Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV)

•Additional sequences revealed that IMNV genome has at least 8226bp and not 7561bp.•These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.•A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.•The hypervariable...

Full description

Saved in:
Bibliographic Details
Published in:Virus research 2015-05, Vol.203, p.66-71
Main Authors: Dantas, Márcia Danielle A., Chavante, Suely F., Teixeira, Dárlio Inácio A., Lima, João Paulo M.S., Lanza, Daniel C.F.
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Brazil
Cluster Analysis
Decapoda
dsRNA virus
Gene Order
Genome, Viral
Hypervariable region
IMNV Brazil
IRES
Molecular Sequence Data
Nucleic Acid Conformation
Open Reading Frames
Penaeidae - virology
Phylogeny
Protein Biosynthesis
RNA, Viral - genetics
Sequence Analysis, DNA
Sequence Homology
Shrimp diseases
Totiviridae - classification
Totiviridae - genetics
Totiviridae - isolation & purification
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:•Additional sequences revealed that IMNV genome has at least 8226bp and not 7561bp.•These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.•A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.•The hypervariable region coincides with the region that encodes virion protrusions. Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643bp and 22bp, at 5′ and 3′ ends of IMNV genome respectively, confirming that its actual size is at least 8226bp long. Considering these additional sequences in genome extremities, ORF1 can starts at nt 470, encoding a 1708 aa polyprotein. Computational predictions reveal two stem loops and two pseudoknots in the 5′ end and a putative stem loop and a slippery motif located at 3′ end, indicating that these regions can be involved in the start and termination of translation. Through a careful phylogenetic analysis, a higher genetic variability among Brazilian isolates could be observed, comparing with Indonesian IMNV isolates. It was also observed that the most variable region of IMNV genome is located in the first half of ORF1, coinciding with a region which probably encodes the capsid protrusions. The results presented here are a starting point to elucidate the viral's translational regulation and the mechanisms involved in virulence.
ISSN:0168-1702
1872-7492
DOI:10.1016/j.virusres.2015.03.015