LINE1 transfected and mock infected 293T cells
HEK293T cells were obtained from ATCC (CRL-3216) and cultured in DMEM supplemented with 10% heat-inactivated FBS (Hyclone, SH30396.03) and 2mM L-glutamine (MP Biomedicals, IC10180683) following ATCCs method. Plasmid pBS-L1PA1-CH-mneo was a gift from Astrid Roy-Engel (Addgene plasmid # 51288 ; http://n2t.net/addgene:51288 ; RRID:Addgene_51288). Transfection was done with Lipofectamine 3000 (Invitrogen L3000001) following manufacturers protocol.    SARS-CoV-2 USA-WA1/2020 (Gen Bank: MN985325.1) was obtained from BEI Resources and expanded and tittered on Vero cells. Cells were infected in DMEM +2% FBS.    Cellullar DNA extraction was done using a published method (Lee et al. Nature, 563, 639645(2018)).    We constructed libraries for HEK293T cell whole genome sequencing using the Tn5 based Illumina DNA Prep kit (Illumina 20018704).     The libraries were loaded onto an SP flowcell on an Illumina NovaSeq 6000 and run for 2X150 cycles according to the manufacturer's instructions.     Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (Illumina).