Identification and genetic characterization of Zika virus isolated from an imported case in China

Zika virus (ZIKV) is a reemerging flavivirus that stroke Brazil in 2015 and appeared in China for the first time in 2016. Sequencing and genomic analysis are essential for Zika virus study. However, the complete genome length of Zika virus is still a disputable issue. In this study, we reported the complete genomic sequence of Zika virus strain ZKC2/2016 from an imported case in China, in February 2016. The virus was isolated and virus characteristics were identified by cytopathic effect, quantitative real time-PCR, immunofluorescence assay and electronic microscopy. Next generation sequencing (NGS) technique and 5′ and 3′ Rapid Amplification cDNA Ends (RACE) PCR were used to sequence the complete genome. The genome length of this newly obtained Zika virus strain is 10,807 base pairs (bp). Genetic analysis showed that ZKC2/2016, along with other Chinese Zika virus strains in 2016, formed three clusters within Asian linage. Multiple sequence alignment and prediction of RNA secondary structure of untranslated regions (UTRs) of ZKC2/2016 and several other ZIKV strains indicated that the difference of ZIKV genome length mainly laid in UTRs. Besides, those genomes shorter than 10,790 bp were probably incomplete due to lacking conserved secondary RNA structures in untranslated regions which were playing important roles in flavivirus replication. Our findings benefited the disease control of Zika fever in China and the study of Zika virus genome.