Large-scale testing and tracking of SARS-CoV-2 infection and evolution by deep sequencing

The global pandemic of Coronavirus infectious disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented an acute and global health challenge of a magnitude not experienced in over a century. To combat the COVID-19 pandemic, countries are relying on non-pharmaceutical interventions (quarantines, social distancing, shutdown of non-essential businesses), which are having a dramatic social and economic impact. A central problem is the lack of diagnostics and surveillance capacities, which are essential for detecting SARS-CoV-2 infections and subsequently reducing transmission chains through effective NPI. Current molecular diagnostics (qRT-PCR assays) are limited in throughput (e.g., 7'000 total per day in Switzerland) and do not provide viral molecular sequence information for epidemiology.To overcome the limitations in current COVID-19 testing, we will develop a molecular barcoding method to tag individual patient RNA samples, which will then be highly multiplexed and tested for detection of virus by deep sequencing and bioinformatics. The importance of molecular barcodes is that they will be connected to a patient identification sample, meaning that on a single deep sequencing run (e.g., Illumina MiSeq) we will be able to multiplex and test up to 4,800 patient samples (Aim 1). Furthermore, our deep sequencing-based testing assay will also allow us to perform evolutionary analysis; by selectively sequencing regions of viral diversity, we will obtain molecular sequence information tracking the spread and evolution of the virus throughout Switzerland (Aim 2). This sequencing data will then be used to recreate transmission chains and inform further quarantine and social distancing measures. Our preliminary estimates suggest that we can sequence 4,800 samples (50 distinct 96-well plates) within a single MiSeq run in less than 24 hours. This can easily be scaled up based on the number of available patient samples by either increasing the number of sequencing runs in parallel (across multiple machines) or by using a higher throughput sequencing machine. This simple molecular biology assay can also be transferred to almost any diagnostics lab in the world, within Switzerland there are at least 30 sites where testing centers could be established and the sequencing infrastructure is available to likely achieve 2,000,0000 samples per week. With this capacity, it would only take 4 weeks for all of Switzerland to be tested for SARS-CoV-2 infection.