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Open Access Research article

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

Tingsong Hu1, Ying Zheng1, Yan Zhang2, Gangshan Li1, Wei Qiu1, Jing Yu1, Qinghua Cui1, Yiyin Wang1, Chaoxiong Zhang1, Xiaofang Zhou1, Ziliang Feng1, Weiguo Zhou1, Quanshui Fan1* and Fuqiang Zhang1*

Author Affiliations

1 Centre for Disease Control and Prevention, Chengdu Military Region, Kunming, 650032, China

2 Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, 200030, China

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BMC Microbiology 2012, 12:305  doi:10.1186/1471-2180-12-305

Published: 27 December 2012

Abstract

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.

Keywords:
Getah virus; Identification; Virus-Discovery; cDNA RAPD