Pandemic Preparedness (GDSC)

Pandemic Preparedness and Pathogen Genomic Surveillance

We advance pandemic preparedness by building the scientific, technical, and operational capability to rapidly turn pathogen genomic data into reliable public-health intelligence. Our team supports the full surveillance pathway from data submission, validation, and curation to sequence analysis, mutation interpretation, visualization, reporting, and stakeholder engagement. Our work maintains and improves pathogen data resources and analytical services while expanding support for priority pathogens of regional and global importance. We provide real-time quality assurance and curation of genome sequences and associated metadata across the regions, helping ensure that surveillance data are complete, consistent, and ready for downstream analysis.

Influenza surveillance tools

Influenza and other respiratory viruses is a longstanding scientific focus of the programme. Our FluSurver platform is used by researchers and surveillance experts worldwide as a comprehensive resource for influenza mutation analysis. It enables users to investigate mutations in the context of antiviral drug resistance, viral fitness, host adaptation, antigenic change, and available structural or functional evidence. FluCluster-AI extends these capabilities with near-real-time surveillance and visualization of influenza variants. The tool supports the identification of emerging variant clusters, estimates their growth patterns, examines likely antigenic drift, and helps reveal relationships between viral genomic changes and clinical or epidemiological information. Together, these tools help turn continuously accumulating sequence data into interpretable evidence for surveillance and research.

Disease x readiness

The programme is designed to support a rapid response to Disease X: a future, unknown pathogen with the potential to cause an epidemic or pandemic. Preparedness requires more than pathogen-specific expertise. It depends on reusable infrastructure, tested analytical workflows, clear coordination across teams, and the ability to deploy trusted data services under severe time pressure. To test this capability, we conducted a Disease X preparedness exercise using a Nipah virus based scenario in January 2026. The exercise modelled the detection of a novel outbreak and demonstrated an end-to-end surveillance capability within one day. Within 24 hours of simulated activation, the workflow was designed to deliver:

• Ingestion, validation, and quality assessment of simulated pathogen genome sequences and metadata. 
• Variant calling, mutation profiling, lineage classification, and phylogenetic placement.
• Deployment of three operational dashboards: a sequence tracker, a lineage and variant dashboard, and a sequence quality monitor. 

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12. Asarnow D, Wang B, Lee WH, Hu Y, Huang CW, Faust B, Ng PML, Ngoh EZX, Bohn M, Bulkley D, Pizzorno A, Ary B, Tan HC, Lee CY, Minhat RA, Terrier O, Soh MK, Teo FJ, Yeap YYC, Seah SGK, Chan CEZ, Connelly E, Young NJ, Maurer-Stroh S, Renia L, Hanson BJ, Rosa-Calatrava M, Manglik A, Cheng Y, Craik CS, Wang CI. Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia. Cell. 2021 Jun 10;184(12):3192-3204.e16. doi: 10.1016/j.cell.2021.04.033. Epub 2021 Apr 24.
13. Ooi KH, Liu MM, Tay JWD, Teo SY, Kaewsapsak P, Jin S, Lee CK, Hou J, Maurer-Stroh S, Lin W, Yan B, Yan G, Gao YG, Tan MH. An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing. Nature Commun. 2021 Mar 19;12(1):1739. doi: 10.1038/s41467-021-21996-6.
14. Chua AQ, Al Knawy B, Grant B, Legido-Quigley H, Lee WC, Leung GM, Looi MK, Maurer-Stroh S. How the lessons of previous epidemics helped successful countries fight covid-19. BMJ. 2021 Mar 11;372:n486. doi: 10.1136/bmj.n486
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16. Pung R, Chiew CJ, Young BE, Chin S, Chen MI, Clapham HE, Cook AR, Maurer-Stroh S, Toh MPHS, Poh C, Low M, Lum J, Koh VTJ, Mak TM, Cui L, Lin RVTP, Heng D, Leo YS, Lye DC, Lee VJM; Singapore 2019 Novel Coronavirus Outbreak Research Team. Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures. Lancet. 2020 Mar 28;395(10229):1039-1046. doi: 10.1016/S0140-6736(20)30528-6. Epub 2020 Mar 17