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 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.

Virome of Giant Panda-Infesting Ticks Reveals Novel Bunyaviruses and Other Viruses That Are Genetically Close to Those from Giant Pandas

“…5 ). At an amino acid level, the Reps of 15 tick-associated CRESS-DNA viruses showed homology to that of the sequences from giant pandas, red pandas, wild birds, or mosquitoes sampled adjacent to this study ( 11 , 28 , 33 ). For example, within the circovirus group the Reps of two Sichuan tick-associated circoviruses (STaCV-1, strain Tick114CircoC2 and STaCV-2, strain Tick094CircoC5) were most closely related to that of a circovirus (GenBank no.…”

Metatranscriptomic Comparison of Viromes in Endemic and Introduced Passerines in New Zealand

“…In Europe they have a high prevalence of arboviruses, commonly acting as amplifying hosts [ 18 , 19 ], while in North America they have played an important role in the establishment and spread of the West Nile virus [ 20 ]. However, the virome of wild passerines has received little research attention, with the first metagenomic analysis published in 2019 and 2020 from samples collected in French Guiana and Spain [ 21 , 22 , 23 ], followed by a study from China in 2022 [ 24 ]. Multiple highly divergent viruses were identified in these studies, including new groups of avastroviruses and a highly divergent gyrovirus.…”

Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand

“…In Europe they have a high prevalence of arboviruses, commonly acting as amplifying hosts [16,17], while in North America they have played an important role in the establishment and spread of West Nile virus [18]. However, the virome of wild passerines has received little research attention, with the first metagenomic analysis published in 2019 and 2020 from samples collected in French Guiana and Spain [19-21], followed by a study from China in 2022 [22]. Multiple highly divergent viruses were identified in these studies, including new groups of avastroviruses and a highly divergent gyrovirus.…”

“…followed by a study from China in 2022 [22]. Multiple highly divergent viruses were identified in these studies, including new groups of avastroviruses and a highly divergent gyrovirus.…”