We apply long-read nanopore sequencing and a new tool, TLDR (Transposons from Long Dirty Reads), to directly infer CpG methylation of new and extant human transposable element (TE) insertions in hippocampus, heart, and liver, as well as paired tumour and nontumour liver. Whole genome TLDR analysis greatly facilitates studies of TE biology as complete insertion sequences and their epigenetic modifications are readily obtainable. Main Transposable elements (TEs) pervade our genomic architecture and broadly influence human biology and disease 1. Recently, Oxford Nanopore Technologies (ONT) long-read DNA sequencing has enabled telomere-to-telomere chromosome assembly at base pair resolution, including of high copy number TEs previously refractory to short-read mapping 2-4. While most evolutionarily older TEs have accumulated sufficient nucleotide diversity to be uniquely identified, recent TE insertions are often indistinguishable from their source elements when assayed with short-read approaches. Each diploid human genome contains 80-100 potentially mobile long interspersed element 1 (LINE-1) copies, referred to here as L1Hs (L1 Human-specific) 5,6. L1Hs elements encode proteins required to retrotranspose 7 in cis, and to trans mobilise Alu and SVA retrotransposons and processed mRNAs 8-10. While the reference genome assembly contains thousands of human-specific TE copies, the vast majority of germline polymorphic 1

1 We apply long-read nanopore sequencing and a new tool, TLDR (Transposons from Long 2 Dirty Reads), to directly infer CpG methylation of new and extant human transposable 3 element (TE) insertions in hippocampus, heart, and liver, as well as paired tumour and non-4 tumour liver. Whole genome TLDR analysis greatly facilitates studies of TE biology as 5 complete insertion sequences and their epigenetic modifications are readily obtainable. 6 7 Main 8Transposable elements (TEs) pervade our genomic architecture and broadly influence 9 human biology and disease 1 . Recently, Oxford Nanopore Technologies (ONT) long-read 10

A recent study proposed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2, and do not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolve 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV) positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions via ONT sequencing. That we find no evidence of SARS-CoV-2 integration suggests such events are, at most, extremely rare in vivo , and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.