scholarly journals Corona Viruses and Human Leukocyte Antigen (HLA) alleles

2021 ◽  
Vol 11 (1-s) ◽  
pp. 83-85
Author(s):  
Nihad Elsadig Babiker ◽  
Alsadig Gassoum ◽  
Sawsan A. Hamed ◽  
Sara Elsadig Babiker ◽  
Imad Fadl-Elmula

Major histocompatibility complex (MHC) is consisted of cluster of genes known as human leukocyte antigen HLA, these genes are committed to process and present antigens to T lymphocyte. Corona viruses, belonging to a genus of the corona viridae family, are enveloped viruses containing single stranded RNA 27-32 kb. This study was conducted to highlight some observations that may help other researcher for rapid research advances; the new corona virus genome sequence was obtained from Virus pathogen database, the spike protein (surface glycoprotein)  was aligned with   SPIKE_CVHSA Spike glycoprotein OS=Human SARS coronavirus OX=694009 GN=S PE=1 SV=1 which was retrieved from Uniprot data base Distribution of HLA alleles was obtained from allele frequencies database, IEDB server was used for MHC 1 prediction. The distribution of HLA-A alleles among population revealed that, the most common wasHLA-A*11:01. The affinity prediction of HLA-A*03:01(AAAYFVGYLK) and HLA-A*11:01(AAYFVGYLK) alleles to the spike peptide were positive.  The two positive predicted peptides for both 2 alleles showed mutation of K245Q, This mutation may affect the binding affinity of the protein peptides to HLA-A alleles. Keywords: HLA. MHC, alleles, Corona viruses, SARS, APS

2008 ◽  
Vol 68 (1) ◽  
pp. 107-109 ◽  
Author(s):  
K A Guthrie ◽  
N R Tishkevich ◽  
J L Nelson

Objectives:Some patients with rheumatoid arthritis (RA) lack RA-associated human leukocyte antigen (HLA) alleles. Prior studies investigated non-inherited maternal HLA alleles (NIMA) in RA risk with conflicting results.Methods:We examined NIMA in a large cohort of families from the North American Rheumatoid Arthritis Consortium (NARAC).Results:Among 620 patients with 1 or both parents having a HLA genotype, patients with RA informative for analysis included 176 without HLA-DRB1*04 and 86 without the HLA shared epitope (SE). The frequency of NIMA encoding HLA-DR4 or the SE was compared to the non-inherited paternal allele (NIPA). DR4-encoding NIMA vs NIPA revealed no significant difference (27% vs 20%). However, parity is known to modulate RA risk and analyses stratified by sex and age of onset showed significant variation among women. Interestingly, among women with onset <45 years DR4-encoding NIMA was increased compared to NIPA; among women ⩾45 years at onset the reverse was observed (31% vs 16% compared to 10% vs 60%, p = 0.008). DR4 encoding NIMA vs NIPA did not differ in men. The SE did not differ in men or women.Conclusions:Risk of RA was associated with HLA-DR4 encoding NIMA in younger-onset women but not in older-onset women or men. These observations could help explain conflicting prior results of NIMA in RA.


2019 ◽  
Vol 72 (1-2) ◽  
pp. 119-129 ◽  
Author(s):  
Kirsten Geneugelijk ◽  
Eric Spierings

AbstractHuman leukocyte antigen (HLA) mismatches between donors and recipients may lead to alloreactivity after solid organ transplantation. Over the last few decades, our knowledge of the complexity of the HLA system has dramatically increased, as numerous new HLA alleles have been identified. As a result, the likelihood of alloreactive responses towards HLA mismatches after solid organ transplantation cannot easily be assessed. Algorithms are promising solutions to estimate the risk for alloreactivity after solid organ transplantation. In this review, we show that the recently developed PIRCHE-II (Predicted Indirectly ReCognizable HLA Epitopes) algorithm can be used to minimize alloreactivity towards HLA mismatches. Together with the use of other algorithms and simulation approaches, the PIRCHE-II algorithm aims for a better estimated alloreactive risk for individual patients and eventually an improved graft survival after solid organ transplantation.


2020 ◽  
Vol 245 (9) ◽  
pp. 815-822
Author(s):  
Kwesi Z Tandoh ◽  
Kwadwo A Kusi ◽  
Timothy N Archampong ◽  
Isaac Boamah ◽  
Osbourne Quaye

Chronic hepatitis B infection is an important medical problem in sub-Saharan Africa. With increasing concerns of dwindling access to needed care, increasing cost of treatment, and rising prevalence of dire outcomes like liver cirrhosis and hepatocellular cancer, the need to determine the genetic associations underpinning hepatitis B virus persistence or clearance in a population comes to the fore. Genetic association studies have suggested a variation in human leukocyte antigen alleles associated with hepatitis B virus outcome along geo-ethnic lines. We investigated the association of human leukocyte antigen alleles to hepatitis B virus outcome against this backdrop. We used targeted next generation sequencing to type the human leukocyte antigen class I and II alleles of 173 study participants. These comprised of 92 cases with chronic hepatitis B infection and 81 healthy controls with serological evidence of naturally cleared hepatitis B virus infection. We have identified human leukocyte antigen alleles associated with hepatitis B virus clearance and persistence for the first time in a Ghanaian population. The class 1 allele C*16:01 (odds ratio (OR) = 3.4, confidence interval (CI) = 1.6–7.0, P-value = 0.01) was associated with hepatitis B virus persistence. Four class I alleles and one class II allele: A*34:02 (OR = 0.1, CI = 0.04–0.2, P-value = 3.4e-05), A*74:01 (OR = 0.3, CI = 0.2–0.7, P-value = 0.0135), B*13:02 (OR = 0.04, CI = 0.01–0.2, P-value = 0.000172), C*08:04 (OR = 0.06, CI = 0.01–0.2, P-value = 7.83e-05), and DRB1*08:04 (OR = 0.2, CI = 0.03–0.27, P-value = 0.000252) were associated with hepatitis B virus clearance. Our data show that previously reported human leukocyte antigen alleles associations to hepatitis B virus outcome are not found in this Ghanaian study. This study has therefore identified human leukocyte antigen types that are associated with either hepatitis B virus persistence or clearance and highlights the importance of geo-ethnic pivoted studies in determining the genetic associations to acute hepatitis B virus infection outcome. Impact statement Genetic association studies can determine the effect size of gene loci on disease outcomes. In the arena of HBV infections, HLA alleles that associate with HBV outcomes can be used in clinical management decisions. This potential translational utility can shape the future management of HBV infections by identifying at-risk individuals and tailoring medical interventions accordingly. This precision medicine motif is currently only a nascent idea. However, it has stakes that may well override the current “wait and see” approach of clinical management of HBV infections. Here, we have identified HLA alleles associated with HBV outcome in a Ghanaian cohort. Our findings support the motif that HLA alleles associate with HBV outcome along geo-ethnic lines. This buttresses the need for further population pivoted studies. In the long term, our findings add to efforts towards the development of an HLA molecular-based algorithm for predicting HBV infection outcomes.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 3491-3491
Author(s):  
Basem M William ◽  
Tao Wang ◽  
Michael D Haagenson ◽  
Marcos J de Lima ◽  
Marcelo Anibal Fernandez-Vina ◽  
...  

Abstract Even in the modern era of targeted therapies, allo-HCT remains a strategy that offers a chance of extended survival in B-NHL who relapsed after, or are deemed ineligible for, autologous transplantation (auto-HCT). Moreover, it was shown that efficacy of auto-HCT in extending survival in patients with diffuse large B-cell lymphoma is limited in the post-rituximab era. The use of allo-HCT for salvage of relapsed/refractory B-NHL is likely to increase with the wide adoption of reduced intensity conditioning (RIC) since transplant-related mortality (TRM) is lower while preserving the benefit of graft vs lymphoma (GVL) effect. Further understanding of the factors likely to predict a more robust GVL response, and potentially better clinical outcomes, would be very useful in selecting patients with B-NHL who are likely to benefit from allo-HCT. Multiple prior studies have shown that the presence of certain human leukocyte antigen (HLA) alleles may be instrumental in modulating the outcomes of B-NHL after immunochemotherapy and/or allo-HCT. We hypothesized that certain HLA alleles may have superior ability to present antigens to cytotoxic T-cells or possibly modulate natural killer (NK) cell activity. We undertook a retrospective analysis of CIBMTR data to evaluate whether the presence of HLA-A2, HLA-C1C1, HLA-DRB1*01:01 or HLA-DRB1*13 alleles and HLA-A1+, HLA-A2- and HLA-B44- haplotypes were associated with outcomes of patients with relapsed/refractory B-NHL after transplantation from HLA-8/8 matched sibling (MRD) or unrelated (MUD) donors. The primary outcome was time to progression. Secondary outcomes included progression-free (PFS) and overall survival (OS), TRM, and incidence and severity of acute and chronic graft versus host disease (GVHD). Multivariate analyses were performed using Cox proportional hazards models adjusting for multiple disease and transplant related characteristics. HLA-A*02 was tested individually; HLA-DRB1*0101 and HLA-DRB1*13 were tested in 4 combinations; HLA-A1+/A2-, B44- vs. A2+ vs. neither. Because of multiple comparisons, p<0.01 is considered significant. The final analysis population was restricted to 1314 patients who received the first allo-HCT during the years of 1995-2012 for indolent (N=506), aggressive (N=514), and mantle (N=294) B-NHLs from MRD (N=708) or MUD (N=606) utilizing myeloablative; MA (N=636), RIC (N=434), non-myeloablative; NMA (N=196) or other (n=48) conditioning. The different HLA allele analysis groups were well-balanced for all disease, patient, transplant and donor characteristics. In multi-variate analysis, we have observed no significant association between any of the HLA alleles or combinations we tested with any of the primary or the secondary end-points. A power calculation suggested very large numbers would be needed to reach statistical significant based on the data analyzed so far. The marked heterogeneity of different lymphoma subtypes, conditioning regimens, donor choices, GVHD prophylaxis, supportive regimens or other center-related characteristics likely limited the ability to detect effects of differences in individual recipient HLA alleles. In conclusion, this study represents the largest reported series of allo-HCT outcomes of B-cell NHL patients based on HLA type. Further study of other variables will be required to delineate the immunologic impact of donor-host interactions on outcomes of allo-HCT for B-cell NHL. Disclosures No relevant conflicts of interest to declare.


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