In silico evaluation of ten monoclonal antibodies neutralization power of SARS-CoV-2 variants EG.5 and BA.2.86 DOI Open Access
Dana Ashoor, M. Dahmani Fathallah

Опубликована: Дек. 14, 2023

The current globally dominant SARS-CoV-2 variants are showing immune escape and reduced susceptibility to antiviral drugs. Therefore, agencies responsible for drug evaluation regula-tion such as the FDA EMA revising their emergency authorization use of several COVID-19 neutralizing antibodies. These NAbs proved be unlikely effective against new espe-cially Omicron descendants pharmaceutical companies pursuing development more potent To address issue using in silico prediction rapid assessment anti-SARS-CoV-2 MAbs neutralization power, we used a computational method developed previously, evaluate 10 antibodies propensity neutralize Omicron’s subvariants Eris (EG.5) Pirola (BA.2.86) based on comparative binding affinity previous experimental clinical observations. Nine these were once granted authorization, one is currently under investigation. rapid, cost-effective provided reliable predictions consistent with published data. Furthermore, our data showed potential therapeutic combi-nation that could treatment countermeasure (BA.2.86).

Язык: Английский

Genomic Surveillance for SARS-CoV-2 Variants: Dominance of XBB Replacement — China, January–June 2023 DOI Creative Commons

Yenan Feng,

Qiudong Su,

Lili Li

и другие.

Deleted Journal, Год журнала: 2024, Номер 6(15), С. 324 - 331

Опубликована: Янв. 1, 2024

Introduction In the first half of 2023, a global shift was observed towards predominance XBB variants. China faced significant epidemic between late 2022 and early 2023 due to Omicron subvariants BA.5.2 BF.7. This study aims depict evolving variant distribution among provincial-level administrative divisions (PLADs) in explore factors driving replacement. Methods Sequences from local imported coronavirus disease 2019 (COVID-19) cases recorded January 1 June 30, were included. The analyzed changing viral variants assessed how prior dominance specific variants, subvariants, influenced prevalence replacement variant. Results A total 56,486 sequences obtained cases, 8,669 cases. Starting April, there with varying PLADs. PLADs previously high BF.7, rise delayed. positive correlation found proportions March April. pattern differed within same PLAD. No differences noted rates subvariants. Conclusions timing various correlating closely

Язык: Английский

Процитировано

5
The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran DOI Creative Commons

Mehdi Shabani,

Ahmad Nejati, Jila Yavarian

и другие.

Frontiers in Microbiology, Год журнала: 2025, Номер 15

Опубликована: Янв. 29, 2025

Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant public health issue worldwide in recent years. The most recently circulating variant of SARS-CoV-2, Omicron, and its rapid evolution into various sub-lineages have raised concerns regarding the effects immunity on virus epitopes, human population. present study evaluated compared these important variations among different Omicron Iran. Methodology From October 2023 to August 2024, high coverage whole genome sequences 49 SARS-CoV-2 strains were subjected phylogenetic analysis evaluation B cell, CD4 + , CD8 T cell epitopes Iran National Influenza Centre. Results tree exhibited eight Nextstrain clades (21L, 22F, 23B, 23H, 23D, 24A, 24B, 24C) 48 studied strains, one recombinant strain (XDK.1). all revealed 31, 65, 78%, conservation, respectively. low conservation rate underscored escaping from neutralizing humoral immunity. considerably preserved across major sub-lineages. Conservation levels varied based epitope class (higher for vs. ), protein non-spike spike), 21L, 24B 24A 24C). Conclusion Herein, increased is probably attributable shorter length peptides associated with epitopes. T-cell proteins this highlighted importance cell-mediated suggested that might be more attractive targets future vaccines.

Язык: Английский

Процитировано

0
Identifying and Validating Prognostic Hyper-Inflammatory and Hypo-Inflammatory COVID-19 Clinical Phenotypes Using Machine Learning Methods DOI Creative Commons

Xiaojing Ji,

Yiran Guo,

Lujia Tang

и другие.

Journal of Inflammation Research, Год журнала: 2025, Номер Volume 18, С. 3009 - 3024

Опубликована: Фев. 1, 2025

COVID-19 exhibits complex pathophysiological manifestations, characterized by significant clinical and biological heterogeneity. Identifying phenotypes may enhance our understanding of the disease's diverse trajectories, benefiting practice trials. This study included adult patients with from Xinhua Hospital, affiliated Shanghai Jiao Tong University School Medicine, between December 15, 2022, February 2023. The k-prototypes clustering method was employed using 50 variables to identify phenotypes. Machine learning algorithms were then applied select key classifier for phenotype recognition. A total 1376 met inclusion criteria. K-prototypes revealed two distinct subphenotypes: Hypo-inflammatory subphenotype (824 [59.9%]) Hyper-inflammatory (552 [40.1%]). Patients in younger, predominantly female, low mortality shorter hospital stays. In contrast, older, male, exhibiting a hyperinflammatory state higher rates organ dysfunction. AdaBoost model performed best prediction (Accuracy: 0.975, Precision: 0.968, Recall: 0.976, F1: 0.972, AUROC: 0.975). "CRP", "IL-2R", "D-dimer", "ST2", "BUN", "NT-proBNP", "neutrophil percentage", "lymphocyte count" identified as top-ranked model. analysis based on symptoms comorbidities. These can be accurately recognized machine models, being optimal predicting in-hospital mortality. play role subphenotypes. Use subphenotypes risk stratification practice. closely monitored, preventive measures such early admission intensive care unit or prophylactic anticoagulation taken.

Язык: Английский

Процитировано

0
Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron’s several subvariants and the current rise of KP.3.1.1 and XEC DOI
Chiranjib Chakraborty, Manojit Bhattacharya, Ali S. Abdelhameed

и другие.

Virology, Год журнала: 2025, Номер unknown, С. 110508 - 110508

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Engineered Multivalent Nanobodies Efficiently Neutralize SARS-CoV-2 Omicron Subvariants BA.1, BA.4/5, XBB.1 and BQ.1.1 DOI Creative Commons
Jiali Wang,

Bingjie Shi,

Hanyi Chen

и другие.

Vaccines, Год журнала: 2024, Номер 12(4), С. 417 - 417

Опубликована: Апрель 15, 2024

Most available neutralizing antibodies are ineffective against highly mutated SARS-CoV-2 Omicron subvariants. Therefore, it is crucial to develop potent and broad-spectrum alternatives effectively manage Here, we constructed a high-diversity nanobody phage display library identified nine nanobodies specific the receptor-binding domain (RBD). Five of them exhibited cross-neutralization activity wild-type (WT) strain subvariants BA.1 BA.4/5, one demonstrated marked efficacy even BQ.1.1 XBB.1. To enhance therapeutic potential, engineered panel multivalent with increased potency breadth. The most nanobody, B13-B13-B13, cross-neutralized all tested pseudoviruses, geometric mean 50% inhibitory concentration (GM IC50) value 20.83 ng/mL. An analysis mechanism underlying enhancement neutralization breadth by representative that strategic engineering approach combining two or three into molecule could improve affinity between single spike, tolerance toward escape mutations such as R346T N460K. Our may be promising drug candidates for treating preventing infection future variants.

Язык: Английский

Процитировано

2
Prompt-engineering enabled LLM or MLLM and instigative bioinformatics pave the way to identify and characterize the significant SARS-CoV-2 antibody escape mutations DOI
Chiranjib Chakraborty, Manojit Bhattacharya, Soumen Pal

и другие.

International Journal of Biological Macromolecules, Год журнала: 2024, Номер unknown, С. 138547 - 138547

Опубликована: Дек. 1, 2024

Язык: Английский

Процитировано

2
Age-dependent decrease of circulating T follicular helper cells correlates with disease severity in elderly patients with COVID-19 DOI
Yihan Wang, Qiu Wang, Furong He

и другие.

Clinical Immunology, Год журнала: 2024, Номер 266, С. 110329 - 110329

Опубликована: Сен. 1, 2024

Язык: Английский

Процитировано

0
In Silico Evaluation of Ten Monoclonal Antibodies Neutralization Power of SARS-CoV-2 Variants EG.5, BA.2.86 and JN.1 DOI Open Access
Dana Ashoor

Опубликована: Авг. 19, 2024

The current globally dominant SARS-CoV-2 variants are showing immune escape and reduced susceptibility to antiviral drugs. Therefore, agencies responsible for drug evaluation regulation such as the FDA EMA revising their emergency authorization use of several COVID-19 neutralizing antibodies. These MAbs proved be unlikely effective against new especially Omicron descendants pharmaceutical companies pursuing development more potent To address this issue, we used In Silico method previously developed assess 10 anti-SARS-CoV-2 antibodies propensity neutralize Omicron’s subvariants EG.5, BA.2.86 JN.1, based on comparative binding affinity 3D generated models previous experimental clinical observations. Nine these were once granted authorization, one is currently under investigation. results showed that antibody a marked increase energy EG.5 compared two significant with Pirola (BA.2.86) JN.1. This data indicates variant escapes neutralization most available therapeutic NAbs. Furthermore, potential combination could treatment countermeasure or novel variants.

Язык: Английский

Процитировано

0
In silico evaluation of ten monoclonal antibodies neutralization power of SARS-CoV-2 variants EG.5, BA.2.86 and JN.1 (Preprint) DOI
Dana Ashoor

Опубликована: Дек. 3, 2024

BACKGROUND The current globally dominant SARS-CoV-2 variants are showing immune escape and reduced susceptibility to antiviral drugs. Therefore, agencies responsible for drug evaluation regulation such as the FDA EMA revising their emergency authorization use of several COVID-19 neutralizing antibodies. These NAbs proved be unlikely effective against new especially Omicron descendants pharmaceutical companies pursuing development more potent OBJECTIVE aim this study is evaluate antibodies neutralization power assess effectiveness available on newly emerged Eris, Pirola JN.1. METHODS Previously developed In Silico method w 10 anti-SARS-CoV-2 propensity neutralize Omicron’s subvariants EG.5, BA.2.86 JN.1, based comparative binding affinity 3D generated models previous experimental clinical observations. Nine these were once granted authorization, one currently under investigation. RESULTS Our results showed that EG.5 there was either a decrease or no change energy with 9 significant increase antibody. For (BA.2.86) observed two This data indicates variant escapes most therapeutic NAbs. However, an in may considered use. silico predictions usefulness anti consistent published data. CONCLUSIONS Computational potential existing SARS-Cov-2 very useful defining combination could treatment countermeasure Eris (EG.5), JN.1 novel variants.

Язык: Английский

Процитировано

0
In silico evaluation of ten monoclonal antibodies neutralization power of SARS-CoV-2 variants EG.5 and BA.2.86 DOI Open Access
Dana Ashoor, M. Dahmani Fathallah

Опубликована: Дек. 14, 2023

The current globally dominant SARS-CoV-2 variants are showing immune escape and reduced susceptibility to antiviral drugs. Therefore, agencies responsible for drug evaluation regula-tion such as the FDA EMA revising their emergency authorization use of several COVID-19 neutralizing antibodies. These NAbs proved be unlikely effective against new espe-cially Omicron descendants pharmaceutical companies pursuing development more potent To address issue using in silico prediction rapid assessment anti-SARS-CoV-2 MAbs neutralization power, we used a computational method developed previously, evaluate 10 antibodies propensity neutralize Omicron’s subvariants Eris (EG.5) Pirola (BA.2.86) based on comparative binding affinity previous experimental clinical observations. Nine these were once granted authorization, one is currently under investigation. rapid, cost-effective provided reliable predictions consistent with published data. Furthermore, our data showed potential therapeutic combi-nation that could treatment countermeasure (BA.2.86).

Язык: Английский

Процитировано

1