The genetic polymorphisms of HLA are strongly correlated with the disease severity after Hantaan virus infection in the Chinese Han population

Narrative Review Explaining the Role of HLA-A, -B, and -C Molecules in COVID-19 Disease in and around Africa

The coronavirus disease 2019 (COVID-19) has left a devasting effect on various regions globally. Africa has exceptionally high rates of other infectious diseases, such as tuberculosis (TB), human immunodeficiency virus (HIV), and malaria, and was not impacted by COVID-19 to the extent of other continents Globally, COVID-19 has caused approximately 7 million deaths and 700 million infections thus far. COVID-19 disease severity and susceptibility vary among individuals and populations, which could be attributed to various factors, including the viral strain, host genetics, environment, lifespan, and co-existing conditions. Host genetics play a substantial part in COVID-19 disease severity among individuals. Human leukocyte antigen (HLA) was previously been shown to be very important across host immune responses against viruses. HLA has been a widely studied gene region for various disease associations that have been identified. HLA proteins present peptides to the cytotoxic lymphocytes, which causes an immune response to kill infected cells. The HLA molecule serves as the central region for infectious disease association; therefore, we expect HLA disease association with COVID-19. Therefore, in this narrative review, we look at the HLA gene region, particularly, HLA class I, to understand its role in COVID-19 disease.

Influence of Disease Severity and Gender on HLA-C Methylation in COVID-19 Patients

In the pathophysiology of COVID-19, immunomodulatory factors play a vital role. Viruses have epigenetic effects on various genes, particularly methylation. Explaining the changes in immunological factor methylation levels during viral infections requires substantial consideration. HLA-C is a crucial determinant of immune function and NK cell activity and is primarily implicated in viral infections. This research focused on studying HLA-C methylation in COVID-19 patients with different severity. Peripheral blood samples were collected from 470 patients (235 men and 235 women) with RT-qPCR-confirmed COVID-19 test and classified into moderate, severe, and critical groups based on WHO criteria. Also, one hundred (50 men and 50 women) healthy subjects were selected as the control group. Peripheral blood mononuclear cells were used for DNA extraction, and the methylation-specific PCR (MSP) method and gel electrophoresis were used to determine the methylation status of the HLA-C. Significant statistical differences in HLA-C methylation were observed among cases and controls and various stages of the disease. HLA-C methylation in men and women has decreased in all stages (p < 0.05). In comparison with control, HLA-C methylation in both genders were as follows: moderate (women: 41.0%, men: 52.33%), severe (women: 43.42%, men: 64.86%), critical (women: 42.33%, men: 60.07%), and total patients (women: 45.52%, men: 56.97%). Furthermore, the methylation levels in men were higher than in women in all groups (p < 0.05). Significantly, among all groups, the severe group of men participants showed the highest methylation percentage (p < 0.05). No significant differences were detected for different disease severity in the women group (p > 0.1). This study found that HLA-C methylation was significantly lower in COVID-19 patients with different disease severity. There were also significant differences in HLA-C methylation between men and women patients with different severity. Therefore, during managing viral infections, particularly COVID-19, it is critical to consider patient gender and disease severity.

COVID-19 2022 update: transition of the pandemic to the endemic phase

COVID-19, which is caused by the SARS-CoV-2, has ravaged the world for the past 2 years. Here, we review the current state of research into the disease with focus on its history, human genetics and genomics and the transition from the pandemic to the endemic phase. We are particularly concerned by the lack of solid information from the initial phases of the pandemic that highlighted the necessity for better preparation to face similar future threats. On the other hand, we are gratified by the progress into human genetic susceptibility investigations and we believe now is the time to explore the transition from the pandemic to the endemic phase. The latter will require worldwide vigilance and cooperation, especially in emerging countries. In the transition to the endemic phase, vaccination rates have lagged and developed countries should assist, as warranted, in bolstering vaccination rates worldwide. We also discuss the current status of vaccines and the outlook for COVID-19.

Comparative Immunoreactivity Analyses of Hantaan Virus Glycoprotein-Derived MHC-I Epitopes in Vaccination

MHC-I antigen processes and presentation trigger host-specific anti-viral cellular responses during infection, in which epitope-recognizing cytotoxic T lymphocytes eliminate infected cells and contribute to viral clearance through a cytolytic killing effect. In this study, Hantaan virus (HTNV) GP-derived 9-mer dominant epitopes were obtained with high affinity to major HLA-I and H-2 superfamilies. Further immunogenicity and conservation analyses selected 11 promising candidates, and molecule docking (MD) was then simulated with the corresponding MHC-I alleles. Two-way hierarchical clustering revealed the interactions between GP peptides and MHC-I haplotypes. Briefly, epitope hotspots sharing good affinity to a wide spectrum of MHC-I molecules highlighted the biomedical practice for vaccination, and haplotype clusters represented the similarities among individuals during T-cell response establishment. Cross-validation proved the patterns observed through both MD simulation and public data integration. Lastly, 148 HTNV variants yielded six types of major amino acid residue replacements involving four in nine hotspots, which minimally influenced the general potential of MHC-I superfamily presentation. Altogether, our work comprehensively evaluates the pan-MHC-I immunoreactivity of HTNV GP through a state-of-the-art workflow in light of comparative immunology, acknowledges present discoveries, and offers guidance for ongoing HTNV vaccine pursuit.

OUP accepted manuscript

Hantavirus-induced diseases are emerging zoonoses with endemic appearances and frequent outbreaks in different parts of the world. In humans, hantaviral pathology is characterized by the disruption of the endothelial cell barrier followed by increased capillary permeability, thrombocytopenia due to platelet activation/depletion and an overactive immune response. Genetic vulnerability due to certain human leukocyte antigen haplotypes is associated with disease severity. Typically, two different hantavirus-caused clinical syndromes have been reported: hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The primarily affected vascular beds differ in these two entities: renal medullary capillaries in HFRS caused by Old World hantaviruses and pulmonary capillaries in HCPS caused by New World hantaviruses. Disease severity in HFRS ranges from mild, e.g. Puumala virus-associated nephropathia epidemica, to moderate, e.g. Hantaan or Dobrava virus infections. HCPS leads to a severe acute respiratory distress syndrome with high mortality rates. Due to novel insights into organ tropism, hantavirus-associated pathophysiology and overlapping clinical features, HFRS and HCPS are believed to be interconnected syndromes frequently involving the kidneys. As there are no specific antiviral treatments or vaccines approved in Europe or the USA, only preventive measures and public awareness may minimize the risk of hantavirus infection. Treatment remains primarily supportive and, depending on disease severity, more invasive measures (e.g., renal replacement therapy, mechanical ventilation and extracorporeal membrane oxygenation) are needed.

Perspectives Concerning Various Symptoms of SARS-CoV-2 Detected Individuals

After exposure to SARS-CoV-2, varying symptoms of COVID-19 ranging from asymptomatic symptoms to morbidity and mortality have been exhibited in each individual. SARS-CoV-2 requires various cellular molecules for penetration into a target host cell. Angiotensin-converting enzyme2 (ACE2) acts as the viral receptor molecule. After attachment, SARS-CoV-2 also requires the transmembrane protease serine-2 (TMPRSS-2) and furin molecules, which serve as co-receptors for penetration into the target cell and for subsequent replication. In the meantime, a major histocompatibility complex (MHC) is required for the induction of adaptive immune cells, especially cytotoxic T cells and helper T cells, to clear the virally infected cells. This perspective review article proposes different aspects to explain the varying symptoms of the individuals who have been exposed to SARS-CoV-2, which relates to the polymorphisms of these involved molecules.

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01

BACKGROUND

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors that affect individual immune response to SARS-CoV-2. We sought to evaluate this hypothesis by conducting a multicenter study using HLA sequencing.

METHODS

We analyzed the association between COVID-19 severity and HLAs in 435 individuals from Germany (n = 135), Spain (n = 133), Switzerland (n = 20) and the United States (n = 147), who had been enrolled from March 2020 to August 2020. This study included patients older than 18 years, diagnosed with COVID-19 and representing the full spectrum of the disease. Finally, we tested our results by meta-analysing data from prior genome-wide association studies (GWAS).

FINDINGS

We describe a potential association of HLA-C*04:01 with severe clinical course of COVID-19. Carriers of HLA-C*04:01 had twice the risk of intubation when infected with SARS-CoV-2 (risk ratio 1.5 [95% CI 1.1-2.1], odds ratio 3.5 [95% CI 1.9-6.6], adjusted p-value = 0.0074). These findings are based on data from four countries and corroborated by independent results from GWAS. Our findings are biologically plausible, as HLA-C*04:01 has fewer predicted bindings sites for relevant SARS-CoV-2 peptides compared to other HLA alleles.

INTERPRETATION

HLA-C*04:01 carrier state is associated with severe clinical course in SARS-CoV-2. Our findings suggest that HLA class I alleles have a relevant role in immune defense against SARS-CoV-2.

FUNDING

Funded by Roche Sequencing Solutions, Inc.

Epitope mimicry analysis of SARS-COV-2 surface proteins and human lung proteins

BACKGROUND

Autoimmune response after the infection of SARS-COV-2 is evident as more cases of Guillain Barre syndrome and Kawasaki disease are diagnosed. In this study, we aim to investigate a possible mechanism of autoimmune lung injury.

METHODS

We extracted the peptide sequences of surface proteins of the SARS-COV-2 from the NCBI data protein. We used Blastp to assess the homologous sequences between the human proteins in the UNIPROT database that are associated with respiratory distress. Then, we filtered the homologous sequences to those selectively expressed in the lung and homologous to surface viral proteins. We then assessed the epitope sequences for MHC-I and MHC-II using recommended settings and reference MHC in the IEDB database.

RESULTS

Homeobox protein 2.1 (NKX2-1) and ATP-binding cassette sub-family A member 3 (ABCA3) showed homologous sequence to both surface glycoproteins and envelope proteins. The HLA-DR and HLA-DQ had a similar binding pattern to ABCA3 as surface glycoproteins and envelope proteins, respectively. Other HLA molecules that had a similar binding pattern to SARS-COV-2 as human proteins were HLA-A and HLA-DP.

CONCLUSION

Our study indicates that there is a possible autoimmune mechanism underlying the acute respiratory distress syndrome in SARS-COV-2.

ER-stressed MSC displayed more effective immunomodulation in RA CD4+CXCR5+ICOS+ follicular helper-like T cells through higher PGE2 binding with EP2/EP4

Objectives: To analyze the further immunomodulatory effects of endoplasmic reticulum (ER)-stressed umbilical cord-derived mesenchymal stem cells MSCs (UC-MSCs) on rheumatoid arthritis (RA) CD4⁺CXCR5⁺ICOS⁺ T (follicular helper-like T, Tfh) cells.Methods: MSCs were isolated from umbilical cord and surface markers were identified by flow cytometry. CD4⁺ T cells were purified from RA patients' peripheral blood mononuclear cells (PBMCs) using immunomagnetic beads. Thapsigargin (Tg)-stimulated or unstimulated MSCs were co-cultured with RA CD4⁺ T cells. CD4⁺CXCR5⁺ICOS⁺ T cells were analyzed with fluorescence activating cell sorter (FACS) and major soluble factors secreted by MSCs were detected by qRT-PCR as well as ELISA. Receptors of prostanoid E2 (PGE2), known as EP1-4, on CD4⁺ T cells were tested with RT-PCR and FACS. Proportion of CD4⁺CXCR5⁺ICOS⁺ T cells was determined after EP2/EP4 antagonists and anti-IL-6R antibody was added into co-cultured system, respectively.Results: ER-stressed MSCs further down-regulated peripheral CD4⁺CXCR5⁺ICOS⁺ T cells compared with Tg-stimulated MSCs and CD4⁺ T co-cultured group. PGE2 and IL-6 increased obviously in the supernatants. EP2/EP4 could be detected on CD4⁺ T cells and frequencies of CD4⁺CXCR5⁺ICOS⁺ T cells were upregulated when EP2 and/or EP4 antagonists rather than anti-IL-6R antibody were added.Conclusions: ER-stressed MSCs exhibited better inhibition effect on RA CD4⁺CXCR5⁺ICOS⁺ T cells by releasing PGE2, indicating the immunosuppressive effect of MSCs could be enhanced by induction of ER stress.

Recombinant DNA vaccine of Hantavirus Gn and LAMP1 induced long-term immune protection in mice

BACKGROUND

Prophylaxis is widely adopted the best choice against Hemorrhagic fever with renal syndrome (HFRS) caused by Hantavirus. However, loss of memory immune response maintenance remains as major shortcoming in current HFRS vaccine. A recombinant DNA vaccine, pVAX-LAMP/Gn was previously proved efficient, requiring long-term evaluations.

METHODS & RESULTS

Immune responses of Balb/c mice were assessed by specific and neutralizing antibodies, interferon-γ ELISpot assay, and cytotoxic T-lymphocyte cytotoxicity assay. HTNV-challenge assay identified long-term protection. Safety was confirmed by histological and behavioral analysis. Epitope-spreading phenomenon was noted, revealing two sets of dominant T-cell epitopes cross-species.

CONCLUSION

pVAX-LAMP/Gn established memory responses within a long-term protection. Lysosome-targeted strategy showed promise on Gn-based DNA vaccine and further investigations are warranted in other immunogenic Hantaviral antigens.

Polymorphisms in HLA-DRB1 gene and the risk of tuberculosis: a meta-analysis of 31 studies

PURPOSE

The HLA-DRB1 gene polymorphisms have been implicated in susceptibility to tuberculosis (TB). However, a large number of studies have reported inconclusive results. This study was conducted to investigate the relationship of HLA-DRB1 gene polymorphisms and TB risk by a meta-analysis.

METHODS

A search was performed in Embase, PubMed, Wanfang Database, and China National Knowledge Internet (CNKI) up to Jul 30, 2014. Odds ratio (OR) and 95% confidence interval (95% CI) were used to assess the association. Statistical analyses were calculated by STATA 11.0 software.

RESULTS

All 31 articles involving 3,416 cases and 4,515 controls were identified. The pooled results indicated a significant association between HLA-DRB1*04 (OR 1.22, 95% CI 1.00-1.48, P = 0.048), *09 (OR 1.50, 95% CI 1.08-2.08, P = 0.016), *10 (OR 1.23, 95% CI 1.01-1.49, P = 0.035), *11 (OR 0.72, 95% CI 0.53-0.99, P = 0.044), *15 (OR 1.40, 95% CI 1.14-1.73, P = 0.001), and *16 (OR 1.33, 95% CI 1.08-1.63, P = 0.007) gene polymorphisms and TB risk. In addition, the results also show no significant association between HLA-DRB1*01 (P = 0.748), *03 (P = 0.947), *07 (P = 0.966), *08 (P = 0.440), *12 (P = 0.288), *13 (P = 0.241), and *14 (P = 0.551) gene polymorphisms and TB risk.

CONCLUSIONS

This study suggested that the HLA-DRB1*04, *09, *10, *15, and *16 gene polymorphisms may contribute to the risk of TB, especially in the East Asian. But the HLA-DRB1*11 gene polymorphism may be a protective factor for TB risk. Unfortunately, there is no significant association between the HLA-DRB1*01, *03, *07, *08, *12, *13, and *14 gene polymorphisms and TB risk.

Immunogenetic factors affecting susceptibility of humans and rodents to hantaviruses and the clinical course of hantaviral disease in humans

We reviewed the associations of immunity-related genes with susceptibility of humans and rodents to hantaviruses, and with severity of hantaviral diseases in humans. Several class I and class II HLA haplotypes were linked with severe or benign hantavirus infections, and these haplotypes varied among localities and hantaviruses. The polymorphism of other immunity-related genes including the C4A gene and a high-producing genotype of TNF gene associated with severe PUUV infection. Additional genes that may contribute to disease or to PUUV infection severity include non-carriage of the interleukin-1 receptor antagonist (IL-1RA) allele 2 and IL-1β (-511) allele 2, polymorphisms of plasminogen activator inhibitor (PAI-1) and platelet GP1a. In addition, immunogenetic studies have been conducted to identify mechanisms that could be linked with the persistence/clearance of hantaviruses in reservoirs. Persistence was associated during experimental infections with an upregulation of anti-inflammatory responses. Using natural rodent population samples, polymorphisms and/or expression levels of several genes have been analyzed. These genes were selected based on the literature of rodent or human/hantavirus interactions (some Mhc class II genes, Tnf promoter, and genes encoding the proteins TLR4, TLR7, Mx2 and β3 integrin). The comparison of genetic differentiation estimated between bank vole populations sampled over Europe, at neutral and candidate genes, has allowed to evidence signatures of selection for Tnf, Mx2 and the Drb Mhc class II genes. Altogether, these results corroborated the hypothesis of an evolution of tolerance strategies in rodents. We finally discuss the importance of these results from the medical and epidemiological perspectives.

Virus antibody survey in different European populations indicates risk association between coxsackievirus B1 and type 1 diabetes

Enteroviruses (EVs) have been connected to type 1 diabetes in various studies. The current study evaluates the association between specific EV subtypes and type 1 diabetes by measuring type-specific antibodies against the group B coxsackieviruses (CVBs), which have been linked to diabetes in previous surveys. Altogether, 249 children with newly diagnosed type 1 diabetes and 249 control children matched according to sampling time, sex, age, and country were recruited in Finland, Sweden, England, France, and Greece between 2001 and 2005 (mean age 9 years; 55% male). Antibodies against CVB1 were more frequent among diabetic children than among control children (odds ratio 1.7 [95% CI 1.0-2.9]), whereas other CVB types did not differ between the groups. CVB1-associated risk was not related to HLA genotype, age, or sex. Finnish children had a lower frequency of CVB antibodies than children in other countries. The results support previous studies that suggested an association between CVBs and type 1 diabetes, highlighting the possible role of CVB1 as a diabetogenic virus type.

No gender-related differences in the severity of nephropathia epidemica, Germany

BACKGROUND

The number of cases of hantavirus disease caused by Puumala virus is increasing enormously in Germany within the last years. Men are overrepresented in hantavirus disease and differences in course and symptoms in relation to gender were reported from several countries. This study was conducted to define possible gender-specific risk factors and aspects of severity in hantavirus infections occurring in Germany.

METHODS

Characteristics, clinical parameters and symptoms were recorded in a retrospective analysis of 108 patients with serologically confirmed hantavirus infection treated in our department. This cohort corresponds in regard to age, time of infection and gender ratio to the characteristics of the overall cases reported in Germany.

RESULTS

The frequency of characteristic symptoms of hantavirus disease did not differ between males and females. The median of nadir and peak levels of clinical parameters did not exhibit relevant differences that would point to a more severe course in males or females. The clinical course and duration of hospitalization were similar for both sexes. No relevant differences in renal and pulmonary findings were observed. Males with hantavirus disease exhibited more cardiac findings than females.To compare the unequal gender distribution of the rodent-borne Puumala hantavirus disease with the gender ratio of other infectious diseases, we analyzed the gender ratio for notifiable infections according to their mode of transmission. Our data revealed a general overrepresentation of men in infections carried by arthropods and rodents.

CONCLUSIONS

In contrast to reports from other countries, no crucial differences in the symptoms, course or severity of hantavirus disease between infected men and female were observed in our cohort. However behavioural differences may account for the fact that men are more often affected by certain infectious diseases than females.

HLA-A2 and B35 restricted hantaan virus nucleoprotein CD8+ T-cell epitope-specific immune response correlates with milder disease in hemorrhagic fever with renal syndrome

BACKGROUND

Hantaan virus (HTNV) infection in humans is a serious public health concern in Asia. A potent T cell activation peptide vaccine from HTNV structure protein represents a promising immunotherapy for disease control. However, the T cell epitopes of the HTNV restricted by the HLA alleles and the role of epitope-specific T cell response after HTNV infection remain largely unexplored.

METHODOLOGY/PRINCIPAL FINDINGS

Five well-conserved novel CD8(+) T-cell epitopes of the HTNV nucleoprotein restricted by the most popular HLA alleles in Chinese Han population were defined with interferon-γ enzyme-linked immunospot assay in 37 patients infected with HTNV during hospitalization. Two epitopes aa129-aa137 and aa131-aa139 restricted by HLA-A2 and B35, respectively, were selected to evaluate the epitope-specific CD8(+) T-cell response. HLA-peptide pentamer complex staining showed that the frequency of single epitope-specific CD8(+) T cell could be detected in patients (95% confidence interval for aa129-aa137: 0.080%-0.208%; for aa131-aa139: 0.030%-0.094%). The frequency of epitope-specific pentamer(+) CD8(+) T-cell response was much higher in mild/moderate patients than in severe/critical ones at the acute stage of the disease. Moreover, the frequency of epitope-specific CD8(+) T cells at acute stage was inversely associated with the peak level of serum creatinine and was positively associated with the nadir platelet counts during the hospitalization. The intracellular cytokine staining and the proliferation assay showed that the effective epitope-specific CD8(+) T cells were characterized with the production of interferon-γ, expression of CD69 and the strong capacity of proliferation.

CONCLUSION/SIGNIFICANCE

The novel HLA class I restricted HTNV nucleoprotein epitopes-specific CD8(+) T-cell responses would be closely related with the progression and the severity of the disease, which could provide the first step toward effective peptide vaccine development against HTNV infection in humans.