Identification and genome characterization of a novel picornavirus from ducks in China

The Multi-Kingdom Microbiome of Wintering Migratory Birds in Poyang Lake, China

Wild birds are a natural reservoir for zoonotic viruses. To clarify the role of migratory birds in viruses spread in Poyang Lake, we investigated the microbiome of 250 wild bird samples from 19 species in seven orders. The bacterial and viral content abundance and diversity were preliminarily evaluated by Kraken2 and Bracken. After de novo assembly by Megahit and Vamb, viral contigs were identified by CheckV. The reads remapped to viral contigs were quantified using Bowtie2. The bacterial microbiome composition of the samples covers 1526 genera belonging to 175 bacterial orders, while the composition of viruses covers 214 species belonging to 22 viral families. Several taxonomic biomarkers associated with avian carnivory, oral sampling, and raptor migration were identified. Additionally, 17 complete viral genomes belonging to Astroviridae, Caliciviridae, Dicistroviridae, Picornaviridae, and Tombusviridae were characterized, and their phylogenetic relationships were analyzed. This pioneering metagenomic study of migratory birds in Poyang Lake, China illuminates the diverse microbial landscape within these birds. It identifies potential pathogens, and uncovers taxonomic biomarkers relevant to varied bird habitats, feeding habits, ecological classifications, and sample types, underscoring the public health risks associated with wintering migratory birds.

Isolation and complete genome analysis of a novel duck picornavirus in China

A novel duck picornavirus, designated as duck/AH15/CHN/2015, was isolated and identified from Cherry Valley ducks with short beak and dwarfism syndrome in 2015 in Anhui province of China. Duck/AH15/CHN/2015 has the highest degree of amino acid sequence identity (approximately 43 %) with duck hepatitis A viruses (DHAV) Complete genome analysis revealed that duck/AH15/CHN/2015 possesses a typical picornavirus-like genomic organization, 5' UTR-L-P1 (VP0-VP3-VP1)-P2 (2A1-2A2- 2B-2C)-P3 (3A-3B-3C-3D)-3'UTR-poly (A). The 5'UTR contains a potential type IV internal ribosome entry site, while a conserved "barbell"-like structure is found at the 3'UTR, which is similar to DHAV. Compared to the closest related DHAVs, two unrelated 2A proteins were predicted in duck/AH15/CHN/2015, while three unrelated 2A proteins were presented in DHAVs. Based on the amino acid identity comparison and phylogenetic analysis of P1, 2C, and 3CD (3C and 3D), duck/AH15/CHN/2015 was closely related to but distinct from DHAVs, and it was proposed to be a member of a novel species in the genus Avihepatovirus of the family Picornaviridae.