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Article
Virology
Divya Sharma et al.
Summary: This study assessed the impact of SARS-CoV-2 Omicron sublineages BA.4 and BA.5 on the sensitivity of RT-qPCR assays used for COVID-19 diagnosis. In silico analysis showed mismatches between primers/probes and the Omicron VoC viral genome, potentially leading to false negative results for certain assays.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Wenkai Han et al.
Summary: This study introduces a machine learning-guided method to predict viral fitness landscape and antigenic evolution. Through analyzing existing SARS-CoV-2 variants, the method accurately infers variant order and predicts potential antigenic changes. The predictions were validated through in vitro experiments. This research is significant for vaccine development and preparedness against future SARS-CoV-2 variants.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yunlong Cao et al.
Summary: The Omicron variant of SARS-CoV-2 contains 15 mutations in the receptor-binding domain, leading to evasion of over 85% of tested neutralizing antibodies. Different epitope groups of neutralizing antibodies are affected to varying degrees by single mutations of Omicron. Antibodies targeting the conserved region of sarbecovirus remain most effective against Omicron.
Article
Biochemistry & Molecular Biology
Divya Sharma et al.
Summary: Antibodies against SARS-CoV-2 isolated from vaccinated and convalescent individuals showed potential binding affinity, offering opportunities for designing more effective antibodies against current and emerging variants. A regression model was developed to predict antibody binding affinity using structural features, with a high correlation coefficient of 0.93. The study also identified mutations at the spike protein-antibody interface that may affect immune escape and enhance affinity in current or future variants.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Katherine G. Nabel et al.
Summary: This study evaluates the impact of SARS-CoV-2 variants on neutralizing antibody activity and reveals that simultaneous antibody escape mutations make the virus more resistant to neutralization. Additionally, the study finds that the virus can acquire glycan to escape neutralization.
Article
Virology
Huimin Guo et al.
Summary: The Lambda variant of SARS-CoV-2 shows reduced sensitivity to neutralization by plasma polyclonal antibodies from natural infection or vaccination, emphasizing the importance of ongoing viral mutation monitoring.
JOURNAL OF CLINICAL VIROLOGY
(2022)
Article
Biochemical Research Methods
Puneet Rawat et al.
Summary: Ab-CoV is a database containing manually curated experimental interaction profiles of 1780 coronavirus-related neutralizing antibodies. It provides comprehensive data including IC50, EC50, and K-D, as well as predicted changes in stability and affinity of point mutations of interface residues.
Article
Biology
Puneet Rawat et al.
Summary: This study classified mutation sites of SARS-CoV-2 virus into low and high mutability classes based on viral isolates count and developed machine learning models to predict mutability. The findings are useful for early detection of concerning viral variants and can be applied in pandemic prevention.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Multidisciplinary Sciences
Qian Wang et al.
Summary: SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 have become dominant in the United States and South Africa, raising concerns about their ability to evade neutralizing antibodies and compromise the efficacy of COVID-19 vaccines and therapeutic monoclonals. A systematic antigenic analysis reveals that BA.2.12.1 and BA.4/5 have different levels of resistance to antibodies, with BA.2.12.1 being modestly resistant and BA.4/5 being substantially resistant. Certain mutations in the spike protein facilitate antibody escape, but compromise the spike affinity for the viral receptor. Only bebtelovimab retains full potency against both subvariants.
Article
Biochemistry & Molecular Biology
Pedro B. P. S. Reis et al.
Summary: Antibodies are a versatile tool in molecular biology and nanotechnology due to their ability to specifically recognize molecular antigens. The improvement of structural biology techniques and the emergence of new ones have led to an increase in resolved antibody-antigen structures, allowing for a comprehensive characterization of antibody-antigen interfaces.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Joseph M. Taft et al.
Summary: The development of deep mutational learning (DML), a machine-learning-guided protein engineering technology, allows accurate prediction of the impact of SARS-CoV-2 variants on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified, and this technology can be used for predictive profiling of current and prospective variants, including highly mutated variants such as Omicron, to guide the development of therapeutic antibody treatments and vaccines for COVID-19.
Article
Biochemistry & Molecular Biology
Daria Beshnova et al.
Summary: Coronavirus disease 2019 (COVID-19) caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a severe pandemic worldwide, causing enormous global health and economic damage. Developing effective COVID-19 treatments is an urgent necessity, and the use of computational methods may provide an attractive solution in selecting the top candidates.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Kai Hakala et al.
Summary: This paper addresses the increasing demand for automated protein function prediction by developing an ensemble system that utilizes machine learning models to predict protein functions based on their sequences. The proposed system demonstrates competitive performance in the CAFA3 evaluation.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Cong Sun et al.
Summary: The study demonstrates that the Omicron variant of SARS-CoV-2 has extraordinary potency in immune escape compared to other variants of concern, posing challenges for current antibody therapies and vaccines. Computational interface analysis is shown to be effective in identifying concerning variants early on, providing preliminary guidance for neutralizing antibody therapy.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Biochemical Research Methods
Gen Li et al.
Summary: The study introduces a sequence-based machine learning algorithm SAAMBE-SEQ to evaluate the impact of mutations on protein-protein binding free energy without requiring structural information. The method demonstrates high accuracy in benchmark tests and is suitable for genome-scale investigations.
Article
Biochemical Research Methods
N. R. Siva Shanmugam et al.
Summary: Protein-carbohydrate interactions are crucial in various cellular and biological processes. Factors influencing binding affinity and the free energy of binding can provide insights into the recognition mechanism. This study collected experimental data for 389 protein-carbohydrate complexes to analyze the relationship between binding affinity and structural features, developing regression equations to predict binding affinity with high accuracy. The web server PCA-Pred was created for predicting protein-carbohydrate complex binding affinity, achieving an average correlation of 0.731 and mean absolute error of 1.149 kcal/mol on a jackknife test.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Allison J. Greaney et al.
Summary: Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are key in neutralizing antibody responses, and a deep mutational scanning method was used to assess the impact of all amino-acid mutations in the RBD on antibody binding with 10 human monoclonal antibodies. The study identified the clustered escape mutations in different surfaces of the RBD that correspond to structurally defined antibody epitopes, showing that even antibodies targeting the same surface can have distinct escape mutations.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
Puneet Rawat et al.
Summary: This study compared spike proteins from three strains of coronaviruses and found that the severity of different strains correlated positively with the interaction area, surrounding hydrophobicity, and interaction energy, while inversely correlating with the flexibility of the binding interface. Conserved residues were identified in the binding interface of spike proteins in all three strains, suggesting evolutionary favorability. Understanding the similarities and differences in spike proteins may accelerate the screening of potential lead molecules and the development or repurposing of therapeutic drugs.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Pengfei Wang et al.
Summary: The COVID-19 pandemic has had global repercussions, with promising vaccines and monoclonal antibody therapies. However, newly detected variants of SARS-CoV-2 present challenges to these treatment options.
Article
Multidisciplinary Sciences
R. Prabakaran et al.
Summary: Mitigating the devastating effects of COVID-19 is crucial to control infection and mortality rates, with strategies such as quarantine and lockdown being implemented in most countries. Mathematical models, like the SEIR model, are used to understand disease dynamics, and the inclusion of restrictions is key for their success. A new SEIQR model has been developed to explore the impact of quarantine and lockdown measures on disease propagation, predicting significant differences between reported and actual cases.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Chunyan Yi et al.
Summary: This study identified 33 amino acid positions within four independent antigenic sites of RBD as valuable indicators of antigenic changes. The research confirms widely circulating strains carrying important immune-escape RBD mutations, while also uncovering new immune escape-enabling mutations. Co-mutations may lead to increased resistance to NAbs and convalescent plasma, emphasizing the importance of monitoring the accumulation of co-mutations on distinct major antigenic sites.
Article
Biochemistry & Molecular Biology
Sarah A. Clark et al.
Summary: The study reveals that mutations occurring during the evolution of SARS-CoV-2 virus may lead to resistance against antibodies, posing challenges to long-term efficacy.
Article
Biochemistry & Molecular Biology
Wanwisa Dejnirattisai et al.
Summary: Ending the SARS-CoV-2 pandemic requires global vaccination. New virus strains with mutations impact antibody responses, but some variants are less resistant than others. A monoclonal antibody can neutralize different variants and partially restore neutralization potency for other public antibodies.
Review
Immunology
Lok Bahadur Shrestha et al.
Summary: The emergence of SARS-CoV-2 variants has raised concerns globally, prompting research to find broadly neutralizing monoclonal antibodies to combat these variants. The discovery of these antibodies may help in the development of therapeutic antibodies and guide the discovery of second-generation vaccines.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Bryan E. Jones et al.
Summary: LY-CoV555 is a novel neutralizing antibody derived from a convalescent patient with COVID-19, showing high affinity binding, potent inhibition of ACE2 binding, and strong neutralizing activity. This antibody has entered clinical trials and is being evaluated for various COVID-19 prevention and treatment indications.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Puneet Rawat et al.
Summary: Researchers compared experimentally verified SARS-CoV-2 neutralizing antibodies with commercial therapeutic monoclonal antibodies and identified three potential therapeutic antibodies targeting CTLA4 and IL17A for combating severe SARS-CoV-2 infection. These candidate antibodies have dual activities of viral neutralization and immunosuppression, and could also be utilized in diagnostic test kits for SARS-CoV-2 infection. The in silico workflow to screen and analyze antibodies for repurposing is believed to have broad applications.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Micah Rapp et al.
Summary: Antibodies derived from the VH1-2 gene have been shown to be potent neutralizing antibodies against SARS-CoV-2, with three VH1-2-derived antibodies (2-15, 2-43, and H4) using VH1-2-encoded motifs to recognize the receptor-binding domain (RBD) of the virus spike protein. Despite genetic similarities, these antibodies are able to recognize both up and down conformations of the RBD, with some antibodies using elongated CDRH3s to interact with glycan N343 on a neighboring RBD. The VH1-2 antibody class utilizes modular genetic elements for modular recognition, with VH gene specifying RBD recognition and CDRH3 specifying quaternary interactions.
Article
Immunology
Ruoke Wang et al.
Summary: Research shows that the South African B.1.351 variant exhibits the highest resistance to current monoclonal antibodies and convalescent plasma from COVID-19-infected individuals, and the molecular basis for this resistance and potential antibody escape has been identified.
Review
Microbiology
William T. Harvey et al.
Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Meng Yuan et al.
Summary: Mutations in the RBS residues of new variant strains of the coronavirus can affect the binding and neutralizing effects of antibodies, but have little impact on antibodies targeting more conserved neutralizing sites.
Article
Multidisciplinary Sciences
Allison J. Greaney et al.
Summary: The study found that although the human immune system can produce antibodies that target diverse RBD epitopes, in practice, the polyclonal response to infection tends to be skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Qi Zhang et al.
Summary: The study identifies potent neutralizing antibodies against SARS-CoV-2 with shared genetic features, termed as public antibodies. While one representative antibody demonstrates high protective efficacy in experiments, virus escape analysis reveals challenges faced by these public antibodies.
NATURE COMMUNICATIONS
(2021)
Article
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(2020)
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Review
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Computer Science, Hardware & Architecture
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MOLECULAR BIOSYSTEMS
(2009)
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