WHO EPI-WIN Webinar: Spotlight Dengue
In the WHO EPI-WIN webinar "Pathogen Genomics in Health Emergencies — Spotlight Dengue" (27 August 2024), co-hosted with the International Pathogen Surveillance Network (IPSN), Professor Nuno Faria (Imperial College London / University of São Paulo) and Professor Lee Ching Ng (Environmental Health Institute, National Environment Agency, Singapore) set out how genomic surveillance is reshaping the global response to dengue at a moment of unprecedented transmission — with nearly 11.5 million cases and over 7,000 deaths reported to WHO by August 2024, and active circulation in more than 90 countries.
WHO EPI-WIN Webinar Pathogen Genomics in Health Emergencies: Spotlight Dengue.
The webinar opens with the global picture and the biology that makes dengue so difficult to contain: four antigenically distinct serotypes, broad genotypic diversity within each, a rapid evolutionary rate (around 10⁻³ substitutions per site per year, comparable to SARS-CoV-2), and the well-known risk that sequential infections with different serotypes can drive antibody-dependent enhancement and severe disease. Against that backdrop, he argues, genomic surveillance is no longer optional.
Dengue is now the most-sequenced arbovirus and the fifth most-sequenced viral threat overall — over 43,000 sequences shared publicly, although only about 10% are whole genomes and African data make up just 4% of the total. To bring order to that growing dataset, a recently proposed two-tier "major lineage / minor lineage" nomenclature is presented to give the field a shared vocabulary for tracking strains of epidemiological or clinical importance (Hill et al. PLoS Biology 2025).
Six concrete ways genomics is already changing dengue public health are presented:
Reconstructing serotype, genotype and lineage spread at scales from neighbourhoods to intercontinental air-travel networks;
Augmenting traditional surveillance — including using infected travellers as sentinels, as in the detection of cryptic DENV-3 circulation in the Caribbean before it surfaced in Florida;
Informing vaccine development, where trial data show that the efficacy of the licensed Dengvaxia vaccine is lower against strains genotypically distant from the strains used for this vaccine’s design.
Improving molecular diagnostics, using a Burkina Faso study that revealed pervasive primer–probe mismatches (especially for DENV-2 in Africa) that can produce false negatives;
supporting phylodynamic modelling, including work in Yunnan, China, showing that dengue does not persist locally year-round but is reintroduced from neighbouring countries each season; and, finally,
Strengthening preparedness for "pathogen X" through targeted metagenomics — illustrated by a Brazilian study in which metagenomic sequencing of fatal undiagnosed cases in São Paulo identified the highly pathogenic Sabiá arenavirus, a finding with direct treatment implications.
The webinar moves from global framing to the operational reality of running an integrated arbovirus programme in a hyperendemic city-state. Singapore — where dengue has been recorded since 1901 — treats virus, vector and human surveillance as a single system, layered with vector control (environmental source reduction, complemented in recent years by Wolbachia-based mosquito suppression), mandatory clinician and laboratory case notification, outbreak management and public communication. Within that system, genomic surveillance does specific, decision-relevant work.
Several examples drawn from Singapore's long sequencing record. Historically, switches in the dominant circulating serotype have foreshadowed outbreaks three to six months later — a pattern observed repeatedly between 2004 and the late 2010s — but the 2019–2020 surge broke the rule, occurring without a serotype switch and instead reflecting the rising dominance of DENV-3, which then drove a major outbreak in 2022.
Plotting the cumulative growth of individual viral variants lets Singapore flag candidates with unusually high epidemic potential early; in the 2022 case, vector-competence experiments showed the emerging DENV-3 variant had a notably short extrinsic incubation period in mosquitoes, comparable to a DENV-2 strain that had previously caused a large outbreak.
Linking sequence data to clinical outcomes through the UNITEDengue programme has begun to suggest genotype-level differences in severity (for example, milder profiles for some DENV-3 and DENV-4 lineages), and phylogeographic analyses help identify connectivity hubs that can be prioritised for vector-control investment — an approach that informed the geographic targeting of Singapore's Wolbachia rollout. The same toolkit, applied to chikungunya and Zika, has reassured Singapore that recent cases reflect repeated transient introductions rather than silent endemic transmission — a conclusion corroborated by low (1–5%) IgG seroprevalence.
Together, the talks make a consistent case: dengue genomics is now mature enough to inform vaccine design, sharpen diagnostics, anticipate outbreaks, target interventions, and detect novel threats — but its public-health value depends on closing persistent surveillance gaps (especially in Africa), standardising lineage nomenclature, and integrating sequence data with epidemiological, clinical, vector and environmental information. The session also featured Dr. Gamou Fall (Institut Pasteur de Dakar) on Senegal's sentinel surveillance network and the role of genomics in detecting sylvatic DENV-2 in Kédougou, with opening remarks by Dr Josefina Campos (WHO Berlin Hub, International Pathogen Surveillance Network) and closing remarks by Dr Diana Rojas Alvarez (WHO Health Emergencies team).
This webinar was attended by 1233 participants from 144 countries, with over 400 organisations, including Ministry of Health members from at least 29 countries, CDC members from at least 11 countries, WHO members from at least 37 different countries/regions, and universities from 49 countries/regions throughout the world.