推断病毒传播时间从已知传输对的种系推断
Emma E Goldberg1, Erik J Lundgren1, Ethan O Romero-Severson1
1Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
Molecular biology and evolution
|December 27, 2023
概括
我们开发了一个马尔科夫模型,用基因数据估计人类免疫缺陷病毒 (HIV) 传播时间. 这种方法提供了准确和精确的HIV传播时间估计,有助于了解传播动态.
科学领域:
- 流行病学 流行病学
- 计算生物学 计算生物学
- 病毒学 病毒学
背景情况:
- 估计人类免疫缺陷病毒 (HIV) 传播时间对于理解传播动态和为公共卫生干预提供信息至关重要.
- 病毒遗传数据的遗传学分析提供了一个强大的工具来推断当直接观察是不可能的传染事件.
研究的目的:
- 开发和评估一种新的单参马尔科夫模型,以从基因数据推断艾滋病毒传播时间.
- 将拟议的马尔科夫模型的性能与现有的传输时间估计方法进行比较.
主要方法:
- 开发一个单参数马尔科夫模型,从艾滋病毒的基因组推断传播时间.
- 使用来自传染对中的个体的多个病毒序列构建族系.
- 使用模拟对比马尔科夫模型的性能与基于树的逻辑间隔,储蓄式规则和凝聚模型.
主要成果:
- 马尔科夫时间切片模型在各种模拟场景中提供了与现有方法相比更准确,更窄的传输时间估计.
- 确定了特定的条件,例如来源感染后的延迟传播和传播后的延迟采样,这些条件挑战了任何方法的准确时间推断.
- 对艾滋病毒传播对的现实应用显示与病例调查数据一致,尽管基因时间校准带来了显著的不确定性.
结论:
- 开发的马尔科夫模型是准确的HIV传播时间推断的宝贵工具.
- 基因时间校准的不确定性是当前传输时间估计的一个主要限制,比模型推断本身更重要.
- 需要进行进一步的研究,以开发充分利用族系拓和节点时间的方法,以改进传输推断.
相关概念视频
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
00:36Viral Mutations
32.3K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
32.3K
02:33Retroviruses
12.3K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
12.3K
00:57Viral Recombination
23.4K
Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
23.4K
03:21Phylogenetic Trees
45.3K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.3K
02:18Types of Genetic Transfer Between Organisms
27.9K
Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and horizontal gene transfer. Vertical gene transfer occurs when genetic information is transferred from one generation to the next, which happens much more frequently than horizontal gene transfer. Both sexual and asexual reproduction are forms of vertical gene transfer, where one or more organisms pass some or all of their genome onto their progeny.
27.9K