Whole genome characterization of an avian calicivirus from broiler chicken farms in Iran: First report

Abstract

Abstract Caliciviruses are (+) RNA viruses with a worldwide distribution and wide host range, including humans and birds. The family caliciviridae consists of eleven genera, two of which, bavovirus and nacovirus, are found in chickens affected by stunting syndrome. In this study, for the first time the presence of calicivirus in Iranian broiler flocks was investigated by viral metagenomics method. Fecal samples were collected from broiler chicken farms affected with diarrhea from Gilan province Iran. Our results showed that some of the diseased chickens carried a genus of calicivirus belonging to bavovirus. The complete 7824 nt genome of this bavovirus, named UT Shahhosseini1 2018, was sequenced and characterized. Phylogenetic analysis revealed that our calicivirus shared 87% similarity to the closest strains, including the German calicivirus chicken/V0021/Bayern/2004, suggesting that the avian- derived strain belongs to the bavoviruses. Conserved motifs shared between bavoviruses further confirmed this finding. Phylogenetic analysis of nonstructural (NS) and VP proteins also revealed similar values. This is the first report and first complete genome sequence of bavovirus in Iran. However, further studies are needed to obtain a better epidemiological picture of the abundance avian-origin caliciviruses of in Iranian bird populations, including poultry. The pathogenic potential of these caliciviruses to affect poultry production should also be investigated.