Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.
Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.
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DOI：
10.1371/journal.ppat.1010023
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发表时间：
2022-05
期刊：
影响因子：
6.7
通讯作者：
中科院分区：
文献类型：
--
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病原体序列数据的可用性和基因组监测的使用正在迅速增加。基因组工具和分类系统需要更新以反映这一点。本文以狂犬病毒为例，展示了更新的基因组工具在加强监测以更好地了解流行病学动态和改善疾病控制方面的潜在价值。先前的研究已经描述了狂犬病毒的进化史，但是所得到的分类缺乏必要的定义来高分辨率地识别入侵、谱系转换和传播途径。在这里，我们提出了一个基于SARS-CoV-2动态命名法的谱系分类系统，通过追踪病毒传播的系统发育方法和跨地理区域的序列比较来定义一个谱系。我们通过应用于全球分布的狂犬病病毒世系来证明这一系统，在该世系中定义了96个总谱系，超出了之前报道的22个。我们进一步展示了该工具与新的狂犬病毒序列数据资源（RABV-GLUE）的集成如何实现快速应用，例如，突出与控制和消除规划相关的谱系动力学，例如确定输入及其来源，以及病毒持续存在的区域和传播途径，包括跨界入侵。在各国努力消除犬媒狂犬病的过程中，这一系统和开发的工具应有助于协调和确定控制规划的目标，并监测进展情况，并有可能更广泛地应用于其他病毒的监测。在SARS-CoV-2大流行期间，以一种可以明确传达的普遍方式跟踪病毒的多样性和传播能力的重要性得到了强调。这一点，加上病原体序列数据的可得性和使用的增加，意味着开发新的基因组工具和分类系统可以加强疫情应对和疾病控制。在这里，我们提出了一种易于使用的客观和可转移的分类工具，用于高分辨率跟踪病毒。狂犬病病毒是一种被忽视的人畜共患疾病，每年导致约5.9万人死亡。我们以狂犬病病毒作为该工具的一个例子。将我们的工具应用于狂犬病病毒的全球进化支，我们发现分辨率从22个亚进化支增加到96个谱系；我们可以对病毒进行分类的定义增加了四倍，这可能使我们能够确定以前不明显的持续存在和传播的区域，并进一步解决病毒传播的模式。在各国努力消除犬类狂犬病的过程中，应用这一工具获得的见解应被证明对有针对性的犬类疫苗接种运动和改善监测具有价值。
The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses. The importance of the ability to track the diversity and spread of viruses in a universal way that can be clearly communicated has been highlighted during the SARS-CoV-2 pandemic. This, accompanied with the increase in the availability and use of pathogen sequence data, means the development of new genomic tools and classification systems can strengthen outbreak response and disease control. Here, we present an easy-to-use objective and transferable classification tool for tracking viruses at high resolution. We use rabies virus, the cause of a neglected zoonotic disease that kills around 59,000 people each year, as an example use case of this tool. Applying our tool to a global clade of rabies virus, we find an increase in resolution from 22 subclades to 96 lineages; this fourfold increase in the definition at which we can classify the virus, may allow us to identify areas of persistence and transmission that were not previously apparent and further resolve patterns of virus spread. Insights from the application of this tool should prove valuable in targeting dog vaccination campaigns and improving surveillance as countries work towards the elimination of dog-mediated rabies.
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影响因子：
11.2
作者：
Boland, Torrey A.;McGuone, Declan;Rosenthal, Eric S.
通讯作者：
Rosenthal, Eric S.
DOI：
10.3390/v12111255
发表时间：
2020-11-04
期刊：
Viruses
影响因子：
--
作者：
Gigante CM;Yale G;Condori RE;Costa NC;Long NV;Minh PQ;Chuong VD;Tho ND;Thanh NT;Thin NX;Hanh NTH;Wambura G;Ade F;Mito O;Chuchu V;Muturi M;Mwatondo A;Hampson K;Thumbi SM;Thomae BG;de Paz VH;Meneses S;Munyua P;Moran D;Cadena L;Gibson A;Wallace RM;Pieracci EG;Li Y
通讯作者：
Li Y
影响因子：
5.3
作者：
Sagulenko P;Puller V;Neher RA
通讯作者：
Neher RA
影响因子：
10.7
作者：
Minh BQ;Nguyen MA;von Haeseler A
通讯作者：
von Haeseler A
影响因子：
5.7
作者：
Lembo, Tiziana;Hampson, Katie;Cleaveland, Sarah
通讯作者：
Cleaveland, Sarah