Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria, 3220, Australia.
Deakin University, Geelong, Victoria, 3220, Australia.
Sci Rep. 2018 Jun 6;8(1):8686. doi: 10.1038/s41598-018-26851-1.
We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the "ribosomal activity microbiome"; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.
我们提出了一种优化的宏基因组学方法，用于检测和描述所有类型的病毒，包括单链和双链 DNA/RNA 以及包膜和非包膜病毒。初步评估包括加标和未加标鸟类粪便样本以及未加标人类粪便样本。从未加标鸟类样本（澳大利亚麝香鸭和太平洋黑鸭）中，我们检测到了 21 种病毒，并且还总结了在人类粪便样本中检测到的几种病毒。然后，我们对在禽类样本中检测到的一些与已知病毒有些相似、具有高质量（Q20 或更高）和大量下一代测序reads、并且从病毒学角度来看具有一定兴趣的病毒序列进行了详细分析，例如，禽冠状病毒和禽副黏病毒 6。其中一些病毒与已知病毒密切相关，而其他病毒与目前已知/测序的病毒的相似度较低，为 70%或更低。除了检测病毒外，该技术还可以对宿主线粒体 DNA 进行特征描述，从而识别宿主物种，而核糖体 RNA 序列则提供了对“核糖体活性微生物组”的了解；肠道寄生虫；以及所吃的食物，如植物或昆虫，我们将这些与非禽类宿主相关的病毒联系起来。
