Tracking dengue virus lineages
Pathoplexus is an open, community-curated platform for sharing pathogen genomic data, built on the Loculus software package to power microbial genomic databases. Rather than locking sequences behind controlled-access portals, Pathoplexus distributes them openly under explicit data-use terms, with full provenance and submitter attribution. DeZi supports this model — open access by default, equitable credit by design — as the foundation for trustworthy genomic surveillance for maximum public health impact.
This approach is also closely aligned with the WHO's recent direction on pathogen data sharing, including its Global Genomic Surveillance Strategy (2022–2032). The shared principle is straightforward: outbreak-relevant genomic data should reach those who can act on it — public health agencies, diagnostic developers, vaccine designers and the research community — as quickly and equitably as possible.
For dengue specifically, this matters in two concrete ways.
First, molecular diagnostics depend on continuously updated reference sequences across all four serotypes and their circulating lineages. Mosquito-borne arboviruses such as DENV and ZIKV are rapidly evolving viruses, and the rapid acquisition of novel mutations and unsampled diversity can render older PCR primers blind to local strains.
Second, vaccine design and evaluation are equally lineage-sensitive: vaccine efficacy varies by serotype and by genotype, and the next generation of dengue vaccines will be informed by the diversity of lineages circulating globally.
The dashboard below is pulled from Pathoplexus and shows live sequence counts across the DeZi partner countries, paired with each country's modelled population at risk for dengue, chikungunya and Zika from ArboRiskMap.
By DeZi country (sorted by total sequences ≥ 7,500 bp)
Pathoplexus is developed and maintained by the Pathoplexus consortium (ETH Zürich, the Swiss Institute of Bioinformatics, the European Bioinformatics Institute and partners), built on the open-source Loculus platform. DeZi links to Pathoplexus as a recommended external toolkit; the platform, code and curated data are maintained by the Pathoplexus team.