Uso de inteligencia artificial en la predisposición genética a enfermedad crítica por COVID-19: evaluación comparativa de modelos de aprendizaje automático

Objetivos

La predicción temprana de enfermedad crítica por COVID-19 es crucial para optimizar el manejo clínico. Este estudio tiene como objetivo optimizar la predicción de enfermedad crítica por COVID-19 mediante la integración de datos clínicos, de laboratorio y polimorfismos genéticos en modelos de inteligencia artificial, evaluando y comparando el rendimiento de distintos algoritmos de aprendizaje automático.

Métodos

Se analizaron 155 pacientes hospitalizados, 23 de los cuales desarrollaron enfermedad crítica. Se realizó un análisis univariante para evaluar la asociación entre siete SNPs y 9 variables clínicas y 10 parámetros de laboratorio en la analítica al ingreso.

Resultados

De los 7 SNPS, solo tres SNPs se asociaron significativamente con enfermedad crítica: rs77534576, rs10774671 y rs10490770. Los modelos de ensemble consiguieron el mejor rendimiento: Random Forest (AUC=0,989), XGBoost (AUC=0,954) y AdaBoost (AUC=0,927). La importancia de las variables varió entre los modelos, destacando la edad, proteína C reactiva, cardiopatías y los tres SNPs en la mayoría de ellos. La incorporación de los SNPs mejoró el poder predictivo en comparación con estudios previos sin datos genéticos. La validación interna confirmó la superioridad y estabilidad de los modelos de ensemble.

Conclusiones

Los modelos de aprendizaje automático pueden ayudar en la predicción por enfermedad crítica por Covid-19. La incorporación de SNPs asociados a gravedad a los datos clínicos y de laboratorio mejora el poder predictivo. Se requieren estudios adicionales con cohortes más grandes y diversas para validar y generalizar estos hallazgos antes de su aplicación clínica.

Use of artificial intelligence to assess genetic predisposition to develop critical COVID-19 disease: a comparative study of machine learning models

Objectives

Early prediction of critical COVID-19 disease is crucial for an optimal clinical management. The objective of this study was to optimize predictive models for critical COVID-19 disease. Clinical data, laboratory data and genetic polymorphisms were integrated into AI models to compare the performance of different machine learning algorithms.

Methods

Data from 155 inpatients were analyzed, 23 of whom developed critical disease. A univariate analysis was performed to assess potential correlations between seven SNPs, nine clinical variables and 10 laboratory parameters at admission.

Results

Of the 7 SNPs, only three SNPs demonstrated a significant association with critical disase, namely: rs77534576, rs10774671 and rs10490770. The ensemble models exhibited the best performance: Random Forest (AUC=0.989), XGBoost (AUC=0.954) and AdaBoost (AUC=0.927). Variable importance varied across models, with age, C-reactive protein, heart diseases and the three SNPs being the most influential features. The predictive power of models improved with the integration of the three SNPs, as compared to previous studies where genetic data were not included. Internal validation confirmed the superiority and stability of the ensemble models.

Conclusions

Machine learning models may help predict progression into critical COVID-19-disease. The predictive power of models improves when SNPs associated with COVID-19 severity are integrated with laboratory and clinical data. Prior to implementation in clinical practice, larger studies in different populations are needed to validate and support the generalization of these results.

Genome-wide association study of long COVID

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association of FOXP4 with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4's role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID.

Association between HLA genetics and SARS-CoV-2 infection in a large real-world cohort

Genetic variation in the human leukocyte antigen (HLA) region is thought to influence susceptibility to and severity of a variety of infectious diseases. Several studies have explored a possible relationship between HLA genetics and SARS-CoV-2 infection, although mixed results, small sample sizes, and difficulty controlling for exposure risk have made it difficult to draw firm conclusions. Here, a dataset of 419,234 subjects with HLA genotype data and COVID-19 PCR test results was studied. A baseline analysis was performed to examine the association of non-HLA factors on COVID-19 positivity. Then, multivariate logistic regressions, incorporating single and paired HLA alleles, were performed and then corrected for significant factors from the baseline analysis. Proxies for socioeconomic status and exposure risk were significantly associated with COVID-19 positivity across all ancestry groups studied. Forty-one single HLA alleles displayed significant association with COVID-19 positivity; after controlling for socioeconomic status and exposure risk, only eight significant associations remained. Additionally, two HLA allele pairs were associated with test positivity after correction. Of all variables, socioeconomic status showed the greatest effect size. The results from this study suggest that many, if not all, of the reported associations between HLA alleles and SARS-CoV-2 infection may be spurious, owing to confounding factors.

Cross-trait GWAS in COVID-19 and systemic sclerosis reveals novel genes implicated in fibrotic and inflammation pathways

OBJECTIVES

Coronavirus disease 2019 (COVID-19) and SSc share multiple similarities in their clinical manifestations, alterations in immune response and therapeutic options. These resemblances have also been identified in other immune-mediated inflammatory diseases where a common genetic component has been found. Thus, we decided to evaluate for the first time this shared genetic architecture with SSc.

METHODS

For this study, we retrieved genomic data from two European-ancestry cohorts: 2 597 856 individuals from The COVID-19 Host Genetics Initiative consortium, and 26 679 individuals from the largest genomic scan in SSc. We performed a cross-trait meta-analyses including >9.3 million single nucleotide polymorphisms. Finally, we conducted functional annotation to prioritize potential causal genes and performed drug repurposing analysis.

RESULTS

Our results revealed a total of 19 non-HLA pleiotropic loci, including 2 novel associations for both conditions (BMP1 and PPARG) and 12 emerging as new shared loci. Functional annotation of these regions underscored their potential regulatory role and identified potential causal genes, many of which are implicated in fibrotic and inflammatory pathways. Remarkably, we observed an antagonistic pleiotropy model of the IFN signalling between COVID-19 and SSc, including the well-known TYK2 P1104A missense variant, showing a protective effect for SSc while being a risk factor for COVID-19, along with two additional novel pleiotropic associations (IRF8 and SENP7). Finally, our findings provide new therapeutic options that could potentially benefit both conditions.

CONCLUSION

Our study confirms the genetic resemblance between susceptibility to and severity of COVID-19 and SSc, revealing a novel common genetic contribution affecting fibrotic and immune pathways.

From Rare to Common: Genetic Insights into TLR7 Variants in a Multicentric Spanish Study on COVID-19 Severity

TLR7, which encodes a key receptor for single-stranded RNA (ssRNA) virus of the innate immune system, was recently associated with X-linked immunodeficiency and COVID-19 susceptibility. This study investigates the association between TLR7 variants and susceptibility to severe COVID-19 in a multicentric Spanish cohort. The TLR7 gene was sequenced in a cohort of 365 COVID-19 patients, stratified into two groups: one comprising mild and asymptomatic patients, considered as controls (n = 87), and the other consisting of moderate to severely affected patients hospitalized due to COVID-19 pneumonia, considered as cases (n = 278). A total of 152 unique TLR7 variants were identified, of note, six rare variants were identified in 11 cases (3.96%), all of whom belonged to the case group. The functional impact of rare TLR7 variants was assessed using a luciferase reporter assay and revealed that N215S is a loss-of-function (LOF) variant, while D332G exhibits an hypomorphic behavior. Conversely, H90Y, V219I, A448V, and R902K maintained normal signaling. No skewed X-inactivation was observed in female carriers of N215S or D332G. In addition, the common variants Q11L (rs179008), c.4-151A>G (rs179009) and c.*881C>G (rs3853839) were associated with severe pneumonia, while c.4-151A>G (rs179009) was specifically linked to Intensive Care Unit (ICU) admission. These findings highlight the role of TLR7 in antiviral immune response and its association with severe COVID-19 in men. The luciferase assay proves to be a reliable tool for evaluating TLR7 signaling, effectively distinguishing between neutral, LOF, and gain-of-function (GOF) variants. Further research is needed to better understand TLR7 variants and its implications in immunodeficiency and immune dysregulation.

Genetic association of ACE2 rs2285666 (C>T) and rs2106809 (A>G) and susceptibility to SARS-CoV-2 infection among the Ghanaian population

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), enters human cells using the angiotensin-converting enzyme 2 (ACE-2) receptor. ACE2 single nucleotide polymorphisms (SNPs) can influence susceptibility by affecting viral binding or gene expression. This study investigated the association between ACE2 SNPs, rs2285666 and rs2106809, and the SARS-CoV-2 infection susceptibility in a Ghanaian population.

Methods

Genomic DNA was extracted, using a magnetic bead-based method, from blood samples of a random-subset of 1,334 participants drawn from a two-stage cluster, population-based household cross-sectional SARS-CoV-2 IgG seroprevalence survey. Data collected included, socio-demographic characteristics, medical history, vaccination, and smoking status. Genotyping of the ACE2 SNPs was performed using Allele-Specific Oligonucleotide Polymerase Chain Reaction (ASO-PCR) combined with melting curve analysis. Logistic regression models were utilized to assess the association between the ACE2 SNPs and the susceptibility to SARS-CoV-2 infection.

Results

The median age of participants was 33 [Interquartile range (IQR) = 24-46] years. Females accounted for the majority of the sampled population, 64.3%. SARS-CoV-2-IgG seropositivity was (58.4%, 95%CI: 52.6%-64.2%) among the male population and (54.1%, 95%CI: 49.54%-58.61%) in the female population. There were no significant differences in overall allele or genotype frequencies of ACE2 SNPs between SARS-CoV-2 IgG seropositive and seronegative individuals for both females and males. Among females, those with the T allele of ACE2 rs2285666 had a 38% decreased susceptibility to SARS-CoV-2 infection under the dominant [adjusted odds ratio (aOR) = 0.62; 95%CI = 0.45-0.85, P = 0.003] and heterozygous advantage models (aOR = 0.62; 95%CI = 0.45-0.86, P = 0.004), after adjusting for confounders, but not thee recessive model (aOR = 0.41; 95%CI = 0.03-5.22, P = 0.490). No significant association was observed among males. Overall, the ACE2 rs2106809 was not associated with the susceptibility to SARS-CoV-2 infection in both males and females.

Conclusion

This study found no association between ACE2 rs2106809 genetic variant and susceptibility to SARS-CoV-2 infection, whilst the rs2285666 T-allele was associated with a decreased frequency for SARS-CoV-2 infection among Ghanaian females. These findings enhance our understanding of genetic factors influencing SARS-CoV-2 susceptibility, which could help identify at-risk populations and inform more targeted public health interventions in future outbreaks.

Genome-wide association study of post COVID-19 syndrome in a population-based cohort in Germany

If health impairments due to coronavirus disease 2019 (COVID-19) persist for 12 weeks or longer, patients are diagnosed with Post-COVID Syndrome (PCS), or Long-COVID. Although the COVID-19 pandemic has largely subsided in 2024, PCS is still a major health burden worldwide, and identifying potential genetic modifiers of PCS remains of great clinical and scientific interest. We therefore performed a case-control type genome-wide association study (GWAS) of three recently developed PCS (severity) scores in 2,247 participants of COVIDOM, a prospective, multi-centre, population-based cohort study of SARS-CoV-2-infected individuals in Germany. Each PCS score originally represented the weighted sum of the binary indicators of all, or a subset, of 12 PCS symptom complexes, assessed six months or later after the PCR test-confirmed SARS-CoV-2 infection of a participant. For various methodical reasons, however, the PCS scores were dichotomized along their respective median values in the present study, prior to the GWAS. Of the 6,383,167 single nucleotide polymorphisms included, various variants were found to be associated with at least one of the PCS scores, although not at the stringent genome-wide statistical significance level of 5 × 10- 8. With p = 6.6 × 10- 8, however, the genotype-phenotype association of SNP rs9792535 at position chr9:127,166,653 narrowly missed this threshold. The SNP is located in a region including the NEK6, PSMB7 and ADGRD2 genes which, however, does not immediately suggest an etiological connection to PCS. As regards functional plausibility, variants of a possible effect mapped to the olfactory receptor gene region (lead SNP rs10893121 at position chr11:123,854,744; p = 2.5 × 10- 6). Impairment of smell and taste is a pathognomonic feature of both, acute COVID-19 and PCS, and our results suggest that this connection may have a genetic basis. Three other genotype-phenotype associations pointed towards a possible etiological role in PCS of cellular virus repression (CHD6 gene region), activation of macrophages (SLC7A2) and the release of virus particles from infected cells (ARHGAP44). All other gene regions highlighted by our GWAS did not relate to pathophysiological processes currently discussed for PCS. Therefore, and because the genotype-phenotype associations observed in our GWAS were generally not very strong, the complexity of the genetic background of PCS appears to be as high as that of most other multifactorial traits in humans.

The common genetic variant rs1278960 determining expression of Interferon-lambda predicts inflammatory response in critically ill COVID-19 patients

The single nucleotide polymorphism rs12979860 is associated with the production of IFNλ4, a type III interferon, which offers protection from viral infection via its proinflammatory properties. We investigated if a genetically determined increase in IFNλ4 affects disease progression in SARS-CoV-2. This prospective, single-center study involved critically ill SARS-CoV-2 patients admitted to the intensive care unit. We performed genotyping for rs12979860 and analyzed daily laboratory data. Genotype frequencies were compared with an external validation cohort. Critically ill individuals with COVID-19 (n = 184; 29.3% women) were included. Median age was 63 years. The TT genotype was present in 11%, CT in 48% and CC in 41%. At baseline, CRP, ferritin, transferrin and neopterin did not differ significantly between groups. Longitudinal analysis revealed significant genotype-dependent differences in CRP, ferritin and neopterin with the highest peak in TT patients after 10-15 days. A higher need for renal replacement therapy (31.6% vs. 11.7%, p = 0.044) and mechanical ventilation (22 days vs. 15 days, p = 0.018) was observed in the TT group. The SNP rs12979860 near IFNL4 is associated with distinct inflammatory trajectories in critically ill COVID-19 patients. Genetic determinants of the immune response influence the severity of inflammation and clinical outcomes in severe COVID-19.

Challenges in interpreting Mendelian randomization studies with a disease as the exposure: Using COVID-19 liability studies as an exemplar

Mendelian randomization (MR) studies using diseases as exposures are increasingly prevalent although any observed associations do not necessarily imply effect of diseases. To illustrate this challenge, we conducted a systematic review of MR studies focusing on COVID-19 consequence. We hypothesized if outcome genome-wide association studies (GWAS) were conducted before COVID-19 pandemic in late 2019, any observed associations in these studies were unlikely to be driven by COVID-19. We systematically searched PubMed, EMBASE, and MEDLINE for all MR studies published between 1 January 2019 and 20 May 2023. Inclusion criteria included MR studies which used COVID-19 as the exposure and designed to assess COVID-19's impact on health outcomes. We extracted relevant information, such as result interpretation and relevance assumption assessment. This review was registered at PROSPERO (CRD42023421079). Amongst 57 included studies, 45 studies used outcome GWAS published prior to 2019 whilst the remaining studies likely used outcome GWAS containing data collected before 2019. Relevance assumption was assessed mainly by p values. A total of 35 studies showed an association of COVID-19 liability with health outcomes. Regardless of the results, 45 studies attributed these as evidence (or lack of evidence) of COVID-19 consequence. In MR studies using disease liability as exposure, relevance assumption should consider the prevalence of the disease in the outcome GWAS in the context of 2 sample Mendelian randomization study rather than p values/F-statistic alone. Even when these are verified, these studies likely suffered from pleiotropy, making corresponding interpretation as effect of disease challenging.

Cardiovascular disease as part of Long COVID: a systematic review

AIMS

Long COVID syndrome has had a major impact on million patients' lives worldwide. The cardiovascular system is an important aspect of this multifaceted disease that may manifest in many ways. We have hereby performed a narrative review in order to identify the extent of the cardiovascular manifestations of the Long COVID syndrome.

METHODS AND RESULTS

An in-depth systematic search of the literature has been conducted for this narrative review. The systematic search of PubMed and Cochrane databases yielded 3993 articles, of which 629 underwent full-text screening. A total of 78 studies were included in the final qualitative synthesis and data evaluation. The pathophysiology of the cardiovascular sequelae of Long COVID syndrome and the cardiac manifestations and complications of Long COVID syndrome are critically evaluated. In addition, potential cardiovascular risk factors are assessed, and preventive methods and treatment options are examined in this review.

CONCLUSION

This systematic review poignantly summarizes the evidence from the available literature regarding the cardiovascular manifestations of Long COVID syndrome and reviews potential mechanistic pathways, diagnostic approaches, preventive measures, and treatment options.

Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network

In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and their GPCRs each share common structural scaffolds, the molecular principles driving selectivity and promiscuity remain elusive. Here, we identify conserved, semi-conserved, and variable determinants (i.e., recognition elements) that are encoded and decoded by chemokines and their receptors to mediate interactions. Selectivity and promiscuity emerge from an ensemble of generalized ("public/conserved") and specific ("private/variable") determinants distributed among structured and unstructured protein regions, with ligands and receptors recognizing these determinants combinatorially. We employ these principles to engineer a viral chemokine with altered GPCR coupling preferences and provide a web resource to facilitate sequence-structure-function studies and protein design efforts for developing immuno-therapeutics and cell therapies.

Context-specific eQTLs provide deeper insight into causal genes underlying shared genetic architecture of COVID-19 and idiopathic pulmonary fibrosis

Most genetic variants identified through genome-wide association studies (GWASs) are suspected to be regulatory in nature, but only a small fraction colocalize with expression quantitative trait loci (eQTLs, variants associated with expression of a gene). Therefore, it is hypothesized but largely untested that integration of disease GWAS with context-specific eQTLs will reveal the underlying genes driving disease associations. We used colocalization and transcriptomic analyses to identify shared genetic variants and likely causal genes associated with critically ill COVID-19 and idiopathic pulmonary fibrosis. We first identified five genome-wide significant variants associated with both diseases. Four of the variants did not demonstrate clear colocalization between GWAS and healthy lung eQTL signals. Instead, two of the four variants colocalized only in cell type- and disease-specific eQTL datasets. These analyses pointed to higher ATP11A expression from the C allele of rs12585036, in monocytes and in lung tissue from primarily smokers, which increased risk of idiopathic pulmonary fibrosis (IPF) and decreased risk of critically ill COVID-19. We also found lower DPP9 expression (and higher methylation at a specific CpG) from the G allele of rs12610495, acting in fibroblasts and in IPF lungs, and increased risk of IPF and critically ill COVID-19. We further found differential expression of the identified causal genes in diseased lungs when compared to non-diseased lungs, specifically in epithelial and immune cell types. These findings highlight the power of integrating GWASs, context-specific eQTLs, and transcriptomics of diseased tissue to harness human genetic variation to identify causal genes and where they function during multiple diseases.

C. Chen L. ABO blood group and COVID-19 severity: Associations with endothelial and adipocyte activation in critically ill patients

BACKGROUND

ABO blood group has been implicated both in susceptibility to, and severity of, SARS-CoV-2 infection. The aim of this study was to explore a potential association between ABO blood group and severity of COVID-19 infection in critically ill patients and the following biological mechanisms: inflammatory cytokines, endothelial injury, and adipokines.

METHODS

We conducted a retrospective study of 128 critically ill COVID-19 patients admitted to Vancouver General Hospital from March 2020-March 2021. Outcomes including 28-day mortality, need for mechanical ventilation and length of intensive care unit (ICU) stay were compared between patients with A & AB blood type vs. B & O blood type. Likewise, serum inflammatory markers, markers of endothelial activation, and adipokines were compared.

RESULTS

The association between ABO and severity of disease was confirmed. Patients with A&AB blood group had more frequent ventilation requirements compared to patients with blood group B&O (N(%): 35 (71%) vs 41 (52%), p = 0.041), higher total ICU mortality (14 (29%) vs 9 (11%), p = 0.018), longer median ICU stay (days, median [interquartile range]: 10 [6-19], vs 7 [3-14], p = 0.016) and longer median hospital stay (26 [14-36] vs. 17 [10-30] p = 0.034). No association was found between ABO blood group and serum inflammatory cytokines or their receptors [IL-6, IL-1b, IL-10, TNF, sIL-6R, sgp130] measured within the first 10 days of ICU stay. No association was found between ABO and plasma markers of endothelial injury [Thrombomodulin, ADAMTS13, sP-Selectin, Factor IX, Protein C, Protein S, vWF]. Among the plasma adipokines, there were no differences between lipocalin-2, PAI-1 or resistin. Notably, however, median adipsin was higher in patients with A&AB blood group compared to O&B (16.3 [4.2-38.5] x106 pg/mL vs. 9.61 [3.0-20.8] x 106 pg/mL, p = 0.048).

CONCLUSIONS

This retrospective single-center study confirms an association between A and AB blood type with more severe COVID-19. While an underlying mechanism was not identified, the finding of higher adipsin levels in patients with type A/AB blood warrants further investigation in larger prospective studies.

Differential immunoregulation by human surfactant protein A variants determines severity of SARS-CoV-2-induced lung disease

Introduction

COVID-19 remains a significant threat to public health globally. Infection in some susceptible individuals causes life-threatening acute lung injury (ALI/ARDS) and/or death. Human surfactant protein A (SP-A) is a C-type lectin expressed in the lung and other mucosal tissues, and it plays a critical role in host defense against various pathogens. The human SP-A genes (SFTPA1 and SFTPA2) are highly polymorphic and comprise several common genetic variants, i.e., SP-A1 (variants 6A2, 6A4) and SP-A2 (variants 1A0, 1A3). Here, we elucidated the differential antiviral and immunoregulatory roles of SP-A variants in response to SARS-CoV-2 infection in vivo.

Methods

Six genetically-modified mouse lines, expressing both hACE2 (SARS-CoV-2 receptor) and individual SP-A variants: (hACE2/6A2 (6A2), hACE2/6A4 (6A4), hACE2/1A0 (1A0), and hACE2/1A3 (1A3), one SP-A knockout (hACE2/SP-A KO (KO) and one hACE2/mouse SP-A (K18) mice, were challenged intranasally with 103 PFU SARS-CoV-2 or MEM medium (Sham).

Results

Infected KO and 1A0 mice had more weight loss and mortality compared to other mouse lines. Relative to other infected mouse lines, a more severe ALI was observed in KO, 1A0, and 6A2 mice. Reduced viral titers were generally observed in the lungs of infected SP-A mice relative to KO mice. Transcriptomic analysis revealed an upregulation in genes that play central roles in immune responses such as MyD88, Stat3, IL-18, and Jak2 in the lungs of KO and 1A0 mice. However, Mapk1 was significantly downregulated in 6A2 versus 1A0 mice. Analysis of biological pathways identified those involved in lung host defense and innate immunity, including pathogen-induced cytokine, NOD1/2, and Trem1 signaling pathways. Consistent with the transcriptomic data, levels of cytokines and chemokines such as G-CSF, IL-6, and IL-1β were comparatively higher in the lungs and sera of KO and 1A0 mice with the highest mortality rate. Furthermore, we observed the complexity of COVID-19, such as the difference between lung and systemic immune response to viral infection and of viral load and mortality among SP-A variants in this model.

Conclusion

These findings demonstrate that human SP-A variants differentially modulate SARS-CoV-2-induced lung injury and disease severity by differentially inhibiting viral infectivity and regulating immune-related gene expressions.

Blood type susceptibility to SARS-CoV-2 at a tertiary hospital in Accra, Ghana

Pandemics from viral outbreaks, such as that caused by SARS-CoV-2, have significant impacts worldwide. The factors that underlie differential susceptibility to severe COVID-19 outcomes are not fully understood. The role of the ABO blood group in the outcome of SARS-CoV-2 infections remains to be clarified in different populations. This study described the SARS-CoV-2 seroprevalence and examined the association of the ABO blood group with COVID-19 disease among apparently healthy and COVID-19 patients at the Korle Bu Teaching Hospital, Accra. The study involved 277 participants comprising 200 healthy individuals and 77 PCR-confirmed COVID-19 patients with mild or severe symptoms. Anti-SARS-CoV-2 antibody assay (IgM/IgG) was performed, and ABO blood grouping was done on plasma samples using the reverse blood grouping method. Statistical analyses were performed in R for the association of socio-demographic parameters and ABO blood groupings of participants with SARS-CoV-2 infection status. The total SARS-CoV-2 seropositivity was 61.4% (157/277). Most of the participants (245/277, 88.4%) were unvaccinated. Of the 245 unvaccinated individuals, 127 (51.8%) were IgG reactive. A significant association was observed between ABO blood group and COVID-19 disease status. Antigen A participants had a higher probability of symptomatic infection than non-antigen A individuals. Blood group O appeared more protective than other blood types among the participants. Seropositivity was high among the participants studied-vaccinated and unvaccinated. Blood group A is associated with an increased risk of COVID-19, whereas blood group O appears protective. Further studies involving larger sample sizes are required to confirm these findings.

IMPORTANCE

The transmissibility and virulence of SARS-CoV-2 and the severity of COVID-19 disease appeared to vary across nations and among populations. However, the factors that account for the differential susceptibility and COVID-19 outcomes are not well understood. The roles of host immune defense mechanisms and genetic makeup have been implicated. This study investigated the seroprevalence of anti-SARS-CoV-2 antibodies (IgM and IgG) in apparently healthy individuals and COVID-19 patients; using a reliable but inexpensive blood group typing based on direct hemagglutination technique and rigorous statistical analyses, we determined the association of ABO blood groups with COVID-19 disease. We found appreciably high seropositivity among the participants studied-both vaccinated and unvaccinated-and showed that blood type significantly influences SARS-CoV-2 infection and COVID-19 severity, with blood group A associated with severe COVID-19 disease, whereas blood group O appears protective. Further studies involving a larger sample size are required to confirm these findings.

Investigating the relationship between cycle threshold of SARS-CoV-2 RT-PCR, clinical features, and laboratory data in hospitalized COVID-19 patients in Semnan, Iran

Introduction

COVID-19, caused by the SARS-CoV-2 virus, has emerged as a global public health crisis. Understanding the factors associated with disease severity and outcomes is crucial for effective patient management. This study aimed to investigate the association between cycle threshold (CT) values, demographic data, medical history, clinical manifestations, and laboratory findings in hospitalized COVID-19 patients in Semnan, Iran.

Methods

A cross-sectional study was conducted on 86 patients with confirmed COVID-19 admitted to two hospitals in Semnan, Iran, between December 2022 and March 2023. Respiratory swab samples were collected RT-PCR was performed, CT values were obtained, and data were collected from medical records, including demographic information, medical history, clinical manifestations, and laboratory results. Statistical analysis was performed using SPSS software.

Results

The study included 86 COVID-19 patients, with a slightly higher representation of females (55.8%) and a mean age of 67.43 years. Pre-existing conditions like hypertension, diabetes mellitus, and ischemic heart disease were prevalent among hospitalized patients. A majority of patients (59.3%) had severe COVID-19, as indicated by lower CT values, while 31.4% exhibited oxygen saturation levels below 90%. Significant differences were observed in FBS, CRP, WBC, Hb, Cr, and SPo2 levels between severe and non-severe patients. Correlation analysis revealed associations between age, CRP, Cr, BUN, FBS, Vitamin D, TG, LDL, HDL, AST, ALP, and SPo2. Reflecting complex interactions between inflammatory markers, organ function, and lipid metabolism in COVID-19 patients.

Conclusion

This study provides valuable insights into the association between CT values, clinical characteristics, and laboratory findings in hospitalized COVID-19 patients. The findings underscore the importance of CT values in assessing disease severity and potential prognostication. Further research is warranted to validate these findings in larger and more diverse patient populations.

Risk Factors Affecting the Severity, Mortality, and Intensive Care Unit Admission of COVID-19 Patients: A Series of 1075 Cases

BACKGROUND

The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is broad; it can range from asymptomatic cases to mild upper respiratory tract illness, respiratory failure, and severe multiorgan failure resulting in death. Therefore, it is important to identify the clinical course of the disease and the factors associated with mortality.

OBJECTIVE

The aim of this study is to identify the risk factors associated with the severity of the disease, intensive care unit admission, and mortality in COVID-19 patients.

METHODS

A total of 1075 patients with clinical and radiological findings compatible with COVID-19 pneumonia and positive SARS-CoV-2 PCR were selected and retrospectively screened. All included patients were classified according to the 7th edition of the 2019 Coronavirus Disease Guidelines published by the National Health Commission of China.

RESULTS

It was observed that elevated white blood count (WBC) increased the severity of COVID-19 by 3.26 times and the risk of intensive care unit (ICU) admission by 3.47 times. Patients with high D-dimer levels had a 91% increased risk, and those with high fibrinogen levels had a 2.08 times higher risk of severe disease. High C-reactive protein (CRP) values were found to increase disease severity by 6.89 times, mortality by 12.84 times, and ICU admission by 3.37 times.

CONCLUSIONS

Identifying the factors associated with disease severity, ICU admission, and mortality in COVID-19 patients could help reduce disability and mortality rates in pandemics.

Association of Endothelial Nitric Oxide Synthase Polymorphisms with Clinical Severity in Patients with COVID-19

Background/Objectives: To elucidate the factors that contribute to individual variability in the progression of COVID-19, experiments on endothelial nitric oxide synthase polymorphisms have been reported. Nitric oxide synthase (NOS3) is located in the endothelium and is involved in the regulation of inflammation and vascular homeostasis. In this study, we investigated the association between COVID-19 severity and NOS3 G894T and NOS3 27-bp VNTR 4b/a genetic polymorphisms. Methods: Patients with COVID-19 (n = 178) were divided into Group 1 (mild disease) and Group 2 (severe disease) based on oxygen saturation levels in room air (Group 1, SpO2 ≥ 93%, n = 107; and Group 2, SpO2 < 93%, n = 73) and hospitalization requirements. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism analysis. Results: Overall, genotype and allele frequencies of the NOS3 genetic polymorphisms were similar across the two study groups (p > 0.05). However, the subgroup analysis showed a notable trend for the 4b/4a allele distribution between Groups 1 and 2. In the younger subgroup of patients (≤50 years old) without chronic obstructive pulmonary disease, Group 2 tended to have a higher frequency of the 4b allele than Group 1 (97.4% vs. 85.4% p = 0.06) and a higher occurrence of 4b/4b genotype (94.7% vs. 74.0%, p = 0.05). Additionally, a rarely observed 4c allele was detected only in two subjects within Group 2 but not in Group 1. Conclusions: These findings suggest a trend of association between COVID-19 severity and NOS3 27-bp VNTR 4b/a genetic polymorphism. Genetic analysis may reveal patient susceptibility to disease, prognosis risk factors, and drug responsiveness.

Genetic Analysis and Predictive Modeling of COVID-19 Severity in a Hospital-Based Patient Cohort

The COVID-19 pandemic has had a devastating impact, with more than 7 million deaths worldwide. Advanced age and comorbidities partially explain severe cases of the disease, but genetic factors also play a significant role. Genome-wide association studies (GWASs) have been instrumental in identifying loci associated with SARS-CoV-2 infection. Here, we report the results from a >820 K variant GWAS in a COVID-19 patient cohort from the hospitals associated with IIS Biobizkaia. We compared intensive care unit (ICU)-hospitalized patients with non-ICU-hospitalized patients. The GWAS was complemented with an integrated phenotype and genetic modeling analysis using HLA genotypes, a previously identified COVID-19 polygenic risk score (PRS) and clinical data. We identified four variants associated with COVID-19 severity with genome-wide significance (rs58027632 in KIF19; rs736962 in HTRA1; rs77927946 in DMBT1; and rs115020813 in LINC01283). In addition, we designed a multivariate predictive model including HLA, PRS and clinical data which displayed an area under the curve (AUC) value of 0.79. Our results combining human genetic information with clinical data may help to improve risk assessment for the development of a severe outcome of COVID-19.

COVID-19 related complications

The COVID-19 pandemic has significantly impacted global healthcare systems, revealed vulnerabilities and prompted a re-evaluation of medical practices. Acute complications from the virus, including cardiovascular and neurological issues, have underscored the necessity for timely medical interventions. Advances in diagnostic methods and personalized therapies have been pivotal in mitigating severe outcomes. Additionally, Long COVID has emerged as a complex challenge, affecting various body systems and leading to respiratory, cardiovascular, neurological, psychological, and musculoskeletal problems. This broad spectrum of complications highlights the importance of multidisciplinary management approaches that prioritize therapy, rehabilitation, and patient-centered care. Vulnerable populations such as paediatric patients, pregnant women, and immunocompromised individuals face unique risks and complications, necessitating continuous monitoring and tailored management strategies to reduce morbidity and mortality associated with COVID-19.

High nasopharyngeal and serum IL-6 levels and the - 573G > C polymorphism (rs1800796) are linked with the risk of severe COVID-19 in a Mexican population: a case‒control study

BACKGROUND

COVID-19 was the leading cause of death in Mexico between 2020 and 2021. SARS-CoV-2 infection varies widely among individuals and populations. Since variations in genes related to the immune response may play a role in the susceptibility to and outcome of COVID-19, the associations of gene polymorphisms (SNPs) of IL-6 (- 573G > C, rs1800796), TNF-α (- 308G > A, rs1800629), and IFN-γ (- 1615 C > T, rs2069705) with the expression levels of these proteins in the nasopharynx and serum were evaluated in a Mexican population with mild, severe, or critical COVID-19.

METHODS

A total of 560 COVID-19 patients (309 mild, 163 severe, and 88 critical cases) and 560 age- and sex-matched COVID-19-negative controls were recruited for this case‒control study. The selected SNPs were genotyped via allelic discrimination. Logistic regression analysis was conducted considering four models of inheritance, and ORs were determined for each genotypic variant, adjusting for associated comorbidities in the multivariate model. The nasopharyngeal mRNA expression levels of IL-6, IFN-γ and TNF-α were determined. The levels of IL-6, IFN-γ, IFN-α2, and TNF-α in the serum were quantified. Significant differences were assessed via the Wilcoxon Mann‒Whitney U test.

RESULTS

The C allele of the IL-6 - 573 SNP was associated with a greater risk of mild and severe COVID-19 (OR: 2.3, CI: 1.897-2.838, p = 0.0001; and OR: 1.5, CI: 1.167-1.949, p = 0.002, respectively), whereas the A allele of the TNF-α - 308 SNP and the T allele of the IFN-γ - 1615 SNP were shown protective roles against severe COVID-19 (OR: 0.3, CI: 0.189-0.537, p = 0.0001; and OR: 0.7, CI: 0.563-1.006, p = 0.05) and against critical COVID-19 (OR: 0.3, CI: 0.158-0.640, p = 0.001; and OR: 0.4, CI: 0.290-0.678, p = 0.0001), adjusting for diabetes and hypertension. Nasopharyngeal IL-6 expression levels were lower in mild COVID-19 patients (p = 0.001) than in critical patients (p = 0.005). Serum IL-6 levels were significantly elevated in the critical cases (p = 0.01).

CONCLUSIONS

Our results revealed that the IL-6 - 573 G > C SNP and increased IL-6 nasopharyngeal and serum levels are associated with the risk of severe COVID-19 in a Mexican population.

Learning from post-COVID-19 condition for epidemic preparedness: a variable catalogue for future post-acute infection syndromes

SCOPE

The emergence of post-COVID-19 condition (PCC) after SARS-CoV-2 infection underscores the critical need for preparedness in addressing future post-acute infection syndromes (PAIS), particularly those linked to epidemic outbreaks. The lack of standardized clinical and epidemiological data during the COVID-19 pandemic has significantly hindered timely diagnosis and effective treatment of PCC, highlighting the necessity of pre-emptively standardizing data collection in clinical studies to better define and manage future PAIS. In response, the Cohort Coordination Board, a consortium of European-funded COVID-19 research projects, has reviewed data from PCC studies conducted by its members. This paper leverages the Cohort Coordination Board's expertise to propose a standardized catalogue of variables, informed by the lessons learned during the pandemic, intended for immediate use in the design of future observational studies and clinical trials for emerging infections of epidemic potential.

RECOMMENDATIONS

The early implementation of standardized data collection, facilitated by the PAIS data catalogue, is essential for accelerating the identification and management of PAIS in future epidemics. This approach will enable more precise syndrome definitions, expedite diagnostic processes, and optimize treatment strategies, while also supporting long-term follow-up of affected individuals. The availability of harmonized data collection protocols will enhance preparedness across European and international cohort studies, and trials enabling a prompt and coordinated response, as well as more efficient resource allocation, in the event of emerging infections and associated PAIS.

COVID-19 and acute limb ischemia: latest hypotheses of pathophysiology and molecular mechanisms

Coronavirus disease 2019 (COVID-19) is a multi-system disease that can lead to various severe complications. Acute limb ischemia (ALI) has been increasingly recognized as a COVID-19-associated complication that often predicts a poor prognosis. However, the pathophysiology and molecular mechanisms underlying COVID-19-associated ALI remain poorly understood. Hypercoagulability and thrombosis are considered important mechanisms, but we also emphasize the roles of vasospasm, hypoxia, and acidosis in the pathogenesis of the disease. The angiotensin-converting enzyme 2 (ACE2) pathway, inflammation, and platelet activation may be important molecular mechanisms underlying these pathological changes induced by COVID-19. Furthermore, we discuss the hypotheses of risk factors for COVID-19-associated ALI from genetic, age, and gender perspectives based on our analysis of molecular mechanisms. Additionally, we summarize therapeutic approaches such as use of the interleukin-6 (IL-6) blocker tocilizumab, calcium channel blockers, and angiotensin-converting enzyme inhibitors, providing insights for the future treatment of coronavirus-associated limb ischemic diseases.

The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. To identify new prognostic markers for the disease, a multicentre prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate (n = 51), and severe/critical (n = 31). Faecal and nasopharyngeal samples were taken, and the microbiota was analysed. Linear discriminant analysis identified Mycoplasma salivarium, Prevotella dentalis, and Haemophilus parainfluenzae as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while Prevotella bivia and Prevotella timonensis were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between P. timonensis (faeces) and P. dentalis and M. salivarium (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.

Immunologic and inflammatory consequences of SARS-CoV-2 infection and its implications in renal disease

The emergence of the COVID-19 pandemic made it critical to understand the immune and inflammatory responses to the SARS-CoV-2 virus. It became increasingly recognized that the immune response was a key mediator of illness severity and that its mechanisms needed to be better understood. Early infection of both tissue and immune cells, such as macrophages, leading to pyroptosis-mediated inflammasome production in an organ system critical for systemic oxygenation likely plays a central role in the morbidity wrought by SARS-CoV-2. Delayed transcription of Type I and Type III interferons by SARS-CoV-2 may lead to early disinhibition of viral replication. Cytokines such as interleukin-1 (IL-1), IL-6, IL-12, and tumor necrosis factor α (TNFα), some of which may be produced through mechanisms involving nuclear factor kappa B (NF-κB), likely contribute to the hyperinflammatory state in patients with severe COVID-19. Lymphopenia, more apparent among natural killer (NK) cells, CD8+ T-cells, and B-cells, can contribute to disease severity and may reflect direct cytopathic effects of SARS-CoV-2 or end-organ sequestration. Direct infection and immune activation of endothelial cells by SARS-CoV-2 may be a critical mechanism through which end-organ systems are impacted. In this context, endovascular neutrophil extracellular trap (NET) formation and microthrombi development can be seen in the lungs and other critical organs throughout the body, such as the heart, gut, and brain. The kidney may be among the most impacted extrapulmonary organ by SARS-CoV-2 infection owing to a high concentration of ACE2 and exposure to systemic SARS-CoV-2. In the kidney, acute tubular injury, early myofibroblast activation, and collapsing glomerulopathy in select populations likely account for COVID-19-related AKI and CKD development. The development of COVID-19-associated nephropathy (COVAN), in particular, may be mediated through IL-6 and signal transducer and activator of transcription 3 (STAT3) signaling, suggesting a direct connection between the COVID-19-related immune response and the development of chronic disease. Chronic manifestations of COVID-19 also include systemic conditions like Multisystem Inflammatory Syndrome in Children (MIS-C) and Adults (MIS-A) and post-acute sequelae of COVID-19 (PASC), which may reflect a spectrum of clinical presentations of persistent immune dysregulation. The lessons learned and those undergoing continued study likely have broad implications for understanding viral infections' immunologic and inflammatory consequences beyond coronaviruses.

Metabolomic profile of severe COVID-19 and a signature predictive of progression towards severe disease status: a prospective cohort study (METCOVID)

Profound metabolomic alterations occur during COVID-19. Early identification of the subset of hospitalised COVID-19 patients at risk of developing severe disease is critical for optimal resource utilization and prompt treatment. This work explores the metabolomic profile of hospitalised adult COVID-19 patients with severe disease, and establishes a predictive signature for disease progression. Within 48 hours of admission, serum samples were collected from 148 hospitalised patients for nuclear magnetic resonance (NMR) spectroscopy. Lipoprotein profiling was performed using the 1H-NMR-based Liposcale test, while low molecular weight metabolites were analysed using one-dimensional Carr-Purcell-Meiboom-Gill pulse spectroscopy and an adaptation of the Dolphin method for lipophilic extracts. Severe COVID-19, per WHO's Clinical Progression Scale, was characterized by altered lipoprotein distribution, elevated signals of glyc-A and glyc-B, a shift towards a catabolic state with elevated levels of branched-chain amino acids, and accumulation of ketone bodies. Furthermore, COVID-19 patients initially presenting with moderate disease but progressing to severe stages exhibited a distinct metabolic signature. Our multivariate model demonstrated a cross-validated AUC of 0.82 and 72% predictive accuracy for severity progression. NMR spectroscopy-based metabolomic profiling enables the identification of moderate COVID-19 patients at risk of disease progression, aiding in resource allocation and early intervention.

Severe COVID-19 disease is associated with genetic factors affecting plasma ACE2 receptor and CRP concentrations

A hyperinflammatory state with highly elevated concentrations of inflammatory biomarkers such as C-reactive protein (CRP) is a characteristic feature of severe coronavirus disease 2019 (COVID-19). To examine a potential role of common genetic factors that may influence COVID-19 outcomes, we investigated whether individuals with a polygenic predisposition for a pro-inflammatory response (in the form of Polygenic Scores) are more likely to develop severe COVID-19. The innovative approach of polygenic scores to investigate genetic factors in COVID-19 severity should provide a comprehensive approach beyond single-gene studies. In our cohort of 156 patients of European ancestry, two overlapping Polygenic Scores (PGS) predicting a genetic predisposition to basal CRP concentrations were significantly different between non-severe and severe COVID-19 cases and were associated with less severe COVID-19 outcomes. Furthermore, specific single nucleotide polymorphisms (SNPs) that contribute to either of the two Polygenic Scores predicting basal CRP levels are associated with different traits that represent risk factors for COVID-19 disease initiation (ACE2 receptor, viral replication) and progression (CRP). We suggest that genetically determined enforced CRP formation may contribute to strengthening of innate immune responses and better initial pathogen control thereby reducing the risk of subsequent hyperinflammation and adverse course of COVID-19.

A lethal disease of the European bison - posthitis is conditionally determined by its genomics

Posthitis is an incurable lethal disease of males of the European bison (Bison bonasus), regarded to be one of the major threats to the survival of the iconic species. Multiple attempts have been undertaken over the last 30 years to identify a source of infection and a primary pathogen. Studies indicated the disease could have a genetic background after tools developed for cattle (Bos taurus) revealed genomic regions that could be associated with its occurrence. In this study, we applied deep coverage targeted sequencing to 74 regions on 10 of the bison's chromosomes (1, 9, 12, 13, 15, 23, 25, 26, 29, and X) in search for species-specific single nucleotide polymorphism (SNP) markers that could help to explain the mechanism of the disease and be used to test for posthitis susceptibility. The association results were ranked based on p-values lower than 0.005 and odds ratios (OR) higher than 1. We obtained 30 SNP markers that met these requirements, all located on chromosome 25. However, none of the SNPs found in the study was significantly associated with posthitis occurrence after Bonferroni correction. The conditional nature of posthitis and 'false negative' sampling represent major difficulties in investigating this disease, and we recommend a complex genomic and environmental factors association assay that could eventually explain the puzzling etiology of posthitis and help mitigate this threat to the European bison.

The HLA-B -21 M/T dimorphism associates with disease severity in COVID-19

Host genetics shape immune responses and influence severity of infectious diseases. The HLA-B -21 M/T dimorphism tunes the functionality of natural killer (NK) cells expressing the inhibitory receptor NKG2A. NKG2A+ NK cells have been reported to recognize SARS-CoV-2-infected cells, but it remains unclear whether the HLA-B -21 M/T dimorphism associates with COVID-19 severity. Here, we investigated the influence of the HLA-B -21 M/T dimorphism in a cohort of 230 unvaccinated patients hospitalized with COVID-19 and requiring respiratory support. We found that HLA-B -21 M/M genotypes were more prevalent in patients with moderate compared to severe COVID-19 (6.0% vs. 0.9%). Comparison of age- and sex-matched sub-groups revealed that patients with M/M genotypes required mechanical respiratory support less frequently (OR = 0.13, 95% CI = 0.01-0.76, P = 0.013). Furthermore, patients with M/M genotypes showed a coordinately shifted signature of clinical laboratory parameters, coinciding with elevated serum levels of the anti-viral cytokine IFN-γ. These findings demonstrate that HLA-B variants associate with COVID-19 severity and suggest that the robust functionality of NKG2A+ NK cells in patients carrying the M/M genotype may contribute to protection from severe disease.

Role and benefits of infectious diseases specialists in the COVID-19 pandemic: Multilevel analysis of care provision in German hospitals using data from the Lean European Open Survey on SARS-CoV-2 infected patients (LEOSS) cohort

PURPOSE

This study investigates the care provision and the role of infectious disease (ID) specialists during the coronavirus disease-2019 (COVID-19) pandemic.

METHODS

A survey was conducted at German study sites participating in the Lean European Open Survey on SARS-CoV-2 infected patients (LEOSS). Hospitals certified by the German Society of Infectious diseases (DGI) were identified as ID centers. We compared care provision and the involvement of ID specialists between ID and non-ID hospitals. Then we applied a multivariable regression model to analyse how clinical ID care influenced the mortality of COVID-19 patients in the LEOSS cohort.

RESULTS

Of the 40 participating hospitals in the study, 35% (14/40) were identified as ID centers. Among those, clinical ID care structures were more commonly established, and ID specialists were always involved in pandemic management and the care of COVID-19 patients. Overall, 68% (27/40) of the hospitals involved ID specialists in the crisis management team, 78% (31/40) in normal inpatient care, and 80% (28/35) in intensive care. Multivariable analysis revealed that COVID-19 patients in ID centers had a lower mortality risk compared to those in non-ID centers (odds ratio: 0.61 (95% CI 0.40-0.93), p = 0.021).

CONCLUSION

ID specialists played a crucial role in pandemic management and inpatient care.

The Investigation of the Distribution of ABO/Rh Blood Group in Hospitalized COVID-19 Patients and Its Association With Disease Severity, Clinical Outcomes, Lab Tests, and Radiologic Findings

Background and Aims

it is important to identify patients at higher risk for severity and poor outcomes of COVID-19 infection, to have better disease management and pandemic control. In this study, we aimed to assess the distribution of ABO and Rh blood groups in hospitalized COVID-19 infected patients and demonstrate its association with severity and outcomes of the disease.

Methods

This is a cross-sectional study at Ziaeian Specialist Hospital, in Tehran, Iran. Of all confirmed COVID-19 infected patients who were admitted to this hospital, 273 patients were enrolled in this study and categorized based on their disease severity or clinical outcomes including intensive care unit (ICU) admission, need for mechanical ventilation and mortality. The distribution of ABO and Rh blood groups was assessed and compared between different groups, to investigate the association of blood group types with disease severity or outcomes. Also, the study population was categorized based on their blood group types to demonstrate the association of laboratory parameters, radiologic findings, and length of hospitalization with blood groups. Sex, age and underlying disease were adjusted in the final model by multivariate regression analysis.

Results

This study showed that Blood group A (35.9%) was the most prevalent among hospitalized COVID-19 patients followed by O (34.8%), B (21.6%), and AB (7.7%) (A > O > B > AB). ABO and Rh blood group was not associated with disease severity, need for mechanical ventilation, or ICU admission, while blood group B was associated with an increased risk of death in comparison with type O, in hospitalized COVID-19 patients (p = 0.02). The number of patients with severe levels of C-reactive protein (CRP) test results was lower in O blood group patients in comparison with non-O blood groups (p = 0.01).

Conclusion

No significant association was found between blood groups and other lab tests, radiologic findings, and length of hospitalization.

The relationship between microRNAs and COVID-19 complications

Over the past three years, since the onset of COVID-19, several scientific studies have concentrated on understanding susceptibility to the virus, the progression of the illness, and possible long-term complexity. COVID-19 is broadly recognized with effects on multiple systems in the body, and various factors related to society, medicine, and genetics/epigenetics may contribute to the intensity and results of the disease. Additionally, a SARS-CoV-2 infection can activate pathological activities and expedite the emergence of existing health issues into clinical problems. Forming easily accessible, distinctive, and permeable biomarkers is essential for categorizing patients, preventing the disease, predicting its course, and tailoring treatments for COVID-19 individually. One promising candidate for such biomarkers is microRNAs, which could serve various purposes in understanding diverse forms of COVID-19, including susceptibility, intensity, disease progression, outcomes, and potential therapeutic options. This review provides an overview of the most significant findings related to the involvement of microRNAs in COVID-19 pathogenesis. Furthermore, it explores the function of microRNAs in a broad span of effects that may arise from accompanying or underlying health status. It underscores the value of comprehending how diverse conditions, such as neurological disorders, diabetes, cardiovascular diseases, and obesity, interact with COVID-19.

Genetic diversity of the immunoglobulin heavy chain locus in cohorts of patients affected with SARS-CoV-2

BACKGROUND

The Immunoglobulin Heavy Chain (IGH) genomic region is responsible for the production of circulating antibodies and warrants careful investigation for its association with COVID-19 characteristics. Multiple allelic variants within and across different IGH gene segments form a limited set of haplotypes. Previous studies have shown associations between some of these haplotypes and clinical outcomes of COVID-19. We typed 445 individuals of European ancestry, stratified for gender, age, and clinical status for 4 SNPs, two of which result in amino acid substitutions in IGHA2 and IGHG4, respectively. We analyzed associations at the single-locus level and for 4-loci haplotypes, inferred by phasing, after stratifying the overall cohort by gender, age, and disease severity.

RESULTS

Only weak evidence of significant differences between subgroups was obtained at the level of a single SNP. However, when the haplotypic data were analyzed for the young and old subgroups separately, uneven partitioning was observed regarding the occurrence of severe cases and Resistors. We then examined the cross-tabulation of disease severity in males and females, based on the presence of each haplotype in the genotype. Two haplotypes were underrepresented in young severe cases compared to old severe ones. The same two haplotypes were overrepresented among young Resistors. These findings provide stronger support for, the weak associations observed at the single locus level.

CONCLUSIONS

Two haplotypes seem to act as protective factors specifically in young individuals, counteracting the general increase in vulnerability with age. This observation aligns with stronger genetic effects seen in young patients for other susceptibility genes. Our findings complement previous research identifying specific genetic variants that influence COVID-19 susceptibility and severity, emphasizing the complex interplay between host genetics and viral infection outcomes. Our results are consistent with a potential causative role of IGH regulatory regions (e.g. HS1.2), which are flanked by the SNP set here analyzed.

Genetic proxies for clinical traits are associated with increased risk of severe COVID-19

Routine use of genetic data in healthcare is much-discussed, yet little is known about its performance in epidemiological models including traditional risk factors. Using severe COVID-19 as an exemplar, we explore the integration of polygenic risk scores (PRS) into disease models alongside sociodemographic and clinical variables. PRS were optimized for 23 clinical variables and related traits previously-associated with severe COVID-19 in up to 450,449 UK Biobank participants, and tested in 9,560 individuals diagnosed in the pre-vaccination era. Associations were further adjusted for (i) sociodemographic and (ii) clinical variables. Pathway analyses of PRS were performed to improve biological understanding of disease. In univariate analyses, 17 PRS were associated with increased risk of severe COVID-19 and, of these, four remained associated with COVID-19 outcomes following adjustment for sociodemographic/clinical variables: hypertension PRS (OR = 1.1, 95%CI 1.03-1.18), atrial fibrillation PRS (OR = 1.12, 95%CI 1.03-1.22), peripheral vascular disease PRS (OR = 0.9, 95%CI 0.82-0.99), and Alzheimer's disease PRS (OR = 1.14, 95%CI 1.05-1.25). Pathway analyses revealed enrichment of genetic variants in pathways for cardiac muscle contraction (genes N = 5; beta[SE] = 3.48[0.60]; adjusted-P = 1.86 × 10-5). These findings underscore the potential for integrating genetic data into epidemiological models and highlight the advantages of utilizing multiple trait PRS rather than a single PRS for a specific outcome of interest.

Neutrophils restricted contribution of CCRL2 genetic variants to COVID-19 severity

The 3p21.31 locus is the most robust genomic region associated with COVID-19 severity. This locus contains a main chemokine receptor (CKR) cluster. We tested expression quantitative trait loci (eQTL) targeting the 3p21.31 CKR cluster linked to COVID-19 hospitalization in Europeans from the COVID-19 HGI meta-analysis. Among these, CCRL2, a key regulator of neutrophil trafficking, was targeted by neutrophil-restricted eQTLs. We confirmed these eQTLs in an Italian COVID-19 cohort. Haplotype analysis revealed a link between an increased CCRL2 expression and COVID-19 severity and hospitalization. By the exposure of neutrophils to a TLR8 ligand, reflecting a viral infection, we revealed specific chromatin domains within the 3p21.31 locus exclusive to neutrophils. In addition, the identified variants mapped within these regions altered the binding motif of neutrophils-expressed transcription factors. These results support that CCRL2 eQTL variants contribute to the risk of severe COVID-19 by selectively affecting neutrophil functions.

Variants in the β-globin locus are associated with pneumonia in African American children

In African American adults, the strongest genetic predictor of pneumonia appears to be the A allele of rs334, a variant in the β-globin gene, which in homozygous form causes sickle cell disease (SCD). No comparable studies have been done in African American children. We performed genome-wide association analyses of 482 African American children with documented pneumonia and 2,048 African American control individuals using genotypes imputed from two reference panels: 1000 Genomes (1KG) (which contains rs334) and TOPMed (does not contain rs334). Using 1KG imputed genotypes, the most significant variant was rs334 (A allele; odds ratio [OR] = 2.76; 95% CI, 2.21-3.74; p = 5.9 × 10-19); using TOPMed imputed genotypes the most significant variant was rs2226952, found in the β-globin locus control region (G allele; OR = 2.14; 95% CI, 1.78-2.57; p = 5.1 × 10-16). After conditioning on rs334, the most strongly associated variant in the β-globin locus, rs33930165 (T allele, 1KG: OR = 4.09; 95% CI, 2.29-7.29; p = 1.7 × 10-6; TOPMed: OR = 3.58; 95% CI, 2.18-5.90; p = 4.7 × 10-7), which as a compound heterozygote with rs334 A allele, can cause SCD. To compare the power of different sample sets we developed a way to estimate the power of sample sets with different sample sizes, genotype arrays, and imputation platforms. Our results suggest that, in African American children, the strongest genetic determinants of pneumonia are those that increase the risk of SCD.

Mucosal immune response in biology, disease prevention and treatment

The mucosal immune system, as the most extensive peripheral immune network, serves as the frontline defense against a myriad of microbial and dietary antigens. It is crucial in preventing pathogen invasion and establishing immune tolerance. A comprehensive understanding of mucosal immunity is essential for developing treatments that can effectively target diseases at their entry points, thereby minimizing the overall impact on the body. Despite its importance, our knowledge of mucosal immunity remains incomplete, necessitating further research. The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has underscored the critical role of mucosal immunity in disease prevention and treatment. This systematic review focuses on the dynamic interactions between mucosa-associated lymphoid structures and related diseases. We delve into the basic structures and functions of these lymphoid tissues during disease processes and explore the intricate regulatory networks and mechanisms involved. Additionally, we summarize novel therapies and clinical research advances in the prevention of mucosal immunity-related diseases. The review also addresses the challenges in developing mucosal vaccines, which aim to induce specific immune responses while maintaining tolerance to non-pathogenic microbes. Innovative therapies, such as nanoparticle vaccines and inhalable antibodies, show promise in enhancing mucosal immunity and offer potential for improved disease prevention and treatment.

Age-dependent phenotypes of cognitive impairment as sequelae of SARS-CoV-2 infection

Cognitive changes associated with PASC may not be uniform across populations. We conducted individual-level pooled analyses and meta-analyses of cognitive assessments from eight prospective cohorts, comprising 2,105 patients and 1,432 controls from Argentina, Canada, Chile, Greece, India, Italy, Russia, and the UK. The meta-analysis found no differences by country of origin. The profile and severity of cognitive impairment varied by age, with mild attentional impairment observed in young and middle-aged adults, but memory, language, and executive function impairment in older adults. The risk of moderate to severe impairment doubled in older adults. Moderately severe or severe impairment was significantly associated with infection diagnoses (chi-square = 26.57, p ≤ 0.0001) and the severity of anosmia (chi-square = 31.81, p ≤ 0.0001). We found distinct age-related phenotypes of cognitive impairment in patients recovering from COVID-19. We identified the severity of acute illness and the presence of olfactory dysfunction as the primary predictors of dementia-like impairment in older adults.

Omega-3 Polyunsaturated Fatty Acids in Chronic Obstructive Pulmonary Disease Patients with COVID-19: A Review

PURPOSE OF THE REVIEW

Mounting evidence indicates that individuals with chronic obstructive pulmonary disease (COPD) face a heightened risk of severe outcomes upon contracting coronavirus disease 2019 (COVID-19). Current medications for COVID-19 often carry side effects, necessitating alternative therapies with improved tolerance. This review explores the biological mechanisms rendering COPD patients more susceptible to severe COVID-19 and investigates the potential of omega-3 polyunsaturated fatty acids (n-3 PUFAs) in mitigating the severity of COVID-19 in COPD patients.

RECENT FINDINGS

Current evidence indicates that COPD patients are at an increased risk of severe COVID-19 due to factors including compromised pulmonary function, dysregulated inflammation, weakened immune response, increased oxidative stress, elevated expression of angiotensin-converting enzyme (ACE2) receptors in the lungs, and genetic predispositions. Remarkably, n-3 PUFAs exhibit the potential in ameliorating the clinical outcomes of COPD patients with COVID-19 by modulating inflammation, reinforcing the body's antioxidant defenses, reducing viral entry and replication, and enhancing immunity. N-3 PUFAs hold potential for improving COVID-19 outcomes in patients with COPD. However, there has been limited investigation into the therapeutic effects of n-3 PUFAs in enhancing clinical outcomes for COPD patients. Rigorous clinical studies are essential to evaluate the impact of n-3 PUFAs on COPD patients with concurrent COVID-19 infection.

Potential associations of selected polymorphic genetic variants with COVID-19 disease susceptibility and severity

In this study, we analyzed the potential associations of selected laboratory and anamnestic parameters, as well as 12 genetic polymorphisms (SNPs), with clinical COVID-19 occurrence and severity in 869 hospitalized patients. The SNPs analyzed by qPCR were selected based on population-wide genetic (GWAS) data previously indicating association with the severity of COVID-19, and additional SNPs that have been shown to be important in cellular processes were also examined. We confirmed the associations of COVID-19 with pre-existing diabetes and found an unexpected association between less severe disease and the loss of smell and taste. Regarding the genetic polymorphisms, a higher allele frequency of the LZTFL1 and IFNAR2 minor variants significantly correlated with greater COVID-19 disease susceptibility (hospitalization) and severity, and a similar tendency was observed for the RAVER1 and the MUC5B variants. Interestingly, the ATP2B4 minor haplotype, protecting against malaria, correlated with an increased disease susceptibility, while in diabetic patients disease susceptibility was lower in the presence of a reduced-function ABCG2 transporter variant. Our current results, which should be reinforced by larger studies, indicate that together with laboratory and anamnestic parameters, genetic polymorphisms may have predictive value for the clinical occurrence and severity of COVID-19.

Tofacitinib Mitigates the Increased SARS-CoV-2 Infection Susceptibility Caused by an IBD Risk Variant in the PTPN2 Gene

BACKGROUND & AIMS

Coronavirus disease (COVID-19), caused by severe acquired respiratory syndrome-Coronavirus-2 (SARS-CoV-2), triggered a global pandemic with severe medical and socioeconomic consequences. Although fatality rates are higher among the elderly and those with underlying comorbidities, host factors that promote susceptibility to SARS-CoV-2 infection and severe disease are poorly understood. Although individuals with certain autoimmune/inflammatory disorders show increased susceptibility to viral infections, there is incomplete knowledge of SARS-CoV-2 susceptibility in these diseases. The aim of our study was to investigate whether the autoimmunity risk gene, PTPN2, which also confers elevated risk to develop inflammatory bowel disease, affects susceptibility to SARS-CoV-2 viral uptake.

METHODS

Using samples from PTPN2 genotyped patients with inflammatory bowel disease, PTPN2-deficient mice, and human intestinal and lung epithelial cell lines, we investigated how PTPN2 affects expression of the SARS-CoV-2 receptor angiotensin converting enzyme 2 (ACE2), and uptake of virus-like particles expressing the SARS-CoV2 spike protein and live SARS-CoV-2 virus.

RESULTS

We report that the autoimmune PTPN2 loss-of-function risk variant rs1893217 promotes expression of the SARS-CoV-2 receptor, ACE2, and increases cellular entry of SARS-CoV-2 spike protein and live virus. Elevated ACE2 expression and viral entry were mediated by increased Janus kinase-signal transducers and activators of transcription signaling and were reversed by the Janus kinase inhibitor, tofacitinib.

CONCLUSION

Collectively, our findings uncover a novel risk biomarker for increased expression of the SARS-CoV-2 receptor and viral entry, and identify a clinically approved therapeutic agent to mitigate this risk.

Casual correlation between overweight, obesity, and severe COVID-19 infection with respiratory failure: A two-sample Mendelian randomization

This study aimed to detect the causal association of overweight and obesity on severe COVID-19 infection with respiratory failure through a two-sample Mendelian randomization (MR) method based on the genome-wide association studies datasets. All genome-wide association studies summary data of exposures and outcome used in this study were obtained from the IEU database derived from Europeans. The study mainly used the inverse variance weighted method to test causal relationship. Simultaneously, MR-PRESSO and MR-EGGER were used to detect the pleiotropy, and sensitivity analysis was performed using leave-one-out analysis. In the inverse variance weighted analyses, we found no causal association between obesity (e.g., OR = 1.15, 95% CIs = 0.96-1.37, P = .13 for obesity-ebi-a-GCST90000255), obesity subtypes (e.g., OR = 1.93, 95% CIs = 0.90-4.14, P = .10 for obesity and other hyperalimentation) as well as overweight (OR = 0.90, 95% CIs = 0.64-1.27, P = .54) and severe COVID-19 infection with respiratory failure. The findings showed no causal association between obesity or overweight and severe COVID-19 infection with respiratory failure. Further validation is needed regarding whether obesity or overweight is a risk factor for it.

Association study of the JAK/STAT signaling pathway with susceptibility to COVID-19 in moroccan patient and in-silico analysis of rare variants

The goal of our study was to explore the association of the polymorphisms in the JAK/STAT pathway among Moroccan COVID-19 patients, using a case-control approach. Next-generation sequencing was employed to investigate the IFNAR1, IFNAR2, JAK1, TYK2, STAT2, and IRF9 genes within the JAK/STAT pathway. We also performed an in silico study to examine the rare variants in this pathway. Statistical analyses were conducted using MedCalc software. Protein 3D structures were determined via the I-TASSER server, with variant structures generated using PyMOL. YASARA View allowed local 3D analysis comparing native and variant structures for pathogenic rare variants. The study encompassed 206 COVID-19 patients, averaging 45.70 ± 12.73 years and a control group (N=118). Among the examined genes, 15 common polymorphisms and 7 rare variants were identified. Adjustment for age and gender revealed a significant association between TYK2 p.Gly363Ser (p=0.036) and COVID-19 infection, where the GA variant exhibited protective effects (0.6361 [0.3405-1.1884], p=0.035). Additionally, STAT2 p.Met594Ile showed an association to COVID-19 risk (p=0.042), with heterozygous GC being linked to infection (p=0.037, OR=2.7135 [0.5684 -12.9532]). Notably, IFNAR1 p.Val168Leu mutated C allele was significantly associated with reduced susceptibility to COVID-19 severity (p=0.028, OR=0.5936 [0.3725 - 0.9461]), under the additive model (p=0.045, OR=0.626 [0.3958 - 0.9899]). Rare variants IFNAR1 p.Trp318Cys, p.Ser476Phe, and IFNAR2 p.Cys271Tyr were predicted deleterious, impacting protein structure via hydrogen bond and hydrophobic interaction alterations. Burden analysis of rare variants revealed a protective cumulative effect against COVID-19 severity for TYK2 (p=0.0013, OR=0.1438 [0.04237 - 0.4803]) under the dominant model. This study underscores the role of genetic factors in COVID-19 susceptibility and advocates further explorations regarding functional impacts of JAK/STAT pathway rare variants.

The Apoprotein E4 isotype does not affect the severity of COVID-19 infection and other flu-like syndromes

Introduction. Apolipoprotein E (ApoE), especially the ApoE4 isotype, is suggested to influence the severity of respiratory viral infections; however, this association is still unclear.Hypothesis. The presence of allele ε4 impacts the development of flu-like syndromes.Aim. This study aimed to evaluate the impact of the Apo E4 isoform on the severity and duration of flu-like syndromes, including the coronavirus disease COVID-19.Methodology. This study comprised 280 individuals presenting flu-like symptoms, all genotyped for ApoE isoforms. Data were collected on clinical course, comorbidities, nutritional status, biochemical and inflammatory markers, SARS-CoV-2 reverse transcription PCR results and disease severity (mild, moderate or severe) according to the World Health Organization criteria. The individuals were analysed as a whole and within subgroups based on the SARS-CoV-2-positive (COVID-19 group) or SARS-CoV-2-negative (flu-like syndrome group) test.Results. The frequency of the ε4 allele was similar across the whole population and in both the COVID-19 and flu-like syndrome subgroups (17 and 18%, respectively). No differences were seen in sex, age range, self-reported skin colour, body mass index (BMI), number of comorbidities, vaccination status, biochemical, cytokine and lipid profiles (except for total cholesterol) in the flu-like group when ε4 allele carriers and non-carriers were compared. In the COVID-19 group, the ε4 allele did not correlate with disease severity or duration, number of comorbidities or inflammatory biomarkers. While gender distribution was equal in the overall COVID-19 population, male gender strongly correlated with COVID-19 severity. Multivariate analysis showed that older individuals, male gender, higher BMI and the presence of comorbidities were linked to increased chances of developing moderate and severe disease. IL-4 was the only factor found to reduce the risk of severe COVID-19.Conclusion. The presence of one ɛ4 allele showed no association with the duration and severity of flu-like syndromes, including COVID-19. Nonetheless, SARS-CoV-2-positive individuals tend to be older men with a higher BMI and a tendency to be overweight or with obesity. Regarding COVID-19 severity, BMI, male sex and the number of associated comorbidities were the factors that increased the chance of developing a more severe form of COVID-19.

Unraveling genetic mysteries: A comprehensive review of GWAS and DNA insights in animal and plant pathosystems

DNA serves as the carrier of genetic information, with sequence variations playing a pivotal role in defining hereditary traits. Genome-Wide Association Studies (GWAS) facilitate the investigation of the links between genetic variations and phenotypes, significantly influencing biological research, particularly in animal and plant pathology. By identifying genetic markers associated with specific traits or diseases, GWAS enhances our understanding of host-pathogen interactions and improves disease-resistant breeding strategies. It has been vital in revealing the genetic basis of disease resistance, pinpointing key genes and DNA loci, which enrich genetic resources for breeding programs and deepen our knowledge of disease resistance mechanisms at the DNA level. Additionally, GWAS contributes to pathogen population genetics, facilitating a thorough exploration of pathogen virulence. Integrating GWAS with marker-assisted selection enhances breeding efficiency and precision in selecting for disease-resistant traits. While previous research has largely focused on host genetics, the genetic variation of pathogens is equally significant. Notably, reports integrating animal and plant pathosystems are still lacking. Given the importance of these systems, this review summarizes key advancements in this field, addresses current challenges, and proposes future directions, thereby offering a vital reference for ongoing research.

Scalable randomized kernel methods for multiview data integration and prediction with application to Coronavirus disease

There is still more to learn about the pathobiology of coronavirus disease (COVID-19) despite 4 years of the pandemic. A multiomics approach offers a comprehensive view of the disease and has the potential to yield deeper insight into the pathogenesis of the disease. Previous multiomics integrative analysis and prediction studies for COVID-19 severity and status have assumed simple relationships (ie linear relationships) between omics data and between omics and COVID-19 outcomes. However, these linear methods do not account for the inherent underlying nonlinear structure associated with these different types of data. The motivation behind this work is to model nonlinear relationships in multiomics and COVID-19 outcomes, and to determine key multidimensional molecules associated with the disease. Toward this goal, we develop scalable randomized kernel methods for jointly associating data from multiple sources or views and simultaneously predicting an outcome or classifying a unit into one of 2 or more classes. We also determine variables or groups of variables that best contribute to the relationships among the views. We use the idea that random Fourier bases can approximate shift-invariant kernel functions to construct nonlinear mappings of each view and we use these mappings and the outcome variable to learn view-independent low-dimensional representations. We demonstrate the effectiveness of the proposed methods through extensive simulations. When the proposed methods were applied to gene expression, metabolomics, proteomics, and lipidomics data pertaining to COVID-19, we identified several molecular signatures for COVID-19 status and severity. Our results agree with previous findings and suggest potential avenues for future research. Our algorithms are implemented in Pytorch and interfaced in R and available at: https://github.com/lasandrall/RandMVLearn.