CLASV: Rapid Lassa virus lineage assignment with random forest.

IF 3.4 2区医学 Q1 PARASITOLOGY

PLoS Neglected Tropical Diseases Pub Date : 2025-09-09 eCollection Date: 2025-09-01 DOI:10.1371/journal.pntd.0013512

Richard Olumide Daodu, Ebenezer Awotoro, Jens-Uwe Ulrich, Denise Kühnert

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Abstract

Lassa fever, caused by the Lassa virus (LASV), is a deadly disease characterized by hemorrhages. Annually, it affects approximately 300,000 people in West Africa and causes about 5,000 deaths. It currently has no approved vaccine and is categorized as a top-priority disease. Apart from its endemicity to West Africa, there have been exported cases in almost all continents, including several European countries. Distinct Lassa virus lineages circulate in specific regions, and have been reported to show varying immunological behaviors and may contribute to differing disease outcomes. It is therefore important to rapidly identify which lineage caused an outbreak or an exported case. We present CLASV, a machine learning-based lineage assignment tool built using a Random Forest classifier. CLASV processes raw nucleotide sequences and assigns them to the dominant circulating lineages (II, III, and IV/V) rapidly and accurately. CLASV is implemented in Python for ease of integration into existing workflows and is freely available for public use.

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分类：随机森林快速拉沙病毒谱系分配。

由拉沙病毒（LASV）引起的拉沙热是一种以出血为特征的致命疾病。它每年影响西非约30万人，造成约5000人死亡。目前还没有批准的疫苗，被列为重点疾病。除了西非的地方性外，几乎所有大陆都出现了输出病例，包括几个欧洲国家。不同的拉沙病毒谱系在特定地区流行，据报道表现出不同的免疫行为，并可能导致不同的疾病结局。因此，重要的是迅速确定是哪个血统引起了疫情或输出病例。我们提出了CLASV，一个使用随机森林分类器构建的基于机器学习的谱系分配工具。CLASV处理原始核苷酸序列，并快速准确地将其分配给优势循环谱系（II， III和IV/V）。CLASV是用Python实现的，以便于集成到现有工作流中，并且可以免费供公众使用。

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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来源期刊

PLoS Neglected Tropical Diseases PARASITOLOGY-TROPICAL MEDICINE

自引率

10.50%

发文量

723

期刊介绍： PLOS Neglected Tropical Diseases publishes research devoted to the pathology, epidemiology, prevention, treatment and control of the neglected tropical diseases (NTDs), as well as relevant public policy. The NTDs are defined as a group of poverty-promoting chronic infectious diseases, which primarily occur in rural areas and poor urban areas of low-income and middle-income countries. Their impact on child health and development, pregnancy, and worker productivity, as well as their stigmatizing features limit economic stability. All aspects of these diseases are considered, including: Pathogenesis Clinical features Pharmacology and treatment Diagnosis Epidemiology Vector biology Vaccinology and prevention Demographic, ecological and social determinants Public health and policy aspects (including cost-effectiveness analyses).