High-throughput Testing of SARS-CoV-2 Infection, Evolution and Immunity by Deep Sequencing

The global spread of COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented a public health crisis of a magnitude not experienced in over a century. A central challenge in mitigating the pandemic is difficulty in detecting the viral infections and subsequently reducing transmission chains. This project aims to develop a high-throughput diagnostic method for detecting the virus, as well as develop a platform for detecting antibody-mediated immunity. The technology has the potential to scale quickly and broadly for possible population-level surveillance of the disease.

To combat the COVID-19 pandemic, countries are relying on non-pharmaceutical interventions (i.e., quarantines, lockdowns, curfews), which have dramatic social and economic impact. However, relaxing these types of interventions would require diagnostics and surveillance capacities that are currently lacking, but essential for detecting infections and subsequently reducing transmission chains.

This consortium brings together molecular engineers, computational biologists and clinical scientists with the aim of overcoming current limitations in diagnostics for SARS-CoV-2. First, the project will develop a molecular barcoding method to tag individual patient RNA (ribonucleic acid) samples, which will then be highly multiplexed (i.e. simultaneously run) and tested for detection of virus by deep sequencing (repetitive sequencing of DNA for detection of rare or weak signal). The importance of molecular barcodes is that they will be connected to a patient identification sample, meaning that on a single deep sequencing run the team will be able to multiplex a large number of patient samples (~5,000). Importantly, diagnostics by sequencing do not require the same collection materials needed for standard tests, thus the sequencing approach should also allow the project to scale to very large patient cohorts and achieve possible population-level surveillance. Second, the consortium aims to develop a high-throughput serology platform based on molecular protein screening and deep sequencing for detecting antibody-mediated immunity to SARS-CoV-2.

These simple molecular biology assays and associated analysis pipelines can be transferred to almost any diagnostics lab in the world. Deep sequencing infrastructure is readily accessible in many different public and private institutions. Thus the project foresees the potential for rapid translation of these diagnostics across Switzerland and other nations, which will greatly benefit the current COVID-19 pandemic but also set the stage for future outbreaks and global health emergencies.


Researchers work on diagnostic methods for detecting the coronavirus.

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