Genome sequence of a Sobemovirus from the feces of Northern Pintail (Anas acuta)

Abstract

Northern pintail (Anas acuta) is a migratory waterfowl that can transmit various viruses. The genome sequence of a Sobemovirus was determined using metagenomic sequencing from the feces of northern pintail (Anas acuta) in Xinjiang, northwest China. The virus possesses a linear RNA molecule of 4177 bp and is most closely related to isolates SoMV-WA (GenBank accession no. HM163159.1) and ATCC PV-109 (GenBank accession no. GQ845002.2), with a nucleotide identity of 86.7%. The virus encodes four open reading frames (ORF) coding for four proteins, and phylogenetic analysis of capsid protein and RNA-dependent RNA polymerase (RdRp) showed that the strain was clustered into the species Sowbane Mosaic Virus (SoMV). The amino acid sequence identity of capsid protein was 89.6-90.9% to other isolates of SoMV, but 17.6-31.4% similar to other strains in the genus Sobemovirus, indicating a strain of Sowbane Mosaic Virus. This is the first report of SoMV in the feces of wild birds and in China, and it suggested that northern pintail likely plays an alternative role in the transmission of SoMV.

Keywords: Genomic comparison; Phylogenetic analysis; Sobemovirus; Wild duck.