Phylodynamics of H5N1 avian influenza virus in Indonesia
Phylodynamics of H5N1 avian influenza virus in Indonesia
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DOI：
10.1111/j.1365-294x.2012.05577.x
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发表时间：
2012-06-01
影响因子：
4.9
通讯作者：
Leung, Frederick Chi-Ching
中科院分区：
文献类型：
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作者：
Lam, Tommy Tsan-Yuk;Hon, Chung-Chau;Leung, Frederick Chi-Ching
了解病原体是如何入侵并在新的宿主群体中形成的，是传染病生态学和进化的核心。流感病毒为研究自然界的这些过程提供了独特的机会，因为它们快速进化、广泛的监测、庞大的数据集和跨越物种边界的倾向。H5N1高致病性禽流感病毒(HPAIV)是一种主要的动物病原体和公共卫生威胁。该病毒在印度尼西亚特别重要，自2003年以来在家禽中造成严重暴发，并造成零星的人感染。然而，关于H5N1 HPAIV是如何在印度尼西亚出现和确立的，人们知之甚少。为了解决这些问题，我们分析了20032007期间分离到的印度尼西亚H5N1 HPAIV基因序列。我们发现，该病毒起源于2002年11月至2003年10月期间在东爪哇的一次传入。这种入侵的特点是最初病毒遗传多样性的迅速爆发，然后是稳定的世系更替速度和遗传多样性的维持。在血凝素基因的早期阶段，几个抗原位点受到正选择的影响，这表明宿主免疫驱动的选择在宿主适应和扩张中发挥了作用。系统地理分析表明，在H5N1最初入侵后，基因变异在爪哇既向东又向西移动，可能涉及人类的长途运输。我们发现的系统动力学与最近研究的其他病毒入侵有相似之处，从而揭示了决定新地理区域疾病出现的生态和进化过程。
Understanding how pathogens invade and become established in novel host populations is central to the ecology and evolution of infectious disease. Influenza viruses provide unique opportunities to study these processes in nature because of their rapid evolution, extensive surveillance, large data sets and propensity to jump species boundaries. H5N1 highly pathogenic avian influenza virus (HPAIV) is a major animal pathogen and public health threat. The virus is of particular importance in Indonesia, causing severe outbreaks among poultry and sporadic human infections since 2003. However, little is known about how H5N1 HPAIV emerged and established in Indonesia. To address these questions, we analysed Indonesian H5N1 HPAIV gene sequences isolated during 20032007. We find that the virus originated from a single introduction into East Java between November 2002 and October 2003. This invasion was characterized by an initially rapid burst of viral genetic diversity followed by a steady rate of lineage replacement and the maintenance of genetic diversity. Several antigenic sites in the haemagglutinin gene were subject to positive selection during the early phase, suggesting that host-immune-driven selection played a role in host adaptation and expansion. Phylogeographic analyses show that after the initial invasion of H5N1, genetic variants moved both eastwards and westwards across Java, possibly involving long-distance transportation by humans. The phylodynamics we uncover share similarities with other recently studied viral invasions, thereby shedding light on the ecological and evolutionary processes that determine disease emergence in a new geographical region.