VIPERA：病毒患者内部演变报告与分析。

IF 5.5 2区医学 Q1 VIROLOGY

Virus Evolution Pub Date : 2024-03-06 eCollection Date: 2024-01-01 DOI:10.1093/ve/veae018

Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá

{"title":"VIPERA：病毒患者内部演变报告与分析。","authors":"Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá","doi":"10.1093/ve/veae018","DOIUrl":null,"url":null,"abstract":"Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae018"},"PeriodicalIF":5.5000,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10953798/pdf/","citationCount":"0","resultStr":"{\"title\":\"VIPERA: Viral Intra-Patient Evolution Reporting and Analysis.\",\"authors\":\"Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá\",\"doi\":\"10.1093/ve/veae018\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.\",\"PeriodicalId\":56026,\"journal\":{\"name\":\"Virus Evolution\",\"volume\":\"10 1\",\"pages\":\"veae018\"},\"PeriodicalIF\":5.5000,\"publicationDate\":\"2024-03-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10953798/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Virus Evolution\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1093/ve/veae018\",\"RegionNum\":2,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"VIROLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Virus Evolution","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1093/ve/veae018","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"VIROLOGY","Score":null,"Total":0}

引用次数: 0

摘要

在慢性感染期间，患者体内的病毒变异孕育了严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）的适应潜力，这是令人担忧的变异体的潜在来源。然而，目前还没有对 SARS-CoV-2 患者内序列样本进行进化分析的综合框架。在本文中，我们介绍了病毒患者内进化报告和分析（VIPERA），这是一款新软件，它将评估 SARS-CoV-2 序列的患者内祖先与分析来自同一病毒感染的序列的进化轨迹整合在一起。我们利用阳性和阴性对照数据集对该软件进行了验证，并成功地将其应用于一个新病例，发现了群体动态和适应性进化的证据。VIPERA 可在 https://github.com/PathoGenOmics-Lab/VIPERA 免费获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

VIPERA: Viral Intra-Patient Evolution Reporting and Analysis.

Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Virus Evolution Immunology and Microbiology-Microbiology

CiteScore

10.50

自引率

5.70%

发文量

108

审稿时长

14 weeks

期刊介绍： Virus Evolution is a new Open Access journal focusing on the long-term evolution of viruses, viruses as a model system for studying evolutionary processes, viral molecular epidemiology and environmental virology. The aim of the journal is to provide a forum for original research papers, reviews, commentaries and a venue for in-depth discussion on the topics relevant to virus evolution.