Research Article: Characterization of the Complete Genome of Chikungunya in Zhejiang, China, Using a Modified Virus Discovery Method Based on cDNA-AFLP

Date Published: December 18, 2013

Publisher: Public Library of Science

Author(s): Yi Sun, JuYing Yan, HaiYan Mao, Lei Zhang, QinFeng Lyu, ZhongHua Wu, Wei Zheng, Cen Feng, YanJun Zhang, Jianming Qiu.


Chikungunya (CHIK) virus is a mosquito-borne emerging pathogen presenting great health challenges worldwide, particularly in tropical zones. Here we report a newly detected strain of CHIK, Zhejiang/chik-sy/2012, in China, a nonindigenous region for CHIK, using a modified approach based on the classic cDNA-AFLP. We then performed etiological and phylogenetic analyses to better understand its molecular characterization and phylogenetic pattern, and also to aid in further evaluating its persistence in Southeast Asia.

By using this modified procedure, we determined for the first time the complete genome sequence of the chikungunya virus strain, Zhejiang/chik-sy/2012, isolated in 2012 from a patient in Zhejiang, China. Sequence analyses revealed that this positive single strand of RNA is 12,017 bp long. We found no single amino acid mutation in A226V, D284E and A316V. Phylogenetic analysis showed that our strain shared the greatest homology with a strain isolated in Taiwan, which was derived from a strain from Indonesia. Chik-sy/2012 is in a different clade from other CHIK viruses found in China previously.

A modified cDNA-AFLP in virus discovery was used to isolate the first CHIK and the first complete genome sequence of virus strain chik-sy/2012 in 2012 from a patient with CHIK fever in Zhejiang, China. The infection displayed great phylogenetic distance from viruses detected in Guangdong, China, in 2008 and 2010, since they were derived from another evolutionary lineage. Additional molecular epidemiology data are needed to further understand, monitor and evaluate CHIK in China.

Partial Text

Chikungunya (CHIK), an Alphavirus in the family Togaviridae, causes human febrile illness accompanied by severe, chronic joint pain. It has emerged and reemerged in Africa and Asia since the mid 1950s and exploded onto the global scene as a major emerging pathogen in a series of devastating outbreaks since 2004 [1], [2]. CHIK is a potential global threat to public health because it is transmitted by mosquitoes in areas where there are large populations of susceptible human hosts. Phylogenetic and phylogeographic analyses showed that CHIK of African origin spread by two distinct routes, one throughout the Indian Ocean and the other moving from India to scattered locations in Southeast Asia and then to Italy [1]. The first incidence of CHIK in mainland China was firstly detected in 2008 [3]. A sudden outbreak among 173 patients was also reported in Guangdong Province, China, in 2010 [4]. In this article, we report the first isolation of CHIK virus in Zhejiang province, China, a nonindigenous region for CHIK, using a modified approach based on the classic cDNA-AFLP in virus discovery. We propose this modification as a better technique because it may improve accuracy in the hunt for viral segments and in determining the genome sequence of both DNA and RNA viruses on a larger scale. Our aims in this study were therefore the following: 1) test our modified work flow of the classic cDNA-AFLP method using CHIK isolation as the study material; 2) determine the entire genome sequence of CHIK; 3) understand the molecular characterization of the CHIK isolate and the phylogenetic patterns of CHIK in Asia to aid in further studies and to evaluate its persistence in China.