Identification and Genome Characterization of the First Sicinivirus Isolate from Chickens in Mainland China by Using Viral Metagenomics

Abstract

Unlike traditional virus isolation and sequencing approaches, sequence-independent amplification based viral metagenomics technique allows one to discover unexpected or novel viruses efficiently while bypassing culturing step. Here we report the discovery of the first Sicinivirus isolate (designated as strain JSY) of picornaviruses from commercial layer chickens in mainland China by using a viral metagenomics technique. This Sicinivirus isolate, which contains a whole genome of 9,797 nucleotides (nt) excluding the poly(A) tail, possesses one of the largest picornavirus genome so far reported, but only shares 88.83% and 82.78% of amino acid sequence identity to that of ChPV1 100C (KF979332) and Sicinivirus 1 strain UCC001 (NC_023861), respectively. The complete 939 nt 5′UTR of the isolate strain contains at least twelve stem-loop domains (A–L), representing the highest set of loops reported within Sicinivirus genus. The conserved 'barbell-like' structure was also present in the 272 nt 3′UTR of the isolate as that in the 3′ UTR of Sicinivirus 1 strain UCC001. The 8,586 nt large open reading frame encodes a 2,862 amino acids polyprotein precursor. Moreover, Sicinivirus infection might be widely present in commercial chicken farms in Yancheng region of the Jiangsu Province as evidenced by all the tested stool samples from three different farms being positive (17/17) for Sicinivirus detection. This is the first report on identification of Sicinivirus in commercial layer chickens with a severe clinical disease in mainland China, however, further studies are needed to evaluate the pathogenic potential of this picornavirus in chickens.

A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds

“…Previous metagenomic studies into the avian gut microbiome have identified multiple picornavirus species in disease-affected and healthy birds, findings which have been echoed in the present study. However, the pathogenic potential of these viruses in avian species remains relatively unknown due to the large amount of genetic variation observed among these viruses Farkas et al, 2012;Bullman et al, 2014;Zhou et al, 2015). In the present study picornaviruses were commonly found alongside the Astroviridae, Caliciviridae, Parvoviridae, and bacteriophage families (Table 1) and seem to be prevalent in growth-stunted birds.…”

“…Within these genera, viral contigs showed similarity to multiple species such as chicken gallivirus 1 (Gallivirus), aichivirus C (Kobuvirus), and chicken megrivirus (Megrivirus). A total of 217 contigs characterized as unclassified Picornaviridae showed similarity to the species sicinivirus 1, a novel picornavirus isolated from commercial broiler chickens in Cork, Ireland (Bullman et al, 2014) and recently reported in mainland China (Zhou et al, 2015). Sicinivirus 1 contigs were almost exclusively associated with RSS-affected samples with only one sicinivirus 1 contig associated with unaffected sample VF14-181 A1.…”

A decade of RNA virus metagenomics is (not) enough

“…Bats have been used to put an upper limitin the hundreds of thousands − of the total number of eukaryotic viruses that remain to be discovered (Anthony et al, 2013). Other insect and arthropod aggregators such as spiders and birds have also yielded many new RNA virus species (Debat, 2017;Ducatez and Guérin, 2015;Shean et al, 2017;Zhou et al, 2015).…”

Near-Complete Genome Sequences of Five Siciniviruses from North America

“…The family comprises 47 genera, with 13 of these identified from avian species ( 1 – 3 ). Avian picornaviruses of the Sicinivirus genus have been identified in both healthy and diseased chickens, and the viruses’ role in disease remains unclear ( 4 – 9 ). Here, we report the sequences of five near-complete genomes of sicinivirus from North America.…”