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Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)

BACKGROUND: The identification of new virus strains is important for the study of infectious disease, but current (or existing) molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of un...

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Detalles Bibliográficos
Autores principales: Hu, Tingsong, Zheng, Ying, Zhang, Yan, Li, Gangshan, Qiu, Wei, Yu, Jing, Cui, Qinghua, Wang, Yiyin, Zhang, Chaoxiong, Zhou, Xiaofang, Feng, Ziliang, Zhou, Weiguo, Fan, Quanshui, Zhang, Fuqiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547691/
https://www.ncbi.nlm.nih.gov/pubmed/23268691
http://dx.doi.org/10.1186/1471-2180-12-305
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author Hu, Tingsong
Zheng, Ying
Zhang, Yan
Li, Gangshan
Qiu, Wei
Yu, Jing
Cui, Qinghua
Wang, Yiyin
Zhang, Chaoxiong
Zhou, Xiaofang
Feng, Ziliang
Zhou, Weiguo
Fan, Quanshui
Zhang, Fuqiang
author_facet Hu, Tingsong
Zheng, Ying
Zhang, Yan
Li, Gangshan
Qiu, Wei
Yu, Jing
Cui, Qinghua
Wang, Yiyin
Zhang, Chaoxiong
Zhou, Xiaofang
Feng, Ziliang
Zhou, Weiguo
Fan, Quanshui
Zhang, Fuqiang
author_sort Hu, Tingsong
collection PubMed
description BACKGROUND: The identification of new virus strains is important for the study of infectious disease, but current (or existing) molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of unknown viruses based on the cDNA - random amplified polymorphic DNA (cDNA-RAPD) technique. Getah virus, belonging to the family Togaviridae in the genus Alphavirus, is a mosquito-borne enveloped RNA virus that was identified using the Virus-Discovery-cDNA RAPD (VIDISCR) method. RESULTS: A novel Getah virus was identified by VIDISCR from suckling mice exposed to mosquitoes (Aedes albopictus) collected in Yunnan Province, China. The non-structural protein gene, nsP3, the structural protein gene, the capsid protein gene, and the 3'-untranslated region (UTR) of the novel Getah virus isolate were cloned and sequenced. Nucleotide sequence identities of each gene were determined to be 97.1–99.3%, 94.9–99.4%, and 93.6–99.9%, respectively, when compared with the genomes of 10 other representative strains of Getah virus. CONCLUSIONS: The VIDISCR method was able to identify known virus isolates and a novel isolate of Getah virus from infected mice. Phylogenetic analysis indicated that the YN08 isolate was more closely related to the Hebei HB0234 strain than the YN0540 strain, and more genetically distinct from the MM2021 Malaysia primitive strain.
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spelling pubmed-35476912013-01-23 Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD) Hu, Tingsong Zheng, Ying Zhang, Yan Li, Gangshan Qiu, Wei Yu, Jing Cui, Qinghua Wang, Yiyin Zhang, Chaoxiong Zhou, Xiaofang Feng, Ziliang Zhou, Weiguo Fan, Quanshui Zhang, Fuqiang BMC Microbiol Research Article BACKGROUND: The identification of new virus strains is important for the study of infectious disease, but current (or existing) molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of unknown viruses based on the cDNA - random amplified polymorphic DNA (cDNA-RAPD) technique. Getah virus, belonging to the family Togaviridae in the genus Alphavirus, is a mosquito-borne enveloped RNA virus that was identified using the Virus-Discovery-cDNA RAPD (VIDISCR) method. RESULTS: A novel Getah virus was identified by VIDISCR from suckling mice exposed to mosquitoes (Aedes albopictus) collected in Yunnan Province, China. The non-structural protein gene, nsP3, the structural protein gene, the capsid protein gene, and the 3'-untranslated region (UTR) of the novel Getah virus isolate were cloned and sequenced. Nucleotide sequence identities of each gene were determined to be 97.1–99.3%, 94.9–99.4%, and 93.6–99.9%, respectively, when compared with the genomes of 10 other representative strains of Getah virus. CONCLUSIONS: The VIDISCR method was able to identify known virus isolates and a novel isolate of Getah virus from infected mice. Phylogenetic analysis indicated that the YN08 isolate was more closely related to the Hebei HB0234 strain than the YN0540 strain, and more genetically distinct from the MM2021 Malaysia primitive strain. BioMed Central 2012-12-27 /pmc/articles/PMC3547691/ /pubmed/23268691 http://dx.doi.org/10.1186/1471-2180-12-305 Text en Copyright ©2012 Hu et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Hu, Tingsong
Zheng, Ying
Zhang, Yan
Li, Gangshan
Qiu, Wei
Yu, Jing
Cui, Qinghua
Wang, Yiyin
Zhang, Chaoxiong
Zhou, Xiaofang
Feng, Ziliang
Zhou, Weiguo
Fan, Quanshui
Zhang, Fuqiang
Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
title Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
title_full Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
title_fullStr Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
title_full_unstemmed Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
title_short Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
title_sort identification of a novel getah virus by virus-discovery-cdna random amplified polymorphic dna (rapd)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547691/
https://www.ncbi.nlm.nih.gov/pubmed/23268691
http://dx.doi.org/10.1186/1471-2180-12-305
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