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.
Highlights
Birds are well known as an important reservoir for emerging pathogens [1], as the limitation of traditional virus isolation and sequencing approaches, it is difficult to find unexpected or unknown viruses
Four pairs of primers were used to perform conventional PCR/reverse transcriptase (RT)-PCR detection, and the results showed that all the samples were negative for infectious bursal disease virus (IBDV) [19], infectious bronchitis virus (IBV) [20], avian encephalomyelitis virus (AEV) [21] and chicken anaemia virus (CAV) [22]
The viral polyprotein of the Sicinivirus isolate only had 88.83% and 82.78% of amino acid sequence identity to that of ChPV1 100C and Sicinivirus 1 strain UCC001, respectively
Summary
Birds are well known as an important reservoir for emerging pathogens [1], as the limitation of traditional virus isolation and sequencing approaches, it is difficult to find unexpected or unknown viruses. Many new avian picornavirus species such as Melegrivirus A [3], Gallivirus A [4], Avisivirus A [5], and the recently accepted genera Sicinivirus [6] have been identified by metagenomic techniques. The family Picornaviridae belongs to the order Picornavirales and is composed of 29 genera, including three new accepted genera Kunsagivirus, Sakobuvirus and Sicinivirus Among these genera, the first member of Sicinivirus was identified and genetically characterized from commercial broiler chickens in Ireland [6]. The order of the encoded polyprotein precursor is L, VP0, VP3, VP1, 2A, 2B, 2C, 3A, 3B, 3C, and 3D, except canine picodicistrovirus (CPDV) of Dicipivirus genera that encode two polyprotein precursors, and possibly Megriviruses which contains a potential second open reading frame (ORF) at the 30 part of the genome [8,9]
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