大规模基因组分析揭示 HIV-1 亚型 F1 西班牙流行株的快速进化率和选择压力
Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1.
机构信息
Joint Research Unit "Infection and Public Health" FISABIO-Universitat de València, València, Spain; CIBER in Epidemiology and Public Health, Madrid, Spain.
HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
出版信息
Infect Genet Evol. 2018 Dec;66:43-47. doi: 10.1016/j.meegid.2018.09.008. Epub 2018 Sep 13.
Abstract
This work is aimed at assessing the presence of positive selection and/or shifts of the evolutionary rate in a fast-expanding HIV-1 subtype F1 transmission cluster affecting men who have sex with men in Spain. We applied Bayesian coalescent phylogenetics and selection analyses to 23 full-coding region sequences from patients belonging to that cluster, along with other 19 F1 epidemiologically-unrelated sequences. A shift in the overall evolutionary rate of the virus, explained by positively selected sites in the cluster, was detected. We also found one substitution in Nef (H89F) that was specific to the cluster and experienced positive selection. These results suggest that fast transmission could have been facilitated by some inherent genetic properties of this HIV-1 variant.
摘要
本研究旨在评估在西班牙影响男男性行为者的快速扩张的 HIV-1 亚型 F1 传播簇中，是否存在正选择和/或进化率变化。我们对属于该簇的 23 例患者的全长编码区序列以及其他 19 例 F1 无流行病学关联的序列应用贝叶斯系统发育和选择分析。检测到病毒的整体进化率发生了变化，这可以用聚类中受正选择影响的位点来解释。我们还发现 Nef 中的一个突变（H89F）是该聚类所特有的，并且经历了正选择。这些结果表明，这种 HIV-1 变体的某些固有遗传特性可能促进了快速传播。
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