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通过近全长测序提高HIV-1亚型的准确性:常见工具的比较

Flavia Smoquina¹, Giulia Berno¹, Federica Forbici¹

¹Laboratory of Virology and Laboratories of Biosafety, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, 00149 Rome, Italy.

International journal of molecular sciences

|December 11, 2025

概括

由于遗传多样性,准确的HIV-1亚型鉴定至关重要. 与部分区域相比,近全长基因组测序可以更好地检测复杂的循环重组形式 (CRF),从而提高自动化工具的性能.

科学领域:

病毒学病毒学
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

人类免疫缺陷病毒1型 (HIV-1) 呈现出广泛的遗传多样性,包括多个亚型和循环复合形式 (CRF).
准确的HIV-1亚型鉴定对于有效的治疗,疫苗开发和流行病学监测至关重要.
由于HIV-1的遗传复杂性,部分基因组测序对精确的亚型分类提出了挑战.

研究的目的:

评估四种自动化HIV-1亚型化工具与分子遗传学分析 (Mphy) 的性能.
为了比较使用不同序列长度的亚型精度:蛋白酶逆转录酶 (PR-RT),多,近全长 (NFL) 基因组.
评估测序深度对循环复合形式 (CRF) 检测的影响.

主要方法:

使用下一代测序 (NGS) 来生成来自100个血样本的序列,用于PR-RT,pol和NFL区域.
将自动化亚型化工具输出 (斯坦福HIVdb,COMET,REGA,Geno2pheno) 与Mphy (黄金标准) 的比较.
评估了不同序列长度和亚型的一致性,灵敏性和特异性.

主要成果:

在NFL测序中,CRF的比例比PR-RT和pol (44.1%) 高 (51.6%),重新分类了13个样本.
自动化工具对PR-RT和pol与Mphy有很好的一致性,特别是对于纯子类型.
对NFL序列的一致性下降,特别是非B亚型和CRF,灵敏度可变但特异性高.

结论:

全基因组或NFL测序显著提高了复杂的HIV-1CRFs的检测.
自动化HIV-1亚型识别工具的准确性受到序列长度和参考数据库完整性的影响.
优化测序策略和数据库更新对于提高HIV-1亚型精度至关重要.

关键词:

艾滋病病毒-1 艾滋病病毒-1 艾滋病毒-1亚型艾滋病毒-1亚型循环的复合形式正在流通.遗传多样性遗传多样性分子系谱的分子发育.几乎是全长的电影.下一代测序的下一代测序.分类自动化工具的子类型整个基因组的测序.

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