HiDRA-seq: High-Throughput SARS-CoV-2 Detection By RNA Barcoding and Amplicon Sequencing. HiDRA-seq: High-Throughput SARS-CoV-2 Detection By RNA Barcoding and Amplicon Sequencing

The recent outbreak of a new coronavirus causing a severe acute respiratory syndrome in humans (SARS-CoV-2) has evolved into a global pandemic with over 5.5 million reported cases and more than 350,000 deaths worldwide. Many countries have been facing shortage of diagnostic kits as well as lack of infrastructure to perform massive testing. Due to these limitations, only patients showing symptoms compatible with infection have been subjected to testing while asymptomatic individuals have broadly contributed to the dispersion of the virus, forcing different countries to massive lockdowns with severe economic and social consequences. The World Health Organization (WHO) has encouraged affected countries to increase testing capabilities to identify new cases and be ready for future rebounds. Here, we propose a rapidly implementable solution that uses basic NGS lab infrastructure and reagents and provides enough throughput for population scale SARS-CoV-2 testing. The method is based on the use of indexed oligo-dT primers to generate barcoded cDNA from a high number of patient samples. Highly multiplexed NGS libraries are prepared from SARS-CoV-2 specific amplicons and sequenced. The low amount of sequencing data required allows the combination of thousands of samples in a sequencing run, while reducing the cost to approximately 2 CHF per test. In this paper, we describe in detail the first version of the protocol, which can be improved in the future to increase its sensitivity and to identify other respiratory viruses or analyze individual genetic features associated with disease progression.