优化基因距离值以推断基于下一代测序的CRF01_AE分子网络
Lijuan Hu1,2,3,4,5, Bin Zhao1,2,3,4,5, Mingchen Liu1,2,3,5
1State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China.
Frontiers in cellular and infection microbiology
|June 7, 2024
概括
优化艾滋病毒CRF01_AE网络的遗传距离值可以改善最近传播事件的识别. 一个0.008-0.013替代/部位范围准确地预测了最近的艾滋病毒感染.
科学领域:
- 流行病学 流行病学
- 病毒学 病毒学
- 生物信息学是一种生物信息学.
背景情况:
- 艾滋病毒分子网络对于理解传播动态至关重要.
- 现有的遗传距离 (GD) 值是特定于亚型的,需要对非B亚型 (如CRF01_AE.AE) 进行优化.
研究的目的:
- 优化基因距离 (GD) 值以推断CRF01_AE分子网络.
- 准确识别CRF01_AE亚型中最近发生的艾滋病毒传播事件.
主要方法:
- 利用了来自12个传输对的59个样本中部分CRF01_AE极序的下一代测序数据.
- 使用Tamura-Nei 93模型计算配对GD以确定GD值范围.
- 使用2019个CRF01_AE序列构建的分子网络,以评估最近艾滋病毒感染 (RHI) 的门预测准确性.
主要成果:
- 为了推断CRF01_AE分子网络,确定了0.008-0.013个替代/位点的GD值范围.
- 这个范围准确地识别了过去三年内的传输事件.
- 增加GD值从0.001到0.02的替代/站点与网络内的RHI比例从16.6%增加到92.3%.
结论:
- 0.008-0.013个替代/站点的GD值范围适用于推断CRF01_AE分子传输网络.
- 这一优化值有助于识别非B亚型的最近艾滋病毒传播事件.
- 为在HIV分子流行病学中选择适当的GD值提供了有价值的数据.
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