ConvMut: A Web tool to analyze viral convergent mutations along phylogenies DOI Creative Commons
Anna Bernasconi,

Emma Fanfoni,

Tommaso Alfonsi

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 16, 2024

Abstract Convergent evolution in protein antigens is common across pathogens and has also been documented SARS-CoV-2; the most likely reason need to evade selective pressure exerted by previous infection- or vaccine-elicited immunity. There a pressing for tools that allow automated analysis of convergent mutations. In response this need, we developed ConvMut, tool identifying patterns recurrent mutations SARS-CoV-2 evolution. To end, exploited granular phylogenetic tree representation PANGO, allowing us observe what call deltas, i.e., groups are acquired on top immediately upstream nodes. Deltas comprise both amino acid substitutions deletions. ConvMut can perform individual identify single independently given subtree (starting from user-selected root). Such represented barplot be sorted frequency position filtered region interest. Lineages then gathered into clusters according their sets shared Finally, an interactive graph orders clusters, details changes each sublineage, allows evolutive path until selected lineage. Other unique paired with main functionality support complete analysis, such as nucleotide at residue subtree. We expect will facilitate design antiviral anti-Spike monoclonal antibodies Spike-based vaccines longer-lasting efficacy, minimizing development marketing failures.

Язык: Английский

Sipavibart: when a success changes into a failure DOI
Daniele Focosi, Arturo Casadevall

The Lancet Infectious Diseases, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

0

Development of antiviral drugs for COVID-19 in 2025: unmet needs and future challenges DOI
Daniele Focosi, David J. Sullivan, Massimo Franchini

и другие.

Expert Review of Anti-infective Therapy, Год журнала: 2025, Номер unknown

Опубликована: Фев. 25, 2025

The success in the COVID-19 pandemic containment largely originated from vaccine- and infection-elicited immunity, with SARS-CoV-2 infection only marginally mitigated by availability of antiviral drugs. current lack effective prophylactic therapeutic agents immunocompromised patients highlights need for a radical change design both drug manufacturing clinical trials. In this review authors summarize their suggestions manufacturers, reviewing classes small molecule antivirals passive immunotherapies highlighting limitations unexploited potential. Molecular serological testing can improve appropriateness. Efficacy be improved combining different while preserving economical sustainability. Respiratory delivery should better investigated

Язык: Английский

Процитировано

0

Limited Biomarker Potential for IgG Autoantibodies Reactive to Linear Epitopes in Systemic Lupus Erythematosus or Spondyloarthropathy DOI Creative Commons
S. Janna Bashar, Zihao Zheng, Aisha M. Mergaert

и другие.

Antibodies, Год журнала: 2024, Номер 13(4), С. 87 - 87

Опубликована: Окт. 12, 2024

Autoantibodies are commonly used as biomarkers in autoimmune diseases, but there limitations. For example, autoantibody have poor sensitivity or specificity systemic lupus erythematosus and do not exist the spondyloarthropathies, impairing diagnosis treatment. While autoantibodies suitable for strong may these conditions, another possibility is that technology has limited their discovery. The purpose of this study was to use a novel high-density peptide array enables evaluation IgG binding every possible linear antigen entire human peptidome, well machine learning approach incorporates ELISA validation predictability order discover could be developed into sensitive specific markers spondyloarthropathy.

Язык: Английский

Процитировано

0

EVOLVE: A Web Platform for Evolutionary Phase Analysis and New Variant Exploration from Multi-Sequence Data DOI Creative Commons
Satyam Sangeet,

Anushree Sinha,

Madhav B. Nair

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 26, 2024

Abstract Recurrent updates from the World Health Organization (WHO) on refining definitions for Variants of Concern (VOCs), Interest (VOIs), and Under Monitoring (VUMs) underscore need systematic investigations to develop quantifiable metrics that differentiate critical phases variant evolution. This study illustrates how protein data can be systematically analyzed by applying phase transition principles statistical mechanics, where quantifying mutational response function (MRF) helps identify concerning variants along evolutionary paths. To support exploration like entropy, MRF, other relevant indicators novel or uncharacterized viruses pathogenic bacteria, we introduce EVOLVE—a web platform empowers researchers across diverse fields access sequence-based analyses. EVOLVE streamlines upload analysis with a user-friendly interface comprehensive tutorials. Overcoming challenges large sequence-space its AI-driven data-learning module integrates dynamics microscopic information, enabling prediction future site-specific mutations in prospective missense variants. Access free at https://www.evolve-0fm3.onrender.com .

Язык: Английский

Процитировано

0

ConvMut: A Web tool to analyze viral convergent mutations along phylogenies DOI Creative Commons
Anna Bernasconi,

Emma Fanfoni,

Tommaso Alfonsi

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 16, 2024

Abstract Convergent evolution in protein antigens is common across pathogens and has also been documented SARS-CoV-2; the most likely reason need to evade selective pressure exerted by previous infection- or vaccine-elicited immunity. There a pressing for tools that allow automated analysis of convergent mutations. In response this need, we developed ConvMut, tool identifying patterns recurrent mutations SARS-CoV-2 evolution. To end, exploited granular phylogenetic tree representation PANGO, allowing us observe what call deltas, i.e., groups are acquired on top immediately upstream nodes. Deltas comprise both amino acid substitutions deletions. ConvMut can perform individual identify single independently given subtree (starting from user-selected root). Such represented barplot be sorted frequency position filtered region interest. Lineages then gathered into clusters according their sets shared Finally, an interactive graph orders clusters, details changes each sublineage, allows evolutive path until selected lineage. Other unique paired with main functionality support complete analysis, such as nucleotide at residue subtree. We expect will facilitate design antiviral anti-Spike monoclonal antibodies Spike-based vaccines longer-lasting efficacy, minimizing development marketing failures.

Язык: Английский

Процитировано

0