The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: July 25, 2023

Over three years’ pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and subvariants have emerged successively, outcompeted earlier become predominant. The sequential emergence reflects the evolutionary process mutation-selection-adaption severe acute respiratory syndrome 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in spike protein causes altered viral antigenicity, transmissibility, pathogenicity SARS-CoV-2. Early pandemic, D614G mutation conferred virus with advantages over previous increased it also laid a conservative background for subsequent substantial mutations. role genomic recombination evolution SARS-CoV-2 raised increasing concern occurrence recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, XBB.1.16 late phase pandemic. Co-circulation different co-infection immunocompromised patients accelerate recombinants. Surveillance variations, particularly recombination, is essential to identify ongoing changes genome antigenic epitopes thus leads development new vaccine strategies interventions.

Language: Английский

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Genomics and Bioinformatics in One Health: Transdisciplinary Approaches for Health Promotion and Disease Prevention

International Journal of Environmental Research and Public Health, Journal Year: 2024, Volume and Issue: 21(10), P. 1337 - 1337

Published: Oct. 9, 2024

The One Health concept underscores the interconnectedness of human, animal, and environmental health, necessitating an integrated, transdisciplinary approach to tackle contemporary health challenges. This perspective paper explores pivotal role genomics bioinformatics in advancing initiatives. By leveraging genomic technologies tools, researchers can decode complex biological data, enabling comprehensive insights into pathogen evolution, transmission dynamics, host-pathogen interactions across species environments (or ecosystems). These are crucial for predicting mitigating zoonotic disease outbreaks, understanding antimicrobial resistance patterns, developing targeted interventions promotion prevention. Furthermore, integrating data with epidemiological information enhances precision public responses. Here we discuss case studies demonstrating successful applications contexts, such as including integration, standardization, ethical considerations research. fostering collaboration among geneticists, bioinformaticians, epidemiologists, zoologists, scientists, harness full potential safeguard global health. necessity continued investment interdisciplinary education, research infrastructure, policy frameworks effectively employ these service a healthier planet.

Language: Английский

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

Deleted Journal, Journal Year: 2024, Volume and Issue: 6(15), P. 324 - 331

Published: Jan. 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

Language: Английский

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Stand Up to Stand Out: Natural Dietary Polyphenols Curcumin, Resveratrol, and Gossypol as Potential Therapeutic Candidates against Severe Acute Respiratory Syndrome Coronavirus 2 Infection

Nutrients, Journal Year: 2023, Volume and Issue: 15(18), P. 3885 - 3885

Published: Sept. 6, 2023

The COVID-19 pandemic has stimulated collaborative drug discovery efforts in academia and the industry with aim of developing therapies vaccines that target SARS-CoV-2. Several novel have been approved deployed last three years. However, their clinical application revealed limitations due to rapid emergence viral variants. Therefore, development next-generation SARS-CoV-2 therapeutic agents a high potency safety profile remains priority for global health. Increasing awareness “back nature” approach improving human health prompted renewed interest natural products, especially dietary polyphenols, as an additional strategy treat patients, owing its good profile, exceptional nutritional value, health-promoting benefits (including potential antiviral properties), affordability, availability. Herein, we describe biological properties pleiotropic molecular mechanisms polyphenols curcumin, resveratrol, gossypol inhibitors against variants observed vitro vivo studies. Based on advantages disadvantages obtain maximal benefits, several strategies such nanotechnology (e.g., curcumin-incorporated nanofibrous membranes antibacterial-antiviral ability), lead optimization methylated analog curcumin), combination specific plant extracts micronutrients), broad-spectrum activities broadly inhibits coronaviruses) also emphasized positive factors facilitation anti-SARS-CoV-2 support effective long-term management control.

Language: Английский

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Longitudinal Analysis of Humoral and Cellular Immune Response up to 6 Months after SARS-CoV-2 BA.5/BF.7/XBB Breakthrough Infection and BA.5/BF.7-XBB Reinfection

Vaccines, Journal Year: 2024, Volume and Issue: 12(5), P. 464 - 464

Published: April 26, 2024

The rapid mutation of SARS-CoV-2 has led to multiple rounds large-scale breakthrough infection and reinfection worldwide. However, the dynamic changes humoral cellular immunity responses several subvariants after remain unclear. In our study, a 6-month longitudinal immune response evaluation was conducted on 118 sera 50 PBMC samples from 49 healthy individuals who experienced BA.5/BF.7/XBB or BA.5/BF.7-XBB reinfection. By studying antibody response, memory B cell, IFN-γ secreting CD4+/CD8+ T cell variants, we observed that each component exhibited distinct kinetics. Either induces relatively high level binding neutralizing titers against Omicron at an early time point, which rapidly decreases over time. Most 6 months post-breakthrough completely lost their activities BQ.1.1, CH.1.1, BA.2.86, JN.1 XBB subvariants. Individuals with exhibit imprinting shifting recall pre-existing BA.5/BF.7 neutralization antibodies. BA.5 group, frequency XBB.1.16-RBD specific cells, resting intermediate cells gradually increased On other hand, induced by WT/BA.5/XBB.1.16 spike trimer remains stable Overall, research indicates have declining levels but can provide some degree protection future exposure new antigens.

Language: Английский

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Advancing Real-time Pandemic Forecasting Using Large Language Models: A COVID-19 Case Study

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: May 3, 2024

Forecasting the short-term spread of an ongoing disease outbreak is a formidable challenge due to complexity contributing factors, some which can be characterized through interlinked, multi-modality variables such as epidemiological time series data, viral biology, population demographics, and intersection public policy human behavior. Existing forecasting model frameworks struggle with multifaceted nature relevant data robust results translation, hinders their performances provision actionable insights for health decision-makers. Our work introduces PandemicLLM, novel framework multi-modal Large Language Models (LLMs) that reformulates real-time text reasoning problem, ability incorporate real-time, complex, non-numerical information -- textual policies genomic surveillance previously unattainable in traditional models. This approach, unique AI-human cooperative prompt design representation learning, encodes LLMs. By redefining process ordinal classification task, PandemicLLM yields more trustworthy predictions, facilitating decision-making. The applied COVID-19 pandemic, trained utilize policies, surveillance, spatial, subsequently tested across all 50 states U.S. duration 16 weeks. Empirically, shown high-performing pandemic effectively captures impact emerging variants provide timely accurate predictions. proposed opens avenues incorporating various pandemic-related heterogeneous formats exhibits performance benefits over existing study illuminates potential adapting LLMs learning enhance forecasting, illustrating how AI innovations strengthen responses crisis management future.

Language: Английский

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Real-world effectiveness of sotrovimab in preventing hospitalization and mortality in high-risk patients with COVID-19 in the United States: A cohort study from the Mayo Clinic electronic health records

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(7), P. e0304822 - e0304822

Published: July 16, 2024

To describe outcomes of high-risk patients with coronavirus disease 2019 (COVID-19) treated sotrovimab, other monoclonal antibodies (mAbs), or antivirals, and who did not receive early COVID-19 treatment. We also evaluate the comparative effectiveness sotrovimab versus no treatment in preventing severe clinical outcomes.

Language: Английский

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COVID-19 Outcomes Among Hematopoietic Cell Transplant and Chimeric Antigen Receptor T-cell Recipients in the Era of SARS-CoV-2 Omicron Variants and COVID-19 Therapeutics

Transplantation and Cellular Therapy, Journal Year: 2024, Volume and Issue: 30(11), P. 1108.e1 - 1108.e11

Published: Aug. 23, 2024

Language: Английский

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Effectiveness of a bivalent mRNA vaccine dose against symptomatic SARS-CoV-2 infection among U.S. Healthcare personnel, September 2022–May 2023

Vaccine, Journal Year: 2023, Volume and Issue: 42(10), P. 2543 - 2552

Published: Nov. 14, 2023

Bivalent mRNA vaccines were recommended since September 2022. However, coverage with a recent vaccine dose has been limited, and there are few robust estimates of bivalent VE against symptomatic SARS-CoV-2 infection (COVID-19). We estimated COVID-19 among eligible U.S. healthcare personnel who had previously received monovalent doses.

Language: Английский

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Molecular mechanistic exploration of conformational shifts induced by class IV anti-RBD antibody IY2A

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 141417 - 141417

Published: Feb. 1, 2025

Language: Английский

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