The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3

Abstract

Avian nephritis virus (ANV) is classified in the <i>Avastroviridae</i> family with disease associations with nephritis, uneven flock growth and runting stunting syndrome (RSS) in chicken and turkey flocks, and other avian species. The whole genome of ANV genotype 3 (ANV-3) of 6959 nucleotides including the untranslated 5' and 3' regions and polyadenylated tail was detected in a metagenomic virome investigation of RSS-affected chicken broiler flocks. This report characterises the ANV-3 genome, identifying partially overlapping open reading frames (ORFs), ORF1a and ORF1b, and an opposing secondary pseudoknot prior to a ribosomal frameshift stemloop structure, with a separate ORF2, whilst observing conserved astrovirus motifs. Phylogenetic analysis of the <i>Avastroviridae</i> whole genome and ORF2 capsid polyprotein classified the first complete whole genome of ANV-3 within <i>Avastroviridae</i> genogroup 2.