Genomic characterization of a novel picornavirus in Pekin ducks

A novel picornavirus was detected from Pekin ducks (Anas platyrhynchos domestica) and completely sequenced. The virus was most closely related to megriviruses, with amino acid identities of 32-68%, 35-45%, 51-57%, 41-50%, and 61-63% in the P1, P2, P3, polyprotein, and 2C and 3CD regions, respectively. The virus was thus identified as an additional species in the genus Megrivirus and named Duck megrivirus (DMV). Sequence analyses indicated that the DMV genome possessed a megrivirus-like organization and also exhibited several unique features. The polyadenylated genome comprised 9700nt, one of the largest among known picornaviruses. A notable feature was the 2A region, which had an association of two distinct, function-unknown 2As (2A1 and 2A2) and a parechovirus-like 2A3. The 5' untranslated region (UTR) contained a variant type IVB internal ribosome entry site (IRES), which possessed a long helix III4 ending with the "8"-like 20-nt-long conserved structure at the top of domain III. The secondary structure model of inferred domain III of DMV-like IRES was also conserved in quail picornavirus, pigeon picornavirus B, and megriviruses. Domain II in DMV contained the conserved internal and apical loops previously identified in groups A and C of hepacivirus/pestivirus like IRESs. Moreover, DMV was closely related to different megriviruses in different genomic regions. These findings suggest that recombination events involving exchange of coding and noncoding regions may have occurred. DMV was detected in 28 of 117 (23.9%) ducks from four provinces in China, suggesting a high prevalence of DMV in duck populations.