Early Spread of SARS-Cov-2 in the Icelandic Population

Daniel F Gudbjartsson; Agnar Helgason; Hakon Jonsson; Olafur T Magnusson; Pall Melsted; Gudmundur L Norddahl; Jona Saemundsdottir; Asgeir Sigurdsson; Patrick Sulem; Arna B Agustsdottir; Berglind Eiriksdottir; Run Fridriksdottir; Elisabet E Gardarsdottir; Gudmundur Georgsson; Olafia S Gretarsdottir; Kjartan R Gudmundsson; Thora R Gunnarsdottir; Arnaldur Gylfason; Hilma Holm; Brynjar O Jensson; Aslaug Jonasdottir; Frosti Jonsson; Kamilla S Josefsdottir; Thordur Kristjansson; Droplaug N Magnusdottir; Louise le Roux; Gudrun Sigmundsdottir; Gardar Sveinbjornsson; Kristin E Sveinsdottir; Maney Sveinsdottir; Emil A Thorarensen; Bjarni Thorbjornsson; Arthur Love; Gisli Masson; Ingileif Jonsdottir; Alma Moller; Thorolfur Gudnason; Karl G Kristinsson; Unnur Thorsteinsdottir; Kari Stefansson

Sequencing libraries were pooled (24-36 samples/pool) and quantified using the Qubit dsDNA assay (Thermo Fisher). Samples were diluted appropriately and denatured to a final loading concentration of 10 pM. All samples were sequenced on Illumina MiSeq sequencers using 300-cycle MiSeq v2 reagent kits (Illumina). Each pool was sequenced using dual indexed paired-end sequencing of 150*8*8*150 bp cycles of data acquisition and imaging with a run time of approximately 24 hrs. Basecalling was done in real time using MCS v3.1 and FASTQ files were generated using MiSeq Reporter. At least 15M PF reads (>4.5Gb) with base qualities of >Q30 for at least 90% of bases were collected for each run.