Virology Unit/National Influenza Centre, Institut Pasteur in Cambodia, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia.
Infect Genet Evol. 2013 Apr;15:87-94. doi: 10.1016/j.meegid.2012.05.013. Epub 2012 Jun 7.
In Cambodia, the first detection of HPAI H5N1 virus in birds occurred in January 2004 and since then there have been 33 outbreaks in poultry while 21 human cases were reported. The origin and dynamics of these epizootics in Cambodia remain unclear. In this work we used a range of bioinformatics methods to analyze the Cambodian virus sequences together with those from neighboring countries. Six HA lineages belonging to clades 1 and 1.1 were identified since 2004. Lineage 1 shares an ancestor with viruses from Thailand and disappeared after 2005, to be replaced by lineage 2 originating from Vietnam and then by lineage 3. The highly adapted lineage 4 was seen only in Cambodia. Lineage 5 is circulating both in Vietnam and Cambodia since 2008 and was probably introduced in Cambodia through unregistered transboundary poultry trade. Lineage 6 is endemic to Cambodia since 2010 and could be classified as a new clade according to WHO/OIE/FAO criteria for H5N1 virus nomenclature. We propose to name it clade 1.1A. There is a direct filiation of lineages 2 to 6 with a temporal evolution and geographic differentiation for lineages 4 and 6. By the end of 2011, two lineages, i.e. lineages 5 and 6, with different transmission paths cocirculate in Cambodia. The presence of lineage 6 only in Cambodia suggests the existence of a transmission specific to this country whereas the presence of lineage 5 in both Cambodia and Vietnam indicates a distinct way of circulation of infected poultry.
在柬埔寨，禽流感病毒 HPAI H5N1 的首次检测发生在 2004 年 1 月，此后家禽中发生了 33 次疫情，报告了 21 例人间病例。这些疫情在柬埔寨的起源和动态仍不清楚。在这项工作中，我们使用了一系列生物信息学方法来分析柬埔寨病毒序列以及来自邻国的序列。自 2004 年以来，已经确定了属于 1 类和 1.1 类的 6 个 HA 谱系。1 谱系与来自泰国的病毒有共同的祖先，在 2005 年后消失，被源自越南的 2 谱系取代，然后被 3 谱系取代。高度适应的 4 谱系仅在柬埔寨出现。5 谱系自 2008 年以来一直在越南和柬埔寨流行，很可能是通过未注册的跨界家禽贸易传入柬埔寨的。6 谱系自 2010 年以来在柬埔寨流行，根据世界卫生组织/国际兽疫局/粮农组织关于 H5N1 病毒命名的标准，可将其归类为一个新的谱系。我们建议将其命名为 1.1A 谱系。2 至 6 谱系之间存在直接的亲缘关系，4 谱系和 6 谱系存在时间演变和地理分化。到 2011 年底，柬埔寨同时流行两种具有不同传播途径的谱系，即 5 谱系和 6 谱系。6 谱系仅在柬埔寨存在表明存在一种特定于该国的传播方式，而 5 谱系在柬埔寨和越南同时存在则表明受感染家禽的流通方式不同。
