The role of <scp>HLA</scp> genetic variants in <scp>COVID</scp>‐19 susceptibility, severity, and mortality: A global review

Hoseinnezhad, Taraneh; Soltani, Nasrin; Ziarati, Sarina; Behboudi, Emad; Mousavi, Mohammad Javad

doi:10.1002/jcla.25005

Cited by 8 publications

(4 citation statements)

References 63 publications

(240 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“… Tables 6 and 7 heavily referenced Table 1 from Hoeseinnezhat et al. ( 65 ). CI, confidence interval.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population

Kim,

Elnaggar,

Varnado

et al. 2024

Front. Immunol.

View full text Add to dashboard Cite

Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8+ epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), and nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] in analyzed MHC class I alleles revealed that SARS-CoV-2 CD8+ epitope conservation was estimated at 87.6%–96.5% in spike (S), 92.5%–99.6% in membrane (M), and 94.6%–99% in nucleocapsid (N). As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1-XBB.1.5 S epitopes experienced decreased predicted binding, as compared with ~3% and ~15% in the earlier strains Delta AY.100–AY.44 and Omicron BA.1–BA.5, respectively. Additionally, we identified several novel candidate HLA alleles that may be more susceptible to severe disease, notably HLA-A*32:01, HLA-A*26:01, and HLA-B*53:01, and relatively protected from disease, such as HLA-A*31:01, HLA-B*40:01, HLA-B*44:03, and HLA-B*57:01. Our findings support the hypothesis that viral genetic variation affecting CD8 T-cell epitope immunogenicity contributes to determining the clinical severity of acute COVID-19. Achieving long-term COVID-19 immunity will require an understanding of the relationship between T cells, SARS-CoV-2 variants, and host MHC class I genetics. This project is one of the first to explore the SARS-CoV-2 CD8+ epitope diversity that putatively impacts much of the United States population.

show abstract

“… Tables 6 and 7 heavily referenced Table 1 from Hoeseinnezhat et al. ( 65 ). CI, confidence interval.…”

Section: Discussionmentioning

confidence: 99%

“…Global summary of HLA Class I allele associated with low risk of or protection from COVID-19 infection.Tables6 and 7heavily referenced Table1from Hoeseinnezhat et al(65). CI, confidence interval.…”

mentioning

confidence: 99%

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population

Kim,

Elnaggar,

Varnado

et al. 2024

Front. Immunol.

View full text Add to dashboard Cite

show abstract

“…The COVID-19 pandemic is one of the major pandemics throughout documented human history, with various variants emerging and affecting different regions [35]. These variants, such as the Omicron variant, have led to changes in the frequency and severity of common symptoms like fever, cough, sore throat, and fatigue [36].…”

Section: Introductionmentioning

confidence: 99%

“…The COVID-19 pandemic is one of the major pandemics throughout documented human history, with various variants emerging and affecting different regions [35].…”

Section: Introductionmentioning

confidence: 99%

Denoising Longitudinal Social Media for Pandemic Monitoring

Lin,

Garay,

Hua

et al. 2024

Preprint

View full text Add to dashboard Cite

ObjectiveCurrent studies leveraging social media data for disease monitoring face challenges like noisy colloquial language and insufficient tracking of user disease progression in longitudinal data settings. This study aims to develop a pipeline for collecting, cleaning, and analyzing large-scale longitudinal social media data for disease monitoring, with a focus on COVID-19 pandemic.Materials and MethodsThis pipeline initiates by screening COVID-19 cases from tweets spanning February 1, 2020, to April 30, 2022. Longitudinal data is collected for each patient, two months before and three months after self-reporting. Symptoms are extracted using Name Entity Recognition (NER), followed by denoising with a combination of Graph Convolutional Network (GCN) and Bidirectional Encoder Representations from Transformers (BERT) model to retain only User Symptom Mentions (USM). Subsequently, symptoms are mapped to standardized medical concepts using the Unified Medical Language System (UMLS). Finally, this study conducts symptom pattern analysis and visualization to illustrate temporal changes in symptom prevalence and co-occurrence.ResultsThis study identified 191,096 self-reported COVID-19-positive cases from COVID-19-related tweets and retrospectively collected 811,398,280 historical tweets, of which 2,120,964 contained symptoms information. After denoising, 39% (832,287) of symptom-sharing tweets reflected user-related mentions. The trained USM model achieved an F1 score of 0.926. Further analysis revealed a higher prevalence of upper respiratory tract symptoms during the Omicron period compared to the Delta and wild-type periods. Additionally, there was a pronounced co-occurrence of lower respiratory tract and nervous system symptoms in the wild-type strain and Delta variant.ConclusionThis study established a robust framework for pandemic monitoring via social media, integrating denoising of user-related symptom mentions and longitudinal data. The findings underscore the importance of denoising procedures in revealing accurate prevalence trends, thereby minimizing biases in symptom analysis.

show abstract

HLA‐B*15 Is Associated With SARS‐CoV‐2 Infection in a Brazilian Population

Facco,

Addas‐Carvalho,

Duarte

et al. 2024

Journal of Medical Virology

View full text Add to dashboard Cite

Studies have suggested an association between polymorphisms in class I genes of the major histocompatibility complex, specifically the human leukocyte antigen (HLA), and susceptibility to SARS‐CoV‐2. To explore this, 135 individuals with positive serological tests for SARS‐CoV‐2 were recruited. All the samples were collected before the advent of vaccines, avoiding immunization effects. Participants were divided into high and low neutralizing antibody titer groups, and polymorphisms in HLA‐A, HLA‐B, and HLA‐DRB1 genes were examined using PCR‐SSO. Allele prevalence in the study population was compared to the National Bone Marrow Volunteer Donors Register (REDOME) in São Paulo and between the high and low titer groups within the study population. Results indicated that the HLA‐B*15 polymorphism was more prevalent in the COVID‐19 positive group compared to the control population (COVID‐19 = 0.1370; Control = 0.0875; p = 0.0067). The HLA‐B*18 polymorphism was less prevalent in the COVID‐19 group (COVID‐19 = 0.0185; Control = 0.0534; p = 0.0064). Additionally, the HLA‐A*30 polymorphism was more prevalent in the high titer group within the (high = 0.10937; low = 0.02816; p = 0.0125). Other polymorphisms showed no significant differences. These findings align with international studies, suggesting these genes plays a role in COVID‐19 pathophysiology, however, further research is required to fully understand their impact.

show abstract

The role of HLA genetic variants in COVID‐19 susceptibility, severity, and mortality: A global review

Cited by 8 publications

References 63 publications

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population

Denoising Longitudinal Social Media for Pandemic Monitoring

HLA‐B*15 Is Associated With SARS‐CoV‐2 Infection in a Brazilian Population

Contact Info

Product

Resources

About