| The novel coronavirus pneumonia pandemic has brought a huge impact on global public health and posed a serious threat to human life and safety.The outbreak of COVID-19 has once again raised concerns about emerging viral infections,and the novel Coronavirus research has found that it may be of wild animal origin.Examples of pathogens being carried and transmitted by wild animals are often reported,with wild birds thought to be natural reservoirs of the virus.Wild birds are found all over the globe,and these animals with large amounts of biomass move around the globe in their annual migration cycles,creating a truly interconnected planet.In addition to wild birds,poultry raised and eaten by humans may be important amplifiers of potentially zoonotic avian influenza viruses such as influenza A.Despite our important relationship with birds,our understanding of the diversity of avian viruses is limited.As wildlife is often associated with important human diseases,it is crucial to identify existing or potential pathogens in these species.In the last two decades,metagenomics,based on high-throughput and low-cost second-generation sequencing technologies,has enabled a quantum leap in virus discovery,not only to trace the origin of a particular epidemic,but also to assess the risk of the most likely source of the disease.In order to understand the diversity and abundance of viral communities in the intestinal tract of wild birds in China,and to explore the dark matter of DNA viruses and analyze their genetic evolution,we conducted a systematic metagenomic analysis of 3,404 cloaca samples from more than 90 species of birds collected from nature reserves,zoos,parks and farms in Heilongjiang,Jiangsu,Zhejiang,Jilin and Hunan provinces of China.The main contents and conclusions of this study are as follows:1.Community analysis of enterovirus in wild birdsA total of 1,518 viruses were detected in the intestinal tract of wild birds,belonging to 157 genera,36 families,26 orders,19 classes,10 phyla,5 kingdoms and4 domains.Riboviria and Monodnaviria viruses accounted for 65.07% and 34.29% of all sequences,respectively,Dicistroviridae,Picornaviridae and Iflaviridae belong to Picornavirales account for a relatively high proportion of the former.The latter were dominated by the families of Parvoviridae and Genomoviridae.Parvoviridae,Dicistroviridae and Picornaviridae were detected in the six groups of birds,including natatores,songbird,scansorial bird,bird of prey,wading bird and cursorial birds,with high abundance.At the species level,nearly half of the viruses can coexist in the intestinal tract of two or more groups of birds.When it comes to the1,146 viruses present in the songbird group,we found that 58.81% of the viruses infect more than one family of birds.At the level of genus and family classification,20 genera and 18 families were shared in the gut of six groups of birds,respectively,suggesting that birds may be the key hosts of these families and genera,and these widespread core viral communities may play an important role in maintaining the stability and function of avian enterovirus communities.2.DNA virus dark matter mining:Through metagenomic sequence analysis,170 parvo-associated viruses belonging to Cossaviricota and 323 circular viruses belonging to Cressdnaviricota were found in the intestinal tract of birds.According to genome structure analysis,phylogenetic analysis and sequence similarity analysis,five of the 170 new parvo-associated viruses were identified as Parvovirinae and 70 were identified as Densovirinae,28 belonged to Hamaparvovirinae,31 belonged to Parvo-like viruses,17 belonged to unclassified Parvoviridae sp.and 19 belonged to Bidnaviridae,which originated from parvoviruses.Eleven of the 323 new circular viruses unearthed belonged to the Circoviridae family,seven belonged to the family Smavoviridae,168 belonged to the family Genomoviridae,and 137 belonged to the unclassified CRESS DNA viruses. |
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