Large scale multiplexing of SARS-CoV-2 genomes using nanopore sequencing

Real-time public health surveillance on the SARS-CoV-2 pandemic is beingperformed using genome sequencing, primarily on the MinION from ONT. Wepresent CoronaHiT for multiplexing samples on long read sequenceras, whichincreases the number of genomes which can be sequenced in a singleexperiment from 24 to 147,456. CoronaHiT is a simpler method with less steps,requires less reagents, and is less labour intensive, with a higher barcoderecovery rate, making it faster and cheaper than standard methods. We presentthe results of sequencing 158 SARS-CoV-2 genomes on a single MinION flowcelland show that the results are comparable to standard ONT multiplexing methodsand Illumina.