Genome characterization and evolutionary analysis of a novel Anativirus from a wild Muscovy duck in Guangdong, China

A novel member of the genus Anativirus was identified and characterized from a naturally deceased wild Muscovy duck (Cairina moschata) collected in Maoming, Guangdong Province, China. This strain, provisionally designated Anativirus GD2411, was detected through metagenomic next-generation sequencing (mNGS), which yielded a complete genome of 8,085 nucleotides. The genome comprises a single open reading frame (nt 413-7,873) encoding the canonical picornaviral polyprotein, flanked by a 5' untranslated region (UTR; 412 nt) and a 3' UTR (209 nt) with a poly(A) tail. Whole-genome nucleotide identity analysis revealed that GD2411 clustered with duck-origin strains, sharing 88.0% identity with CH01 and 81.2% with TW90, but only 50.6% with the chicken-derived strain CHK1. High amino acid conservation was observed across functional regions, particularly in 2C (≥91.9%), 3C (≥92.4%), and 3D (≥97.0%), reflecting the preservation of RNA-dependent RNA polymerase function. Phylogenetic analyses based on complete genomes and 3D protein sequences using maximum likelihood methods consistently placed GD2411 within the duck Anativirus clade, indicating a close evolutionary relationship with TW90 and CH01. Although an experimental infection model was not established, PCR screening revealed broad gastrointestinal distribution of the virus, with the highest viral load detected in the cecum, suggesting fecal-oral transmission as a primary route. These findings provide preliminary evidence of Anativirus infection in wild Muscovy ducks in southern China, though the limited sample size precludes definitive conclusions regarding host range expansion. The highly conserved 3D region is highlighted as a potential target for antiviral therapy or vaccine development.