title: Raw reads: W25Y23Mal
design: DNAse treatment (DNase I, Amplification Grade, Invitrogen) was performed to reduce unspecific amplification before library preparation for Miseq sequencing for samples between week 30-34. The COVIDSeq Assay kit [EM1] (Illumina) was used to generate the libraries. Samples from weeks 22, 23, 33, and 34 were amplified using the Artic V4.1 NCOV-2019 Panel primers (IDTDNA), while the remaining weeks were amplified using the Artic V5.3.2 NCOV-2019 Panel primers (IDTDNA). The resulting libraries were sequenced on the Illumina Miseq platform using the MiSeq Reagent Kit v3 2 x 76 (150-cycle) (Illumina)  at the Functional Microbial Ecology Lab (FUME) within the Swedish University of Agriculture.