Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

• Published in: Microbiome 2022-04, Vol.10 (1), p.60-21, Article 60
• Main Authors: Shan, Tongling, Yang, Shixing, Wang, Haoning, Wang, Hao, Zhang, Ju, Gong, Ga, Xiao, Yuqing, Yang, Jie, Wang, Xiaolong, Lu, Juan, Zhao, Min, Yang, Zijun, Lu, Xiang, Dai, Ziyuan, He, Yumin, Chen, Xu, Zhou, Rui, Yao, Yuxin, Kong, Ning, Zeng, Jian, Ullah, Kalim, Wang, Xiaochun, Shen, Quan, Deng, Xutao, Zhang, Jianmin, Delwart, Eric, Tong, Guangzhi, Zhang, Wen
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Animals; Animals, Wild; Bioinformatics; Birds; Breeding; Cloaca; Complete genome; Coronaviruses; Cross-species infection; Domestic animals; Encephalitis; Ethics; Etiology; Foot & mouth disease; Gene mapping; Genomes; Influenza; Laboratories; Metagenomics; Next-generation sequencing; Parvoviruses; Pathogens; Phylogenetic analysis; Phylogeny; Proteins; Recombinant; Recombination; RNA viruses; RNA Viruses - genetics; Severe acute respiratory syndrome coronavirus 2; Software; Species; Taxonomy; Virome; Virome - genetics; Viruses; Viruses - genetics; West Nile virus; Wild bird; Wildlife; Zoonoses
• ISSN: 2049-2618; 2049-2618
• DOI: 10.1186/s40168-022-01246-7

Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. 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). The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.