Genetic diversity and phylogenetic analyses of Asian lineage of Zika virus whole genome sequencing derived from Culex quinquefasciatus mosquitoes and urine of patients during the epidemic in Thailand

Abstract

Abstract Zika virus (ZIKV) is a mosquito-borne flavivirus that is emerging and re-emerging. Since 2010, sporadic ZIKV cases have been reported annually in Thailand, with over 1,000 confirmed positive cases in 2016. High-throughput sequencing technologies, such as whole genome sequencing (WGS), have recently enabled the rapid sequencing of pathogen genomes. Therefore, this study used multiplex amplicon sequencing by the Illumina Miseq to describe the ZIKV WGS. Six ZIKV WGS were obtained from three samples of field-caught Culex quinquefasciatus mosquitoes and three urine samples collected from human in three different provinces of Thailand. Additionally, one ZIKV isolate was successfully isolated from a female Cx. quinquefasciatus. Based on WGS analysis, the timing of the 2020 outbreak correlates with the acquisition of five amino acid changes in the Asian lineage ZIKV strains from Thailand 2006, Cambodia 2010 and 2019, and Philippines 2012, including C-T106A, prM-V1A, E-V473M, NS1-A188V, and NS5-M872V. This mutation was found in all seven WGS, which was previously reported to be associated with significantly higher mortality rates. Moreover, phylogenetic analysis indicated that the seven ZIKV sequences belonged to the Asian lineage. The genomic region of the E gene showed the highest nucleotide diversity (0.7–1.3%). The data can be applied to develop molecular tools to better understand the virus's patterns and evolution. Furthermore, it could indicate potential targets for development of more effective to control and prevent the zika outbreak.