TY - JOUR
T1 - A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics
AU - Li, Liqiang
AU - Guo, Xiang
AU - Zhang, Xiaoqing
AU - Zhao, Lingzhai
AU - Li, Li
AU - Wang, Yuji
AU - Xie, Tian
AU - Yin, Qingqing
AU - Jing, Qinlong
AU - Hu, Tian
AU - Li, Ziyao
AU - Wu, Rangke
AU - Zhao, Wei
AU - Xin, Sherman Xuegang
AU - Shi, Benyun
AU - Liu, Jiming
AU - Xia, Shang
AU - Peng, Zhiqiang
AU - Yang, Zhicong
AU - Zhang, Fuchun
AU - Chen, Xiao-Guang
AU - Zhou, Xiaohong
N1 - Funding information:
This study was supported by the National Key R&D Program of China (2020YFC120104), the National Institutes of Health, the USA (AI136850), the National Natural Science Foundation of China (82072311), the Guangzhou Synergy Innovation Key Program for Health (201803040006 and 201508020263), and the Guangzhou International Science and Technology Cooperation Program (2012J5100026).
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/10/13
Y1 - 2022/10/13
N2 - 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. Graphical Abstract: [Figure not available: see fulltext.].
AB - 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. Graphical Abstract: [Figure not available: see fulltext.].
KW - Dengue virus serotype-1 (DENV-1)
KW - Molecular epidemiology
KW - Population structure
KW - Phylogeography
KW - Global genotyping framework
KW - Molecular surveillance
UR - http://www.scopus.com/inward/record.url?scp=85139747088&partnerID=8YFLogxK
U2 - 10.1186/s40249-022-01024-5
DO - 10.1186/s40249-022-01024-5
M3 - Journal article
C2 - 36224651
AN - SCOPUS:85139747088
SN - 2095-5162
VL - 11
JO - Infectious Diseases of Poverty
JF - Infectious Diseases of Poverty
M1 - 107
ER -