Leveraging pathogen sequencing and statistical analysis to inform public health - past, present and future
Tanja's keynote lecture at Virus Genomics Evolution and Bioinformatics 2024 in Hinxton, UK, is now available on Youtube!
Abstract
Pathogen sequencing data contains a fingerprint of past evolutionary and epidemiological processes, and thus provides a unique opportunity to extract the encoded knowledge. Phylodynamic tools provide the means to extract this knowledge.
I will outline our sequencing and analysis efforts prior to and during the COVID-19 pandemic. As an example, we traced the detailed transmission dynamics of influenza in a city, revealing important insights relevant to public health policy. The pandemic accelerated advances, and I will outline how we were able to inform and evaluate public health responses based on global sequencing data, complemented by our sequencing efforts in Switzerland.
The unprecedented amount of sequencing data collected during the pandemic posed critical challenges to existing data management and dashboard platforms. To address this gap, we developed novel, queryable data compression schemes, enabling real-time interactive exploration of the full data, available at external page https://genspectrum.org/.
Post-pandemic, we built on these advances and developed – in a major global collaborative effort – a novel data sharing platform, external page https://pathoplexus.org, facilitating global access and sharing of these big datasets. Users can submit their own sequences and download datasets of interest for a growing number of supported viruses. Importantly, this framework is based on the latest technological developments and is run by the community, with transparent governance and data sharing frameworks.
For future genomic surveillance, we envision two complementary strategies. First, a representative set of routinely collected patient samples: I will outline the results of our pilot study, where we targeted respiratory viruses in Switzerland during the 2023/2024 winter season. Second, samples obtained from wastewater: I outline how we started with measuring SARS- CoV-2 concentrations in wastewater and performing genomic sequencing, allowing us to estimate variant-specific reproductive numbers and thereby correctly anticipate future waves.
I close the talk with discussing future core opportunities and open challenges in monitoring pathogens through genomic surveillance and using the full pathogen genomic information to inform public health policies and responses.