Background::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 essential for research studies and collaborative surveillance.Methods::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 and characterized a unified global high-resolution genotyping framework using phylogenetics, population genetics, phylogeography, and phylodynamics.Results::The defined framework was discriminated with three hierarchical layers of genotype, subgenotype and clade with respective mean pairwise distances 2-6%, 0.8-2%, and ≤ 0.8%. The global epidemic patterns of DENV-1 showed strong geographic constraints 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 increasing cross-transmission trends were also demonstrated. 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, where dengue outbreaks were frequently triggered by importation, showed a growing trend of DENV-1 diffusion. The probably hidden epidemics were found especially in Africa and India. Then, our framework can be utilized in an accurate stratified coordinated surveillance based on the defined viral population compositions. Thereby it is prospectively valuable for further hampering the ongoing transition process of epidemic to endemic, addressing the issue of inadequate monitoring, and warning us to be concerned about the cross-national, cross-regional, and cross-continental diffusions of dengue, which can potentially trigger large epidemics.Conclusions::The framework and its utilization in quantitatively assessing DENV-1 epidemics has 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 risk modeling. We will promote it to the public and update it periodically.

Dengue virus serotype-1 (DENV-1);Molecular epidemiology;Population structure;Phylogeography;Global genotyping framework;Molecular surveillance

Li Liqiang;Guo Xiang;Zhang Xiaoqing;Zhao Lingzhai;Li Li;Wang Yuji;Xie Tian;Yin Qingqing;Jing Qinlong;Hu Tian;Li Ziyao;Wu Rangke;Zhao Wei;Xin Sherman Xuegang;Shi Benyun;Liu Jiming;Xia Shang;Peng Zhiqiang;Yang Zhicong;Zhang Fuchun;Chen Xiao-Guang;Zhou Xiaohong

Institute of Tropical Medicine, Southern Medical University, Guangzhou 510515, China;Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou 510515, China;Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou 510060, Guangdong, China;State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou 510515, China;Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China;School of Foreign Studies, Southern Medical University, Guangzhou 510515, China;BSL-3 Laboratory (Guangdong), School of Public Health, Southern Medical University, Guangzhou 510515, China;Laboratory of Biophysics, School of Medicine, South China University of Technology, Guangzhou 510006, China;School of Computer Science and Technology, Nanjing Tech University, Nanjing 211816, China;Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong 999077, China;National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, Shanghai, People’s Republic of China;School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China

贫困所致传染病（英文）

[1]Li Liqiang;Guo Xiang;Zhang Xiaoqing;Zhao Lingzhai;Li Li;Wang Yuji;Xie Tian;Yin Qingqing;Jing Qinlong;Hu Tian;Li Ziyao;Wu Rangke;Zhao Wei;Xin Sherman Xuegang;Shi Benyun;Liu Jiming;Xia Shang;Peng Zhiqiang;Yang Zhicong;Zhang Fuchun;Chen Xiao-Guang;Zhou Xiaohong-.A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics)[J].贫困所致传染病（英文）,2022(05):14-29

arboviral,reproduceable,reconciling,phylodynamics,subgenotype,Subgenotype

unified,global,genotyping,framework,dengue,virus,serotype,stratified,coordinated,surveillance,strategy,epidemics,Background,Dengue,fastest,spreading,disease,posing,great,challenges,public,health,comparable,contextualizing,spatiotemporal,epidemiological,data,DENV,essential,research,studies,collaborative,Methods,Targeting,prominently,recent,decades,qualified,complete,sequences,strains,information,from,countries,areas,ranging,established,characterized,high,resolution,using,phylogenetics,population,phylogeography,Results,defined,was,discriminated,three,hierarchical,layers,clade,respective,mean,pairwise,distances,patterns,showed,strong,geographic,constraints,representing,spatial,pairs,Continent,Genotype,Region,Nation,Clade,thereby,identifying,regions,which,prospectively,facilitates,coordination,increasing,cross,transmission,trends,were,also,demonstrated,traditional,endemic,such,Thailand,Vietnam,Indonesia,displayed,persisting,dominant,source,centers,while,emerging,China,Australia,USA,where,outbreaks,frequently,triggered,importation,growing,probably,hidden,especially,Africa,India,Then,can,be,utilized,accurate,compositions,Thereby,valuable,further,hampering,ongoing,transition,process,addressing,issue,inadequate,monitoring,warning,concerned,about,national,regional,continental,diffusions,potentially,large,Conclusions,its,utilization,quantitatively,assessing,has,laid,foundation,unveiled,urgency,establishing,platform,blocking,This,expected,bridge,classical,genomic,epidemiology,risk,modeling,We,will,promote,update,periodically,Molecular,Population,structure,Phylogeography,Global

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