A unified global genotyping framework of dengue virus serotype-1 for coordinated proposal of stratified surveillance
Liqiang Li#, Xiang Guo#, Xiaoqing Zhang, Lingzhai Zhao, Li Li, Yuji Wang, Tian Xie, Qingqing Yin, Qinlong Jing, Tian Hu, Ziyao Li, Rangke Wu, Wei Zhao, Sherman Xuegang Xin, Benyun Shi, Jiming Liu, Xiaonong Zhou, Zhiqiang Peng, Zhicong Yang, Fuchun Zhang*, Xiao-Guang Chen*, Xiaohong Zhou*
#These authors contributed equally to this work.
- Correspondence: Xiaohong Zhou (daizhouxh@163.com) ; Xiao-Guang Chen (xgchen2001@hotmail.com) ; Fuchun Zhang (gz8hzfc@126.com)
Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is an essential issue for researches and collaborative surveillance. Targeting DENV-1 spreading prominently in recent decades, by reconciling all qualified complete E gene sequences of 5003 DENV-1 strains with epidemiological information from 78 epidemic countries/areas ranging from 1944 to 2018, we established a unified global high-resolution genotyping framework with three hierarchical layers of genotype, subgenotype and clade, and characterized their epidemic patterns representing stratified spatial-genetic epidemic pairs of Continent-Genotype, Region-Subgenotype and Nation-Clade, thereby identifying 12 epidemic regions which prospectively facilitates the region-based coordination. The traditional endemic countries such as Thailand, Vietnam and Indonesia displayed as persisting dominant source centers, while the emerging epidemic countries such as China, Australia, and the USA showed a growing trend of DENV-1 diffusion. The framework and its utilization in quantitatively assessing DENV-1 epidemics laid a foundation and re-unveiled the urgency for establishing a stratified coordinated surveillance platform for blocking global spreading of dengue. This framework is also expected to bridge classical DENV-1 genotyping with genomic epidemiology and even pathogen-mosquito-disease-associated risk modelling.
- Data selection and quality control (01.rBAPS)
- Establishment of a unified high-resolution global genotyping framework of DENV-1 (01.rBAPS, 02.Frame)
- Ancestral state reconstruction and molecular clock phylogenetic analyses (03.BEAST)
- Characterization of the unified global genotyping framework of DENV-1 (04.TRAITS)
- Global geographic distribution and epidemic regional classification (05.GEO)
- Global transmission pattern of DENV-1 at subgenotype level (06.BSSVS)
- Sources and trend of DENV-1 diffusion at clade level (07.PACT)