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Genetic diversity in the yellow head nidovirus complex
Penaeus monodon shrimp collected from across the Indo-Pacific region during 1997–2004 were screened for the presence of yellow head-related viruses. Phylogenetic analyses of amplified ORF1b gene segments identified at least six distinct genetic lineages (genotypes). Genotype 1 (YHV) was detected onl...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Published by Elsevier Inc.
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103379/ https://www.ncbi.nlm.nih.gov/pubmed/18768192 http://dx.doi.org/10.1016/j.virol.2008.07.005 |
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author | Wijegoonawardane, Priyanjalie K.M. Cowley, Jeff A. Phan, Thuy Hodgson, Richard A.J. Nielsen, Linda Kiatpathomchai, Wansika Walker, Peter J. |
author_facet | Wijegoonawardane, Priyanjalie K.M. Cowley, Jeff A. Phan, Thuy Hodgson, Richard A.J. Nielsen, Linda Kiatpathomchai, Wansika Walker, Peter J. |
author_sort | Wijegoonawardane, Priyanjalie K.M. |
collection | PubMed |
description | Penaeus monodon shrimp collected from across the Indo-Pacific region during 1997–2004 were screened for the presence of yellow head-related viruses. Phylogenetic analyses of amplified ORF1b gene segments identified at least six distinct genetic lineages (genotypes). Genotype 1 (YHV) was detected only in shrimp with yellow head disease. Genotype 2 (GAV) was detected in diseased shrimp with the less severe condition described as mid-crop mortality syndrome and in healthy shrimp from Australia, Thailand and Vietnam. Other genotypes occurred commonly in healthy shrimp. Sequence comparisons of structural protein genes (ORF2 and ORF3), intergenic regions (IGRs) and the long 3′-UTR supported the delineation of genotypes and identified both conserved and variant structural features. In putative transcription regulating sequences (TRSs) encompassing the sub-genomic mRNA 5′-termini, a core motif (5′-GUCAAUUACAAC-3′) is absolutely conserved. A small (83 nt) open reading frame (ORF4) in the 3′-UTR of GAV is variously truncated in all other genotypes and a TRS-like element preceding ORF4 is invariably corrupted by a A > G/U substitution in the central core motif (5′-UU(G/U)CAAC-3′). The data support previous evidence that ORF4 is a non-functional gene under construction or deconstruction. The 3′-UTRs also contain predicted 3′-terminal hairpin-loop structures that are preserved in all genotypes by compensatory nucleotide substitutions, suggesting a role in polymerase recognition for minus-strand RNA synthesis. |
format | Online Article Text |
id | pubmed-7103379 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Published by Elsevier Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-71033792020-03-31 Genetic diversity in the yellow head nidovirus complex Wijegoonawardane, Priyanjalie K.M. Cowley, Jeff A. Phan, Thuy Hodgson, Richard A.J. Nielsen, Linda Kiatpathomchai, Wansika Walker, Peter J. Virology Article Penaeus monodon shrimp collected from across the Indo-Pacific region during 1997–2004 were screened for the presence of yellow head-related viruses. Phylogenetic analyses of amplified ORF1b gene segments identified at least six distinct genetic lineages (genotypes). Genotype 1 (YHV) was detected only in shrimp with yellow head disease. Genotype 2 (GAV) was detected in diseased shrimp with the less severe condition described as mid-crop mortality syndrome and in healthy shrimp from Australia, Thailand and Vietnam. Other genotypes occurred commonly in healthy shrimp. Sequence comparisons of structural protein genes (ORF2 and ORF3), intergenic regions (IGRs) and the long 3′-UTR supported the delineation of genotypes and identified both conserved and variant structural features. In putative transcription regulating sequences (TRSs) encompassing the sub-genomic mRNA 5′-termini, a core motif (5′-GUCAAUUACAAC-3′) is absolutely conserved. A small (83 nt) open reading frame (ORF4) in the 3′-UTR of GAV is variously truncated in all other genotypes and a TRS-like element preceding ORF4 is invariably corrupted by a A > G/U substitution in the central core motif (5′-UU(G/U)CAAC-3′). The data support previous evidence that ORF4 is a non-functional gene under construction or deconstruction. The 3′-UTRs also contain predicted 3′-terminal hairpin-loop structures that are preserved in all genotypes by compensatory nucleotide substitutions, suggesting a role in polymerase recognition for minus-strand RNA synthesis. Published by Elsevier Inc. 2008-10-25 2008-09-02 /pmc/articles/PMC7103379/ /pubmed/18768192 http://dx.doi.org/10.1016/j.virol.2008.07.005 Text en Crown copyright © 2008 Published by Elsevier Inc. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Wijegoonawardane, Priyanjalie K.M. Cowley, Jeff A. Phan, Thuy Hodgson, Richard A.J. Nielsen, Linda Kiatpathomchai, Wansika Walker, Peter J. Genetic diversity in the yellow head nidovirus complex |
title | Genetic diversity in the yellow head nidovirus complex |
title_full | Genetic diversity in the yellow head nidovirus complex |
title_fullStr | Genetic diversity in the yellow head nidovirus complex |
title_full_unstemmed | Genetic diversity in the yellow head nidovirus complex |
title_short | Genetic diversity in the yellow head nidovirus complex |
title_sort | genetic diversity in the yellow head nidovirus complex |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103379/ https://www.ncbi.nlm.nih.gov/pubmed/18768192 http://dx.doi.org/10.1016/j.virol.2008.07.005 |
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