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

Amplicon sequences were aligned to the reference genome of the SARS-CoV-2 (NC_045512.2) 2 using bwa mem 14 , possible PCR duplicates were marked with markduplicates from Picard tools 15 and reads with less than 50 bases aligned were omitted from the alignment. The resulting aligned filtered reads were used for variant calling with bcftools 14 . For consensus sequence generation only variants reported as homozygous were used. In regions targeted with primers we allowed variants to have allele frequency below one in individual. The consensus sequence was masked with ambiguous nucleotides (N) at positions if the depth of coverage was strictly less than 5 reads after restricting to bases of quality 20 or higher. Consensus sequences with more than 10,000 ambiguous nucleotides were discarded from analysis. The mutations in Table S3 were used to define haplogroups/clades. . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.