Abstract
Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.
Highlights
The last decades have witnessed a broadening of the global diversity of viruses thanks to rapidly evolving random amplification sequencing technology
Amino acid sequence identity of capsid protein (ORF2) varied from 35% to 93% within the genus Avastrovirus, but we found lower identities when we compared these four novel genomes to one another (24–29%), or when we compared them to other avastroviruses (15–36%)
An ORF1b and ORF2 amino acid distance matrix analysis generated with heatmaps confirmed the clear demarcation between passerine avastroviruses and relatives of other Avastrovirus genus (Fig. 1)
Summary
The last decades have witnessed a broadening of the global diversity of viruses thanks to rapidly evolving random amplification sequencing technology. Given that zoonotic viruses are considered the most probable causative agents of emerging diseases[3] and that mammal and avian species are their main hosts[4,5], the study of the wildlife viral diversity and their ecological context in these remote areas will provide important information for public and animal health to prevent potential new emerging viral epidemics[2,6]. There is growing evidence that the risk of pathogen transfer is increasing in both directions[9,10,11], and a comprehensive characterization of the virome of the local fauna may be instrumental in preventing any harmful impact This important knowledge would hardly become available without exploratory approaches, which address the discovery and describe the diversity of viruses that affect non-model host species. Astroviruses are important for public and environmental health as a causative agent of encephalitis in cattle[25]
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