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First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India.

ABSTRACT: This is the first report of a Papaya ringspot virus (PRSV) isolate from the northeastern region of India. The nucleotide sequence identity of PRSV-Meghalaya was in the range of 72.6 to 82.5% with other Indian PRSV isolates, and the highest identity of 84.4% was with a French isolate. Population genetic analysis indicated positive selection.

SUBMITTER: Mishra R

PROVIDER: S-EPMC5981033 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India.

Mishra Ritesh R Patil Basavaprabhu L BL

Genome announcements 20180531 22

This is the first report of a <i>Papaya ringspot virus</i> (PRSV) isolate from the northeastern region of India. The nucleotide sequence identity of PRSV-Meghalaya was in the range of 72.6 to 82.5% with other Indian PRSV isolates, and the highest identity of 84.4% was with a French isolate. Population genetic analysis indicated positive selection. ...[more]

PMID: 29853500

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Project description:OBJECTIVE:Chicken 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. METHODS:Total 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. RESULTS:The 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

First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India.

Publications

First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India.

Similar Datasets

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