Dataset Information

Complete Genome Sequence of a Class I Newcastle Disease Virus Strain Isolate from a Breeding Chicken Flock in Sichuan, China.

ABSTRACT: A Newcastle disease virus (NDV) strain, APMV-1/Chicken/China(SC)/PT3/2016, was isolated from asymptomatic chickens at a breeding farm in China. The PT3 strain has a genome length of 15,198 nucleotides and is classified as subgenotype 1b of class I. Pathogenicity tests demonstrated that PT3 is a lentogenic strain.

SUBMITTER: Li SY

PROVIDER: S-EPMC6498238 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Complete Genome Sequence of a Class I Newcastle Disease Virus Strain Isolate from a Breeding Chicken Flock in Sichuan, China.

Li Shu-Yun SY You Guo-Jin GJ Du Li-Jing LJ Li Wen-Wen WW Liu Yue-Yue YY Du Ji-Teng JT Xia Jing J Huang Yong Y

Microbiology resource announcements 20190502 18

A Newcastle disease virus (NDV) strain, APMV-1/Chicken/China(SC)/PT3/2016, was isolated from asymptomatic chickens at a breeding farm in China. The PT3 strain has a genome length of 15,198 nucleotides and is classified as subgenotype 1b of class I. Pathogenicity tests demonstrated that PT3 is a lentogenic strain. ...[more]

PMID: 31048383

Similar Datasets

Project description:ObjectiveChicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and "white chicks" condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens.MethodsTotal RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein.ResultsThe consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5'-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3'-UTR which harboured two corona virus stem loop II like "s2m" motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74-98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.

Dataset Information

Complete Genome Sequence of a Class I Newcastle Disease Virus Strain Isolate from a Breeding Chicken Flock in Sichuan, China.

Publications

Complete Genome Sequence of a Class I Newcastle Disease Virus Strain Isolate from a Breeding Chicken Flock in Sichuan, China.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets