Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China.
Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China.
复制标题
中国云南省狂犬病病毒跨境传播、谱系位移和进化率估算
DOI：
10.1186/s12985-017-0769-6
复制
发表时间：
2017-06-03
期刊：
影响因子：
4.8
通讯作者：
Tian H
中科院分区：
文献类型：
--
作者：
Zhang Y;Vrancken B;Feng Y;Dellicour S;Yang Q;Yang W;Zhang Y;Dong L;Pybus OG;Zhang H;Tian H
背景狂犬病是对公共健康的一种重要但被低估的威胁，大多数病例发生在亚洲。自2000年以来，中国西南部的云南省与东南亚三个国家接壤，出现了新一波狂犬病疫情。方法我们利用GenBank中的现有数据估计狂犬病病毒的基因特异性进化速率，然后利用该信息校准狂犬病病毒（RABV）在亚洲传播的时间尺度。我们使用了 452 个公开的地理参考完整核蛋白 (N) 基因序列，其中包括最近从 2008 年至 2012 年在云南收集的样本中生成的 52 个 RABV 序列。结果 RABV N 基因进化率估计为 1.88 × 10−4(1.37–2.41 × 10−4)，95% 贝叶斯可信度间隔，BCI）每年每个站点的替换。系统发育重建表明，目前在云南流行的RABV谱系来自至少7个独立引入（95％BCI：6-9个引入），并且代表亚洲三个主要RABV谱系SEA-1、-2和-3中的每一个。我们发现，云南是RABV国内传播的汇点，连接着华北、华南和东南亚的RABV疫情。从东南亚（SEA）跨境传播到华南地区，以及华北和华南疫情混合也得到了很好的支持。 RABV 从东南亚流入云南的情况没有得到很好的支持，这可能是由于东南亚 RABV 多样性采样较差。我们发现了云南 SEA-1 毒株对云南 SEA-2 和 -3 谱系进行谱系置换的证据，并考虑这是否可归因于适应度差异。结论总体而言，我们的研究有助于更好地了解 RABV 的传播，从而促进未来狂犬病病毒的控制和预防工作。
BackgroundRabies is an important but underestimated threat to public health, with most cases reported in Asia. Since 2000, a new epidemic wave of rabies has emerged in Yunnan Province, southwestern China, which borders three countries in Southeast Asia.MethodWe estimated gene-specific evolutionary rates for rabies virus using available data in GenBank, then used this information to calibrate the timescale of rabies virus (RABV) spread in Asia. We used 452 publicly available geo-referenced complete nucleoprotein (N) gene sequences, including 52 RABV sequences that were recently generated from samples collected in Yunnan between 2008 and 2012.ResultsThe RABV N gene evolutionary rate was estimated to be 1.88 × 10−4(1.37–2.41 × 10−4, 95% Bayesian credible interval, BCI) substitutions per site per year. Phylogenetic reconstructions show that the currently circulating RABV lineages in Yunnan result from at least seven independent introductions (95% BCI: 6–9 introductions) and represent each of the three main Asian RABV lineages, SEA-1, -2 and -3. We find that Yunnan is a sink location for the domestic spread of RABV and connects RABV epidemics in North China, South China, and Southeast Asia. Cross-border spread from southeast Asia (SEA) into South China, and intermixing of the North and South China epidemics is also well supported. The influx of RABV into Yunnan from SEA was not well-supported, likely due to the poor sampling of SEA RABV diversity. We found evidence for a lineage displacement of the Yunnan SEA-2 and -3 lineages by Yunnan SEA-1 strains, and considered whether this could be attributed to fitness differences.ConclusionOverall, our study contributes to a better understanding of the spread of RABV that could facilitate future rabies virus control and prevention efforts.