Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses
Abstract Background Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. Results Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild spec...
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40168-022-01246-7 |
| _version_ | 1818274538887053312 |
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| author | Tongling Shan Shixing Yang Haoning Wang Hao Wang Ju Zhang Ga Gong Yuqing Xiao Jie Yang Xiaolong Wang Juan Lu Min Zhao Zijun Yang Xiang Lu Ziyuan Dai Yumin He Xu Chen Rui Zhou Yuxin Yao Ning Kong Jian Zeng Kalim Ullah Xiaochun Wang Quan Shen Xutao Deng Jianmin Zhang Eric Delwart Guangzhi Tong Wen Zhang |
| author_facet | Tongling Shan Shixing Yang Haoning Wang Hao Wang Ju Zhang Ga Gong Yuqing Xiao Jie Yang Xiaolong Wang Juan Lu Min Zhao Zijun Yang Xiang Lu Ziyuan Dai Yumin He Xu Chen Rui Zhou Yuxin Yao Ning Kong Jian Zeng Kalim Ullah Xiaochun Wang Quan Shen Xutao Deng Jianmin Zhang Eric Delwart Guangzhi Tong Wen Zhang |
| author_sort | Tongling Shan |
| collection | DOAJ |
| description | Abstract Background Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. Results Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). Conclusions The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract |
| first_indexed | 2024-12-12T22:15:27Z |
| format | Article |
| id | doaj.art-48801694acc646ab9369219c6d179523 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-12T22:15:27Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-48801694acc646ab9369219c6d1795232022-12-22T00:10:06ZengBMCMicrobiome2049-26182022-04-0110112110.1186/s40168-022-01246-7Virome in the cloaca of wild and breeding birds revealed a diversity of significant virusesTongling Shan0Shixing Yang1Haoning Wang2Hao Wang3Ju Zhang4Ga Gong5Yuqing Xiao6Jie Yang7Xiaolong Wang8Juan Lu9Min Zhao10Zijun Yang11Xiang Lu12Ziyuan Dai13Yumin He14Xu Chen15Rui Zhou16Yuxin Yao17Ning Kong18Jian Zeng19Kalim Ullah20Xiaochun Wang21Quan Shen22Xutao Deng23Jianmin Zhang24Eric Delwart25Guangzhi Tong26Wen Zhang27Shanghai Veterinary Research Institute, Chinese Academy of Agricultural SciencesSchool of Medicine, Jiangsu UniversitySchool of Geography and Tourism, Harbin UniversityDepartment of Clinical Laboratory, The Affiliated Huai’an Hospital of Xuzhou Medical UniversitySchool of Medicine, Jiangsu UniversityAnimal Science College, Tibet Agriculture and Animal Husbandry UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversityWildlife and Protected Area College/Center of Conservation Medicine and Ecological Safety Northeast Forestry UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversityShanghai Veterinary Research Institute, Chinese Academy of Agricultural SciencesSchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversitySchool of Medicine, Jiangsu UniversityVitalant Research InstituteCollege of Veterinary Medicine, South China Agricultural UniversityVitalant Research InstituteShanghai Veterinary Research Institute, Chinese Academy of Agricultural SciencesSchool of Medicine, Jiangsu UniversityAbstract Background Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. Results Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). Conclusions The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstracthttps://doi.org/10.1186/s40168-022-01246-7Wild birdViromeRecombinantComplete genomePhylogenetic analysisCross-species infection |
| spellingShingle | Tongling Shan Shixing Yang Haoning Wang Hao Wang Ju Zhang Ga Gong Yuqing Xiao Jie Yang Xiaolong Wang Juan Lu Min Zhao Zijun Yang Xiang Lu Ziyuan Dai Yumin He Xu Chen Rui Zhou Yuxin Yao Ning Kong Jian Zeng Kalim Ullah Xiaochun Wang Quan Shen Xutao Deng Jianmin Zhang Eric Delwart Guangzhi Tong Wen Zhang Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses Microbiome Wild bird Virome Recombinant Complete genome Phylogenetic analysis Cross-species infection |
| title | Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses |
| title_full | Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses |
| title_fullStr | Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses |
| title_full_unstemmed | Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses |
| title_short | Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses |
| title_sort | virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses |
| topic | Wild bird Virome Recombinant Complete genome Phylogenetic analysis Cross-species infection |
| url | https://doi.org/10.1186/s40168-022-01246-7 |
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