title: Characterization of the complete genome of chikungunya in Zhejiang, China, using a modified virus discovery method based on cDNA-AFLP.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, P.R.China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, P.R.China.
authors.forename: Juying
authors.initials: J
authors.lastname: Yan
authors.affiliation: Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, P.R.China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Mao
authors.affiliation: Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, P.R.China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Zhejiang International Travel Healthcare Center, Hangzhou, Zhejiang, P.R.China.
authors.forename: Qinfeng
authors.initials: Q
authors.lastname: Lyu
authors.affiliation: Zhejiang International Travel Healthcare Center, Hangzhou, Zhejiang, P.R.China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Zhejiang International Travel Healthcare Center, Hangzhou, Zhejiang, P.R.China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Zhejiang Normal University, Jinhua, Zhejiang, P.R.China.
authors.forename: Cen
authors.initials: C
authors.lastname: Feng
authors.affiliation: Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, P.R.China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods*; D002646:Chikungunya virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D002681:China; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D010802:Phylogeny
chemical_list: D018076:DNA, Complementary