Molecular phylogenetic analyses of imported Zika virus genomes in China

Abstract Background The rapid transmission and potential link to severe neurologica complications and birth defects have made Zika virus infection a serious threat to global public health. However, the initial ancestor of Zika virus and the potential transmission route remain are unknown. Methods We assessed the epidemiological characteristics of 28 confirmed cases of Zika virus infection and analysed the genetic diversity of Zika virus isolates. Findings 28 confirmed cases of Zika virus infection were imported from South America, Central America and south Pacific areas. 18 cases were overseas Chinese people who had emigrated from Jiangmen, Guangdong. The remaining cases were businessman travelling in Venezuela, Samoa, Suriname, Guatemala, and Ecuador. The results of a molecular-clock phylogenetic analysis showed that the evolutionary rate of the Asian lineage was 1·05 × 10 −3 substitutions per site per year. The estimated time-scaled phylogeny contains a well-supported cluster of Zika virus strains (posterior probability [PP]=1·0) that share a common ancestor with the French Polynesia lineage in 2013, which suggests that a common ancestor likely transmitted from French Polynesia to South America, particularly to Brazil. All cases of Zika virus imported into China were located in two independent clusters (PP=1·0). One cluster contained the isolates imported into China from Venezuela. The common ancestor of this clade descended from an ancestral lineage that can be dated to the beginning of 2015; therefore, the imported China isolates from Venezuela were probably already locally endemic before 2015. In another cluster, all the isolates were imported into China from the South Pacific island Samoa. The common ancestor of this cluster can be dated to the middle of 2014. The estimated time-scaled phylogeny indicates that this cluster also shared a common ancestor with French Polynesia strain in 2013 (PP=0·99). Interpretation The present data indicated that the imported Zika virus in China was unlikely to be transmitted from Brazil in 2015. Alternatively, an independent local transmission of Zika virus appears to have been previously established in Venezuela and Samoa after 2014 and 2013, respectively. Funding Guangdong Provincial Science and Technology Program (2015A020213004), Guangdong Provincial Science and Technology (2016A020251001), and National Key Ru0026D Program (2016YFC1200201).