Prevalence and diversity of avian influenza viruses in environmental reservoirs
Prevalence and diversity of avian influenza viruses in environmental reservoirs
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DOI：
10.1099/vir.0.83369-0
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发表时间：
2008-02-01
影响因子：
3.8
通讯作者：
Runstadler, Jonathan A.
中科院分区：
文献类型：
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作者：
Lang, Andrew S.;Kelly, Anke;Runstadler, Jonathan A.
人们对禽流感在自然环境中的生态和进化知之甚少，尽管这些因素如何影响传播的可能性。大多数工作都集中在鉴定从水禽等宿主分离的病毒，也有几个从水和冰等非生物来源分离和检测的例子。我们使用RT-PCR扩增和鉴定了水禽大量使用的池塘沉积物中存在的流感病毒序列。流感病毒检出率较高(50%)。通过对部分血凝素(HA)基因进行测序，对存在的病毒进行了表征，结果表明，这些沉积物中存在着不同的病毒集合。我们从11个样本中对117个部分HA基因克隆进行了测序，并检测到四种不同的HA亚型(H3、H8、H11和H12)，其中约65%的克隆序列是唯一的。这种与培养无关的方法还能够检测到同一年在同一地理区域的禽类抽样中没有发现的一种病毒亚型。在冬季池塘结冰时很容易检测到病毒，这表明这些沉积物可能每年都会储存病毒，利用池塘感染禽类，尽管我们尚未证明这些病毒是可行的。我们证明，这种方法是评估环境中存在的病毒的流行率和多样性的一种可行和有价值的方法，并可以作为更困难的病毒培养的有价值的补充，试图了解流感病毒的生态。
Little is known about the ecology and evolution of avian influenza in the natural environment, despite how these affect the potential for transmission. Most work has focused on characterizing viruses isolated from hosts such as waterfowl, and there have also been several instances of isolation and detection from abiotic sources such as water and ice. We used RT-PCR to amplify and characterize the influenza virus sequences present in sediments of ponds that are used heavily by waterfowl. The detection rate of influenza virus was high (> 50 %). Characterization of the viruses present by sequencing part of the haemagglutinin (HA) gene showed that there is a diverse collection of viruses in these sediments. We sequenced 117 partial HA gene clones from 11 samples and detected four different HA subtypes (H3, H8, H11 and H12), with approximately 65% of clone sequences being unique. This culture-independent approach was also able to detect a virus subtype that was not found by sampling of birds in the same geographical region in the same year. Viruses were detected readily in the winter when the ponds were frozen, indicating that these sediments could be a year-to-year reservoir of viruses to infect birds using the ponds, although we have not shown that these viruses are viable. We demonstrate that this approach is a feasible and valuable way to assess the prevalence and diversity of viruses present in the environment, and can be a valuable complement to more difficult viral culturing in attempting to understand the ecology of influenza viruses.