The close interactions of dogs (Canis lupus familiaris) with humans and surrounding wildlife provide frequent opportunities for cross-species virus transmissions. The co-existence of multiple types of viruses in the reservoir accelerate viral variations. For effective prediction and prevention of future potential viral epidemic or pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505,203,006 valid reads, 150 bp in length) were generated of which 46,832,838 reads were de novo assembled into 325,339contigswhichwere best matched with viral proteins available in the NCBI database. In the aggregate, 9834 contigs were confirmed for virus species, accounting for about 3.02% of the total number of contigs. For all the unique contigs, the top 30 ones with the most reads abundance were assigned to DNA virus families Circoviridae, Parvoviridae and Herpesviridae, and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous dog virome sequences were homologous to the animal virus of the Astroviridae, Coronaviridae, Circoviridae families, etc.; and phages of the Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae families and unclassified phages. Further, several dog virome sequences had homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. These results highlight the high frequency of virus detection possible in extensively contacted animal species and provide viral genomes for further disease-association studies, which is meaningful both for the epidemiological and biological elucidation of companion animals and public health.

中文翻译：

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家犬肠道病毒宏基因组分析捕捉病毒多样性和冠状病毒潜在风险的快照

狗（犬类狼疮）与人类和周围野生动物的密切互动为跨物种病毒传播提供了频繁的机会。水库中多种病毒的共存加速了病毒变异。为了有效预测和预防未来潜在的病毒流行或大流行，采用宏基因组学方法调查了45只与人类有广泛接触的家养健康犬的肠道病毒状态。总共生成了 248.6 GB 数据（505,203,006 个有效读数，长度为 150 bp），其中 46,832,838 个读数从头组装成 325,339 个重叠群，与 NCBI 数据库中可用的病毒蛋白最匹配。共确认病毒种属9834个contigs，约占contigs总数的3.02%。对于所有独特的重叠群，读取丰度最高的前 30 个分别分配给 DNA 病毒科圆环病毒科、细小病毒科和疱疹病毒科，以及 RNA 病毒科星状病毒科、冠状病毒科和小核糖核酸病毒科。许多狗病毒组序列与星状病毒科、冠状病毒科、圆环病毒科等动物病毒同源；和微病毒科、虹吸病毒科、阿克曼病毒科、Podoviridae、Myoviridae 家族的噬菌体和未分类的噬菌体。此外，几个狗病毒组序列与昆虫和植物病毒同源，这反映了狗的饮食和栖息地。值得注意的是，犬冠状病毒在所有高丰度样本中都是唯一鉴定的，因此系统发育分析显示与人冠状病毒株 229E 和 NL63 密切相关，通过获得跨物种传播能力，表明犬冠状病毒感染人类的​​潜在风险。这些结果突出了在广泛接触的动物物种中可能进行的高频率病毒检测，并为进一步的疾病关联研究提供了病毒基因组，这对于伴侣动物的流行病学和生物学阐明以及公共卫生都具有重要意义。