Tracking two decades of global dengue virus lineage dynamics
- 1Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
Abstract
Dengue virus (DENV) is genetically diverse, consisting of four antigenically distinct serotypes and extensive sub-serotype variation that can influence epidemiology and control. As DENV continues to expand globally, there is an urgent need to characterize the dynamics of distinct DENV genetic lineages, including their persistence, establishment, and spread. Using a standardized DENV lineage nomenclature system and 37,828 publicly available DENV genomes sampled from 2000-2024, we classified sequences across nine global regions to construct a comprehensive resource of regional lineage distributions over time. We found marked regional differences in lineage diversity, with higher lineage richness in Southeast and East Asia than in the Americas. We further showed that COVID-19-related disruptions were associated with decreased regional lineage persistence and detection of new lineages during 2020-2021, followed by rebounds after 2022 and, in some regions, substantial lineage turnover. Finally, we identified a small set of globally expansive (cosmopolitan) lineages that are over-represented in available sequences, including five first-order minor lineages detected in at least seven of nine regions: 3III_B.3, 2II_F.1, 2II_A.1, 1III_A.3, and 1I_K.3. Together, these results demonstrate how standardized lineage classification enables global tracking of emerging DENV diversity and supports targeted genomic surveillance.
Related
- Tracking ageing over three decades: preliminary results from the EPIC-Turin Recall Study
- High-resolution lineage tracking maps the multi-phase evolution and adaptive potential of biofilms
- Nationwide Tracking of A‐Lineage Spread in Western Honey Bees Using Haplotype Sharing, Local Ancestry Mapping, and Migration Inference
- Nanotechnology-Enabled Vaccines for Malaria, Tuberculosis, HIV, and Dengue: Translational Evidence and Implementation in the Global South
- Tracking the Global Prevalence and Distribution of the AmpC-β-Lactamase-Carrying pESM Megaplasmid in Salmonella Minnesota
BibTeX
@misc{good2026tracking,
title = {{Tracking two decades of global dengue virus lineage dynamics}},
author = {S. Good and A. J. Porzucek and Y. T. Chew and R. Lopes and N. Rankin and C. V. F. Carrington and E. E. OoI and A. F. Brito and V. Hill and N. D. Grubaugh},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.02.756263},
url = {https://www.biorxiv.org/content/10.64898/2026.10.02.756263v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Tracking two decades of global dengue virus lineage dynamics
AU - S. Good
AU - A. J. Porzucek
AU - Y. T. Chew
AU - R. Lopes
AU - N. Rankin
AU - C. V. F. Carrington
AU - E. E. OoI
AU - A. F. Brito
AU - V. Hill
AU - N. D. Grubaugh
PY - 2026
DA - 2026/10/02
PB - bioRxiv
DO - 10.64898/2026.10.02.756263
UR - https://www.biorxiv.org/content/10.64898/2026.10.02.756263v1
AB - Dengue virus (DENV) is genetically diverse, consisting of four antigenically distinct serotypes and extensive sub-serotype variation that can influence epidemiology and control. As DENV continues to expand globally, there is an urgent need to characterize the dynamics of distinct DENV genetic lineages, including their persistence, establishment, and spread. Using a standardized DENV lineage nomenclature system and 37,828 publicly available DENV genomes sampled from 2000-2024, we classified sequences across nine global regions to construct a comprehensive resource of regional lineage distributions over time. We found marked regional differences in lineage diversity, with higher lineage richness in Southeast and East Asia than in the Americas. We further showed that COVID-19-related disruptions were associated with decreased regional lineage persistence and detection of new lineages during 2020-2021, followed by rebounds after 2022 and, in some regions, substantial lineage turnover. Finally, we identified a small set of globally expansive (cosmopolitan) lineages that are over-represented in available sequences, including five first-order minor lineages detected in at least seven of nine regions: 3III_B.3, 2II_F.1, 2II_A.1, 1III_A.3, and 1I_K.3. Together, these results demonstrate how standardized lineage classification enables global tracking of emerging DENV diversity and supports targeted genomic surveillance.
ER -