VIProDesign: Viral Protein Panel Design for Highly Variable Viruses to Evaluate Immune Responses and Identify Broadly Neutralizing Antibodies.

Tatsiana Bylund, Mohammed El Anbari, Andrew Schaub, Tongqing Zhou, Reda Rawi
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Abstract

Highly mutable viruses continuously evolve, with some posing major pandemic risks. However, standardized neutralization assays and up-to-date viral panels are often lacking, limiting evaluation of immunogens and identification of broadly neutralizing antibodies. Closing these gaps is essential for guiding effective countermeasure development. In this study, we present Viral Protein Panel Design (VIProDesign), a computational tool for designing viral protein panels that address the high sequence diversity of rapidly evolving viruses. VIProDesign uses the Partitioning Around Medoids (PAM) algorithm to select representative strains and applies the elbow-point method based on cumulative Shannon entropy to balance diversity and panel size. We used VIProDesign to generate optimized panels for Betacoronavirus, human immunodeficiency virus-1 (HIV-1), Influenza virus, Norovirus, and Lassa virus. The tool also supports customizable panel sizes, making it suitable for both resource-limited contexts and early-stage research. This flexible approach streamlines viral panel design across diverse pathogens. Although VIProDesign was originally developed for viral proteins, its underlying framework is broadly applicable to the selection of representative protein panels across diverse taxa, including bacterial species, toxins, and other biologically relevant protein families.

VIProDesign:高度可变病毒的病毒蛋白面板设计,用于评估免疫反应和识别广泛中和抗体。
高度易变的病毒不断进化,其中一些病毒构成重大大流行风险。然而,标准化的中和试验和最新的病毒小组往往缺乏,限制了免疫原的评估和广泛中和抗体的鉴定。缩小这些差距对于指导有效的对策制定至关重要。在这项研究中,我们提出了病毒蛋白面板设计(VIProDesign),这是一种用于设计病毒蛋白面板的计算工具,用于解决快速进化病毒的高序列多样性。VIProDesign使用分区围绕介质(PAM)算法来选择具有代表性的应变,并采用基于累积香农熵的肘点法来平衡多样性和面板大小。我们使用VIProDesign生成优化的乙型冠状病毒、人类免疫缺陷病毒-1 (HIV-1)、流感病毒、诺如病毒和拉沙病毒的检测板。该工具还支持可定制的面板大小,使其适用于资源有限的环境和早期研究。这种灵活的方法简化了不同病原体的病毒面板设计。虽然VIProDesign最初是为病毒蛋白开发的,但其基本框架广泛适用于选择不同分类群的代表性蛋白质面板,包括细菌物种,毒素和其他生物学相关的蛋白质家族。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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