The landscape of viral associations in human cancers

1The World Health Organization estimates that 15.4% of all cancers are attributable to infections and 9.9% are linked to viruses,. Cancers that are attributable to infections have a greater incidence than any individual type of cancer worldwide. Eleven pathogens have been classified as carcinogenic agents in humans by the International Agency for Research on Cancer (IARC). After Helicobacter pylori (associated with 770,000 cases worldwide), the four most prominent infection-related causes of cancer are estimated to be viral: HPV (associated with 640,000 cases), HBV (420,000 cases), hepatitis C virus (HCV) (170,000 cases) and EBV (120,000 cases). It has been shown that viruses can contribute to the biology of multistep oncogenesis and are implicated in many of the hallmarks of cancer. Notably, the discovery of links between infection and cancer types has provided actionable opportunities, such as the use of HPV vaccines as a preventive measure, to reduce the global impact of cancer. The following characteristics have been proposed to define human viruses that cause cancer through direct or indirect carcinogenesis: (1) presence and persistence of viral DNA in tumor biopsies; (2) growth-promoting activity of viral genes in model systems; (3) dependence of a malignant phenotype on continuous viral oncogene expression or modification of host genes; and (4) epidemiological evidence that a virus infection represents a major risk for the development of cancer.

2The worldwide efforts of comprehensive genome and whole-transcriptome analyses of tissue samples from patients with cancer have generated appropriate facilities for capturing information not only from human cells but also from other—potentially pathogenic—organisms or viruses that are present in the tissue. A comprehensive collection of whole-genome and whole-transcriptome data from cancer tissues has been generated within the International Cancer Genome Consortium (ICGC) project PCAWG, providing a unique opportunity for a systematic search for tumor-associated viruses.

3The PCAWG Consortium aggregated whole-genome sequencing (WGS) data from 2,658 cancers across 38 tumor types that have been generated by the ICGC and The Cancer Genome Atlas (TCGA) projects. These sequencing data were reanalyzed with standardized, high-accuracy pipelines to align to the human genome (build hs37d5) and identify germline variants and somatically acquired mutations. The PCAWG working group ‘Pathogens’ analyzed the WGS and whole-transcriptome sequencing (RNA-sequencing (RNA-seq)) data of the PCAWG consensus cohort (2,656 donors). Focusing on viral pathogens, we applied three independently developed pathogen-detection pipelines ‘Computational Pathogen Sequence Identification’ (CaPSID), ‘Pathogen Discovery Pipeline’ (P-DiP) and ‘Searching for Pathogens’ (SEPATH) to generate a large compendium of viral associations across 38 cancer types. We extensively characterized the known and novel viral associations by integrating driver mutations, mutational signatures, gene expression profiles and patient survival data of the same set of tumors analyzed by the PCAWG Consortium.

4To identify the presence of viral sequences, we explored the WGS data of 5,354 tumor–normal samples across 38 cancer types, and 1,057 tumor RNA-seq data across 25 cancer types (Supplementary Tables 1, 2, 20). In total, 195.8 billion reads were considered for analysis, as they were not sufficiently aligned to the human reference genome in the PCAWG-generated alignment. The remaining reads ranged from 28,036 to 800 million reads per WGS and up to 120 million reads per RNA-seq tumor sample (Fig. 1a, Extended Data Fig. 1a–c). Viral sequences were detected and quantified independently by the three recently developed pathogen-discovery pipelines CaPSID, P-DiP and SEPATH. The estimated relative abundance of a virus was calculated as viral reads per million extracted reads (PMER) at the genus level to improve consistency between pipelines. To minimize the rate of false-positive hits in virus detection, we applied a strict threshold of PMER > 1 supported by at least three viral reads as suggested in previous studies,. Virus detection in a sample by at least two pipelines was considered to be a consensus hit. In total, 532 genera were considered for the extensive virus search in at least two of the pipelines (Extended Data Fig. 1d, Supplementary Table 18). Filtering of suspected viral laboratory contaminants was achieved through P-DiP, by examining each assembled contig of viral sequence segments for artificial, non-viral vector sequences and inspecting virus genome coverage across all positive samples (Extended Data Fig. 2a). The most frequent hits prone to suspected contamination were lambdavirus, alphabaculovirus, microvirus, simplexvirus, hepacivirus, cytomegalovirus (CMV), orthopoxvirus and punalikevirus; these were observed across many tumor types (Fig. 1b). For example, mastadenovirus showed an uneven genome coverage that could result from contaminating vector sequences. Therefore, we analyzed the virus detections across sequencing dates (Extended Data Fig. 2b) to assess any batch effect indicative of a contaminant; in mastadenovirus, we identified an association with sequencing date in early-onset prostate cancer regardless of tumor–normal state. We conclude that our mastadenovirus detections are due to a contamination that occurred across projects worldwide for which similar patterns could be identified.

5We generally observed a strong overlap of the genera identified across pipelines (Extended Data Fig. 1e, Supplementary Tables 6, 7, 11). From the WGS dataset, we identified 321, 598 and 206 virus–tumor pairs using P-DiP, CaPSID and SEPATH, respectively (Fig. 2a; overlap after random permutation of detections, Extended Data Fig. 3a, Supplementary Tables 3–5). The number of hits derived from the RNA-seq dataset differed between the pipelines (virus–tumor pairs: 101 for P-DiP, 83 for CaPSID, 41 for SEPATH; Fig. 2b, Supplementary Tables 8–10). SEPATH, which used a k-mer approach, detected the lowest number of virus hits and was the least sensitive. Despite this, the identified viruses matched well with the consensus (DNA 90%, RNA 95%). P-DiP, which was based on an assembly and BLAST approach, detected more hits with 59% of the DNA and 54% of the RNA hits in the consensus set, whereas CaPSID, which was the most sensitive, implemented a two-step alignment process complemented with an assembly step and identified 60% (DNA) and 80% (RNA) hits within the consensus set. Although the majority of the virus hits from RNA-seq (n = 61 out of 68 consensus hits based on RNA-seq) overlapped with the WGS data, a lower fraction of detections from the WGS data were present in the RNA-seq data (n = 61 out of 168 of 382 consensus hits based on WGS with available RNA-seq data), emphasizing the importance of DNA sequencing for generating an unbiased catalog of tumor-associated viruses. This difference can also be attributed to the viral life cycle, as viral gene expression can be minimal during incubation or latent phases. Contrasting virus-positive and virus-negative samples within each organ type shows that the organ system, as expected, has a significant influence, but virus positivity does not (P < 2 × 10−16, analysis of variance modeling of candidate reads that are dependent on organ system and virus positivity; Extended Data Fig. 1c). This indicates that virus-positive tumors were not detected owing to a higher number of candidate reads; this is consistent with the fact that the viral reads in most cases do not substantially contribute to the reads analyzed. In total, 86% of the sequence hits detected in WGS and RNA-seq data were found to be from double-stranded DNA viruses and double-stranded DNA viruses with reverse transcriptase (Fig. 1c, Supplementary Table 19). This could be attributed to (1) a higher frequency of tumor-associated viruses from these genome types, (2) a larger sequencing dataset for WGS compared with RNA-seq, (3) a potential limitation of our analysis due to DNA and RNA extraction protocols that are less likely to include single-stranded DNA or RNA viruses or (4) the selection bias of tumor entities included in the PCAWG study (Fig. 1c).

6We used a consensus approach that resulted in a reliable set of 389 distinct virus–tumor pairs from WGS and RNA-seq data (Fig. 2a–d). Overall, 23 virus genera were detected across 356 patients with cancer (13%). The top-five most-prevalent viruses (lymphocryptovirus, orthohepadnavirus, roseolovirus, alphapapillomavirus and CMV) account for 85% of the consensus virus hits in tumors (n = 329 out of 389). Among these five prevalent virus genera, three have been well described in the literature as drivers of tumor initiation and progression: (1) lymphocryptovirus (n = 145 samples (5.5%); for example, EBV) is the most common viral infection across a variety of tumor entities that mainly occur in the gastrointestinal tract and shows a much lower prevalence in the matched non-malignant control samples (n = 82 (3%); Fig. 2c); (2) orthohepadnavirus (n = 67 (2.5%); for example, HBV) is—as expected—the most frequent among liver cancer with HBV present in 62 of 330 donors (18.9%); and (3) alphapapillomavirus (discussed below). Lymphocryptovirus (n = 11), orthohepadnavirus (n = 18) and alphapapillomavirus (n = 32) were detected in both RNA-seq and DNA-sequencing data (Fig. 2c, left), of which alphapapillomavirus was the most frequent (32 out of 39 consensus hits). This is consistent with the constitutive expression of viral oncogenes in cancers associated with these viruses, a parameter that supports a direct role in carcinogenesis. An in-depth analysis of the virus genome equivalents per human tumor genome equivalent, which considers genome sizes, coverage and tumor purity, showed overall low viral genome equivalents even for established tumor viruses (Extended Data Fig. 3c, Supplementary Table 12). Evidence of a mouse mammary tumor virus (MMTV, PMER = 3.4) was detected in one renal carcinoma sample and in none of the 214 analyzed breast cancer samples. Previous work has suggested that MMTV may have a role in breast cancer but our comprehensive search of viral sequences could not identify any MMTV-positive case in breast cancer that would support this claim.

7Roseolovirus and alphatorquevirus show a higher number of hits in non-malignant control samples, which were mainly derived from blood cells (Fig. 2c). For example, we identified 59 patients as roseolovirus-positive (human herpesvirus (HHV)-6A, HHV-6B and HHV-7) in their tumors (pancreas, 6%; stomach, 8%; colon/rectum, 8.3%) and 90 patients positive in the non-malignant control samples. Considering the known cell tropism of roseolovirus for B and T cells, we asked whether immune infiltration would be higher in roseolovirus-positive tumors. However, we could not identify a stronger contribution of immune cells in virus-positive tumor cases as estimated using CIBERSORT (false-discovery rate (FDR)-corrected P > 0.05 for pancreas; Extended Data Fig. 4a). Therefore, consistently with current knowledge (reviewed in ref. ), we cannot confirm a link between roseolovirus and immune-cell content or tumor development. Furthermore, we could not identify actively transcribed viral genes for roseolovirus and alphatorquevirus at the transcriptome level. This is in agreement with the latent state of these viruses in blood mononuclear cells, and their transmission through blood transfusions. CMV was found, as expected, after identification and removal of contaminations in both stomach tumors (n = 13) and the adjacent non-malignant tissue (n = 11). In line with a recent publication, we could not detect CMV in the 294 tumors of the central nervous system (146 medulloblastomas, 89 pilocytic astrocytoma, 41 glioblastomas and 18 oligodendrogliomas) that were analyzed. Therefore, a previously debated role of this virus is not supported. Notably, we did not identify a significant enrichment of co-infection of multiple viruses in any tumor type (Extended Data Fig. 3d).

8HBV was most frequently detected in liver cancers (n = 62). Compared with the histopathological gold-standard HBV PCR test, (n = 228), the WGS-based consensus detections had the same high specificity (96.1%) and a high sensitivity (84.0%), indicating that HBV detection using WGS is reliable (Fig. 3a, Extended Data Fig. 4b, Supplementary Table 13). Furthermore, five out of the seven cases that were positive using WGS but negative for HBV PCR showed positivity for HBAg, indicating that the WGS analysis has a high sensitivity. In summary, the precision (85.7%) and recall (84%) for the detection of HBV based on around 30-fold-coverage WGS data were comparable to those of targeted PCR. We confirmed a significant exclusivity between HBV infection and mutations in CTNNB1, TP53 and ARID1A that was found in a larger liver cancer cohort analyzed by high-throughput sequencing (FDR-corrected P = 5.35 × 10−6, 0.0023 and 0.0023, respectively; DISCOVER).

9EBV was detected in many different tumor entities and normal samples (Fig. 2c). When comparing the PMER of EBV in tumor and matched normal samples, we see a stronger contribution in matched normal samples from matched solid tissue or tissue adjacent to the tumor (Extended Data Fig. 4c). For samples that contained reads for EBV in WGS and with available RNA-seq data, the absolute score for immune cells based on CIBERSORT was not significantly different between virus-positive and virus-negative samples (FDR-corrected P > 0.05 for colon/rectum, head-and-neck, lymphoid and stomach; Extended Data Fig. 4a). In summary, there is no evidence that the detection of EBV is due to infiltrating immune cells. This indicates the presence of EBV in the respective organs. On the basis of the expression data available for the tumor samples, we identified viral transcripts of the latent as well as lytic phase of the viral life cycle (Fig. 3b, Extended Data Fig. 4d, Supplementary Table 13). Eight of the nine tumors that expressed lytic EBV transcripts were from stomach cancers, confirming the active contribution of EBV to gastric cancer.

10Alphapapillomaviruses were mainly detected in head-and-neck cancers (n = 18 out of 57), cervical cancers (n = 19 out of 20) and in two bladder cancer cases out of 23, in agreement with previous studies,,. There is also supporting evidence for 32 out of 39 alphapapillomavirus hits in the whole-transcriptome data (Fig. 2c). We observed only one HPV subtype per tumor according to the P-DiP results and HPV16 was the dominant type in cervical (n = 11) and head-and-neck (n = 15) tumors, followed by HPV18, which was present in only cervical cancer (n = 6). As reported previously, HPV33 was identified in head-and-neck (n = 3) and cervical (n = 1) tumors. Different HPV variants, type 6 and 45, were detected in bladder cancer.

11In head-and-neck cancer, HPV-positive tumors exhibited an almost complete mutual exclusivity with mutations in known drivers such as TP53, CDKN2A and TERT (FDR-corrected P = 1.73 × 10−5, 1.73 × 10−5 and 0.012, respectively; multiple testing corrected for presented mutations in EBV and HPV, DISCOVER) (Fig. 3c, Supplementary Table 13), as reported previously, which could be explained by the mutation-independent inactivation of TP53 due to the human papillomaviruses,,. Furthermore, we found that mutational signature 2 was enriched in alphapapillomavirus-positive cases of head-and-neck cancer (FDR-corrected P = 0.02; Fig. 3d, Supplementary Tables 12, 22). In addition, the expression of APOBEC3B is significantly higher in virus-positive head-and-neck cancers compared with virus-negative cancers (P = 1.6 × 10−4; Fig. 3f). However, we did not observe enrichment of APOBEC signatures and changes in expression in EBV-positive samples found in the cervix or in other tissues.

12Distinct expression profiles between virus-positive and virus-negative tumors in head-and-neck cancer were observed (Fig. 3e, Supplementary Table 23). Analyzing the immune cells estimated by CIBERSORT, we identified a significant increase in macrophages and T-cell signals in alphapapillomavirus-positive head-and-neck cancers (P = 0.004, 0.012 and 0.012 for follicular helper, CD8 and regulatory T cells, respectively, and P = 0.018 for M1 macrophages; FDR corrected for all viruses and cell types tested; Fig. 3g, Supplementary Table 24). Our integrative analysis of HPV reconfirms many of the findings related to HPV infection, illustrating the potential of our systematic approach in identifying and characterizing tumor-associated viruses.

13Human endogenous retroviruses (HERV) are integrations in the human DNA that originate from infection of germline cells by retroviruses over millions of years and contribute over 500,000 individual sites, or 2.7% of the overall sequence the human genome,. ERVs were identified by all three pathogen-detection pipelines but were filtered by CaPSID and SEPATH. In addition, an alignment-based approach was used to detect HERV sequences that were embedded in the human reference genome that could be missed by the pipelines by focusing only on non-human reads. In this study, we quantified the expression of HERV-like long terminal repeat retrotransposons that were categorized into several clades by Repbase as ERVL, ERVL-MaLR, ERV1, ERVK and ERV (Supplementary Table 14). In comparison to the other HERV families, ERV1 shows the strongest expression on average (Fig. 4a) and ERVK the highest fraction of active loci (Fig. 4b). By analyzing the expression of HERVs, we could identify strong expression of ERV1 in chronic lymphocytic leukemia compared with all other tumor tissues and adjacent normal tissues (Fig. 4c). However, we could not identify a link between transcriptionally active stemness markers (OCT3/4, SOX2 and KLF4) and increased HERV expression, in contrast to a previous report (Spearman rank correlation <0.35; Extended Data Fig. 5). New data suggest that expression of HERVs is associated with prognosis in clear cell renal cell carcinoma. Analyzing HERV expression in relation to patient survival, we found that high ERV1 expression in kidney cancer was linked to worse survival outcome (P = 0.0081; log-rank test; Fig. 4d, Extended Data Fig. 6, Supplementary Table 15).

14Viral integration into the host genome has been shown to be a causal mechanism that can lead to the development of cancer. This process is well-established for HPVs in cervical, head-and-neck and several other carcinomas, and for HBV in liver cancer,.

15Low-confidence integration events were detected for HHV4 (gastric cancer and malignant lymphoma) and HPV6b (head-and-neck and bladder carcinoma), whereas integration events with high confidence were demonstrated for HBV (liver cancer), AAV2 (liver), HPV16 and HPV18 (in both cervical and head-and-neck carcinoma). Most of these integration events were found to be distributed across chromosomes and a significant number of viral integrations occurred in the intronic (40%) regions whereas only 3.4% of integrations was detected in gene coding regions (n = 84 intronic versus n = 31 other regions excluding intergenic regions, two-sample test for equality of proportions, P = 7.0 × 10–12; Extended Data Fig. 7a–d).

16HBV was found to be integrated in 36 liver cancer specimens out of 61 patients who were identified to be HBV positive. Notably, genomic clusters of viral integrations were identified in TERT (number of integration sites within a genomic cluster (NGC) of 6), KMT2B (NGC = 4)—which was recently identified to be a likely cancer driver gene,—and RGS12 (NGC = 3) (Extended Data Fig. 7e). Furthermore, two or more integration events in individual samples were observed in the gene (or gene promoter) regions of CCNE1, CDK15, FSIP2, HEATR6, LINC01158 (also known as PANTR1), MARS2 and SLC1A7 (Fig. 5a). Additional events with two integration sites were also detected within a distance of 50 kb from CLMP, CNTNAP2 and LINC00359 genes. Integration events at TERT were found to recur in five different liver cancer samples. One sample had a genomic cluster of three viral integration events within TERT and four samples contained a single integration event in the TERT promoter, or 3′ or 5′ untranslated regions (UTR) (Supplementary Table 17). When comparing gene expression in samples with virus integration to those without, we found that only TERT was overexpressed (fold change ≥2.0) in two liver cancer samples (Fig. 5e). Additional genes with increased expression that were influenced by integration events include TEKT3, CCNA2, CDK15 and THRB (Fig. 5a).

17There was a significant association between HBV viral integrations and somatic copy-number alterations (SCNAs, Fig. 5c). For samples with HBV integration events, the number of SCNAs was higher on average in the vicinity of viral integration sites (within 1 Mb) compared with samples without HBV integration (mean 4.2 versus 2.3, P = 7.4 × 10−3; two-sided paired t-test). No evidence of an SCNA association was seen for other integrated viruses like HPV16 and HPV18 (Extended Data Fig. 8a,b).

18HPV18 integration events were detected in seven tumors in total (Fig. 5b), with the most notable clusters of integration events that affected TALDO1 (NGC = 4) in cervical cancer samples (Extended Data Fig. 7g).

19In 20 samples, HPV16 integration events were detected. Genomic clusters of viral integration sites were identified in cervical and head-and-neck cancer samples (Extended Data Fig. 7f). None of these multiple integration events were observed to recur across patients (Fig. 5b). Integration events were also observed in two different long noncoding RNAs (lncRNAs), LINC00111 and the plasmacytoma variant translocation 1 gene (PVT1), an oncogenic lncRNA,. Expression of both genes is strongly increased in the cases with HPV16 integration (Extended Data Fig. 8f, Supplementary Table 17).

20Using the PCAWG SNV calls, we found a significant increase in the number of mutations that occurred within ±10,000 bp of high-confidence viral integration sites (average number of mutations per sample, 0.41 (HPV16+) versus 0.14 (HPV16−), P = 0.02; one-sided paired t-test, alternative greater, Extended Data Fig. 8c,d). Notably, the integration sites are—compared with a random genome background—enriched in proximity (<1,000 bp) to common fragile sites (P = 0.0018, Kolmogorov–Smirnov test). These results suggest that HPV16 integration reflects either characteristics of chromatin features that favor viral integration, such as fragile sites or regions with limited access to DNA repair complexes, or the influence of integrated HPV16 on the host genome. Such a correlation was not seen for the integration sites of other viruses (Extended Data Fig. 8e). Finally, a single AAV2 integration event located in the intronic region of the cancer driver gene KMT2B was detected in one liver cancer sample.

21De novo analysis using the CaPSID pipeline has generated 56 different contigs that have been classified into taxonomic groups at the genus level by CSSSCL. After filtering de novo contigs for their homology to known reference sequences, we identified 29 contigs in 28 different tumor samples that showed low sequence similarity (on average 63%) to any nucleotide sequence contained in the BLAST database. In this respect, our analysis has shown that WGS and RNA-seq can be used to identify isolates from potentially new viral species. However, the total numbers of novel isolates were low in comparison to viral hits to well-defined genera (Fig. 2c). These de novo contigs were not enriched for a specific tumor entity but rather were distributed across cancer types including bladder, head-and-neck and cervical cancers (Extended Data Fig. 9).

22Searching large pan-cancer genome and whole-transcriptome datasets enabled the identification of a high percentage of virus-associated cases (16%). In particular, analysis of tumor genomes, which were sequenced on average to a depth of at least 30-fold coverage, identified considerably more virus-positive cases than investigations of whole-transcriptome data alone, which is the search space analyzed in most previous virome studies. This is probably mainly due to viruses with no or only weak transcriptional activity in the given tumor tissue. Co-infections, generally believed to indicate a weak immune system, were very rare (Extended Data Fig. 3d). This could, however, also be the result of selection processes during tumorigenesis.

23Although universal criteria for a causality of viral pathogens are prone to errors, it is worthwhile to look at individual features that might support a potentially pathomechanistic contribution of a given pathogen. These include aspects that affect the expression of host factors (for example, after viral integration) or the mutual exclusivity of the presence of viral genomes and other host factors, which are already known to have a role in the etiology of a given tumor type. Such aspects need to be carefully considered when discussing what strengthens the potentially pathogenic role of a virus.

24Not surprisingly, known tumor-associated viruses, such as EBV, HBV, HPV16 and HPV18, were among the most frequently detected targets. Notably, viral detection based on WGS showed similar performance with respect to precision and recall as a targeted PCR for HBV, indicating that this approach is sensitive to detect viruses. This is particularly true for the common integration verified for HBV, HPV16 and HPV18 in our study. In addition, the common theme of potential pathomechanistic effects by the genomic integration of viruses, which were also supported by the observations of multiple nearby integration sites in a given tumor genome that we report in the present study, has gained further momentum. By analyzing the effect of viral integrations on gene expression, we identified several links to genes nearby the integration site. In this regard, the frequently observed integration of HBV at the TERT promoter accompanied with the transcriptional upregulation of TERT constitutes an intriguing mechanistic example, as the increased activity of TERT is a well-understood driver of carcinogenesis. Furthermore, we also linked viral integrations to increased mutations (SNVs and SCNAs) nearby the integration site.

25The known causal role of HPV16 and HPV18 in several tumor entities, which triggered one of the largest measures in cancer prevention, has been the motivation for extensive elucidation of the pathogenetic processes involved. Nevertheless, comprehensive analyses of WGS and RNA-seq datasets revealed additional novel findings. While we confirmed the exclusivity of HPV infection and TP53, CDKN2A and TERT mutations in head-and-neck tumors, we could also link virus presence to an increase in mutations attributed to the mutational signature 2 (ref. ). These are explained by the activity of APOBEC, which—among other effects—changes viral genome sequences as a mechanism of cellular defense against viruses,. This activation could have an important function in introducing further host genome alterations and, thus, constitute an important mechanism that drives tumorigenesis,. In liver cancer, mutations in CTNNB1, TP53 and ARID1A, major primary oncogenes in this cancer type and HBV infections were confirmed to occur significantly mutually exclusive. Furthermore, the virus-positive head-and-neck cancer samples had a significantly higher abundance of T-cell and M1 macrophage expression signals, which is in agreement with recently described subtypes of head and neck squamous cell carcinoma that differ—among other features—in virus infection and inflammation features.

26To reduce the number of reads to be considered for the pathogen search, we identified potential pathogenic reads by using P-DiP (https://github.com/mzapatka/p-dip). On the basis of reads aligned to hg19 by BWA or STAR using the standard PCAWG approach, we identified read pairs for which at least one read did not map well to the human genome (longest stretch of mapped bases from 20 to 30 bases) and read pairs that were unmapped or mapped to NC_007605 (human herpesvirus 4, which is contained in the 1000 Genomes version of the hg19 human reference genome), and extracted these for further processing. To speed up the extraction, we used bamcollate2 from Biobambam2 (v.2.08) as an input stream to the Python script.

27The expression of ERVs was analyzed using RNA-seq data and aligned STAR sequences based on the settings developed within PCAWG (hg19 and Gencode 19). In contrast to the standard pipeline, the reference transcripts from Gencode 19 were enriched by adding HERV locations extracted from RepeatMasker (http://www.repeatmasker.org, rmsk from UCSC, version 17/08/03) and Featurecounts (subread-1.5.3) applied to identify reads mapping to the modified reference transcripts. Resulting reads counts were converted into TPM according to Wagner et al..

28Our starting point is to take reads that are not mapped to the human genome, using the extracted potentially pathogenic reads. Low quality bases (q < 30) were trimmed from the read ends and the TruSeq indexed adapter and TruSeq universal adapter were removed using Cutadapt (v.1.8.1). Reads less than 32 bp were discarded. Additional filtering was performed to remove reads that contained more than 5% of Ns or those with low complexity (dust method with maximum score of 10) by using Prinseq (v.0.20.3). Metagenomic Phylogenic Analysis (MetaPhlAn), was then applied to identify and quantify the presence of bacterial and viral populations. MetaPhlAn comes with a curated marker database of around 1 million unique clade-specific marker genes identified from reference genomes (version 2.0 of the database was used). Reads were aligned against the unique marker gene database by using Bowtie2 (v.2.2.1) with presets set to sensitive. Reads were then counted and normalized giving an estimation of the relative abundance for each level of the phylogenetic tree.

29The assembly-based pipeline (P-DiP) was further developed based on a version implemented by M.A. and A.G.. In summary, the pipeline runs preprocessing, assembly and BLAST searches and stores processing details and final results in a postgreSQL database. For the WGS and RNA-seq analyses, we started with the potentially pathogenic reads extracted from the BWA-aligned WGS BAM files. As a first step, reads were trimmed based on quality using trimmomatic. Thereafter, host reads were subtracted by aligning to the human reference genome (WGS: hg19 excluding NC_007605 and hs37d5 and adding phiX; RNA sequencing: Homo_sapiens.GRCh37.dna.primary_assembly) using Bowtie2 (v.2.2.8). Trinity (v.2.0.6) was used for the read assembly of WGS reads that were not aligned by Bowtie with sufficient quality (not aligned with --very-fast (-D 5 -R 1 -N 0 -L 22 -i S,0,2.50) to Homo_sapiens.GRCh37.ncrna, Homo_sapiens.GRCh37.cdna.all or PhiX); for the RNA-seq data we applied idba assembler (v.1.1.3). Assembled contigs were filtered by size (minimal length of 300 bp). Abundance was estimated by remapping all of the reads that did not align to the human reference to the assembled contigs by using Bowtie2. Putative PCR duplicates identified by mapping location were removed from the abundance count. The taxonomic classification of the size-filtered contigs was performed using the BLAST+ package (v.2.2.30) and nucleotide databases nt (ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz, accessed 15 May 2015) and nr (https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz, accessed 20 April 2015). For the extraction of pathogen hits R-scripts were used to filter the BLAST results (https://github.com/mzapatka/p-dip). In summary, for each of the contigs, the best BLAST hits for each segment of the contig were considered and the reads aligning to these segments identified. Potential contaminants were defined based on the taxonomy annotation in NCBI taxonomy. Any taxonomy ID below plasmids (36,549), transposons (2,387), midivariant sequences (31,896), insertion sequences (2,673), artificial sequences (81,077) and synthetic viruses (512,285) was annotated as potential contamination. Segments with higher read counts of these sequences compared to pathogen hits were flagged as contaminants and not further considered.

30The metagenomic analysis pipeline of CaPSID starts by first processing a BAM file that contains the reads sequenced from a tumor (or normal) sample aligned to the human reference sequence (GRCh37/hg19). Reads that did not map to the human reference were extracted and filtered for low complexity and quality using the SGA preprocessing module and then aligned in single-end mode using the Bowtie2 aligner to 5,652 NCBI viral reference sequences (RefSeq) and a filter sequence reference database composed of 5,242 bacterial and 1,138 fungal reference sequences that were also downloaded from the NCBI. To improve the sensitivity and specificity with which viral sequences were detected, reads that did not map to any reference with Bowtie2 were realigned to the same viral RefSeq database, using the more-sensitive aligner SHRiMP2 in local alignment mode. At the completion of this two-step alignment process, reads that aligned to viral reference sequences were annotated using the information stored in the genome database of CaPSID, which contains full NCBI GenBank and taxa information. Using information from each aligned read, CaPSID then calculates the following four metrics: (1) the total number of reads (or hits) that aligned across any given viral genome, (2) the total number of reads that aligned only across gene regions within any given viral genome, (3) the total coverage across each viral genome and (4) the maximum coverage across any of the genes in a given viral genome.

31For the analysis of the tumor WGS or RNA-seq samples, CaPSID reports candidate sequences from dozens of different viral genomes, some of which are not related to the cancer phenotype. Some of these reported viral hits are also due to a series of experimental and computational artifacts. To reduce the number of potential false-positive hits, the CaPSID pipeline flags viral genomes that could be the result of artifacts present in the sequencing data or those with no obvious relation to cancer phenotype and that could be filtered in subsequent steps. The following criteria were used to flag and filter for potential viral candidates: (1) flag viral candidates with low coverage, (2) flag bacteriophage viral genome sequences, (3) report only viral candidates with a read composition different from the one expected when generated from the host’s reference GRCh37/hg19 sequence, (4) flag viral candidates that are typically not known to infect humans and those with low read abundance and/or low overall alignment read accuracy.

32In the first step, CaPSID flagged viral genomes with low read count and/or coverage using three metrics, including total number of uniquely aligned reads <3, total genome coverage <10% and maximum gene coverage <50%. Viral genomes with low read count can arise as a result of (1) low read/transcript abundance in the human sequenced sample, (2) unspecific alignment between sequenced short reads (for example, low complexity reads) and viral reference sequences and (3) for RNA-seq library preparation in which highly expressed transcripts generally dominate over low abundance targets. To limit the reporting of viral genomes with very low coverage, we chose to flag all genomes for which the maximum gene coverage was <50%. As this lower bound on the maximum gene coverage applied to individual genes and not to the complete viral genome, it appears to be unlikely that viruses with such low coverage are biologically important. The second step in our filtering approach was to flag bacteriophage viral genomes that are most likely not related to any cancer phenotype. Bacteriophages are detected as a result of the presence of bacteria (or bacterial contamination) in human sequenced samples. The third step was used to determine whether the genome coverage observed for each viral candidate was different from the one expected to arise from reads that originated exclusively from the human reference DNA GRCh37/hg19 sequence. To build the CaPSID background model, we used the ART NGS read simulator. The entire GRCh37/hg19 sequence reference file is first fed to the ART simulator (parameters: art_illumina [Illumina platform] -l [read length=100 bp] -f [the fold of read coverage to be simulated=100] with default values for indels and substitution rates), which then generates single-end (or paired-end) reads and base quality values.

33Reads simulated by ART were then aligned to the viral reference sequence database using the same alignment approach for reads that originated from tumor samples (see above). CaPSID then calculated the four metrics for the GRCh37/hg19 background model using the alignment information from simulated reads that aligned to viral reference sequences. The fourth step consisted of flagging viral candidates that were typically not known to infect humans using a dictionary of around 130 terms that we compiled from a database of all viruses known to infect humans. In addition to the above filtering criteria, CaPSID also considered the read abundance associated with each viral candidate sequence (abundance is expressed in terms of aligned reads in parts-per million of total number of unmapped reads) and the average read percentage identity with which reads aligned to a given viral candidate reference sequence.

34The purpose of this analysis step is to attempt to characterize potential novel viral sequences at the species or subspecies level. Unaligned reads that could not be aligned to any of the filter/host or viral reference sequences were assembled into contigs using the IDBA algorithm. Assembled contigs were then masked for repeat regions by using RepeatMasker and then filtered for their size and read coverage (contig length ≥500 bp and coverage >5×). Resulting contigs were then assigned to taxonomic groups at the genus level by using the CSSSCL algorithm. Contigs lacking sequence homology to reference sequences contained in the CaPSID or BLAST nucleotide databases with percentage identity <90% were then selected as suggestive of the presence of new viral strains/isolates or species.

35Identification of the consensus hits was achieved by optimizing two features of the individual genus hits: PMER 1 as cut-off (Supplementary Note) and percentage identity >90%. The 90% percentage identity threshold was determined based on our benchmarking study that indicated that an alignment-based approach can still accurately characterize viral sequences with up to 10% mutation rate (compared with sequences stored in a reference database). Lowering the threshold, with which short reads align to any given reference sequence below 90% identity on average, results in a drop of sequence coverage due to a high attrition rate of aligned reads, lowering the detection rate and thus providing more uncertain characterizations of viral candidates. Notably, there was no difference in the PMER distribution of common hits across the three pipelines, indicating that a common detection cut-off is reasonable (Extended Data Fig. 3b).

36The consensus set was restricted to genera that were covered in at least two detection pipelines (Extended Data Fig. 1b). Notably, we could not detect any more hits with high PMER using the unique search space of P-DiP, indicating that almost all of the viral hits from individual pipelines were also screened by another pipeline.

37A subset of viral candidates identified to be present in tumor samples by the CaPSID analysis pipeline (parameters used: PMER ≥ 1.1 and genome coverage > simulated background model) was selected for the detection of viral integration events using the VERSE algorithm. This subset of viruses included: herpesviruses (HHV1, HHV2, HHV4, HHV5, HHV6A/B), simian virus 40 (SV40) and 12 (SV12), human immunodeficiency virus (HIV1), human and simian T-cell lymphotropic virus type 1 (HTLV1 and STLV1), BK polyomavirus (BKP), human parvovirus B19, mouse mammary tumor virus, murine type C retrovirus, Mason–Pfizer monkey virus, HBV, HPV (HPV16, HPV18 and HPV6a) and AAV2. Below we describe the steps used for the viral integration detection analysis.

38Viral integration events in the host can be detected by using paired-end NGS technologies that facilitate the detection of genomic rearrangements, as well as gene fusions and novel transcripts. VERSE is capable of determining virus integration sites within a single base resolution by requiring the presence of both chimeric and soft clipped reads. In addition, VERSE improves the detection through customizing reference genomes and was shown to substantially enhance the sensitivity of the detection of virus integration sites. VERSE categorizes its predictions into one of two classes: (1) a high confidence hit with a single base resolution—if there was a sufficient number of soft-clipped reads to support an integration locus so that CREST was able to detect it; or (2) a low confidence hit with a 10-bp resolution for which CREST failed to detect an integration event because of the lack of high-quality soft-clipped reads.

39To further limit the false-positive rate associated with viral integration sites, we compared results obtained with VERSE to those from a previous study. Out of 64 WGS liver cancer samples with HBV integration events that were reported previously, 50 were part of the PCAWG dataset analyzed in this study. Of those, 45 out of 50 tested positive for HBV when analyzed by CaPSID (filtering criteria used: PMER ≥ 1.0, genome coverage > host background model and read percentage identity ≥89%). In addition, 50 of these WGS samples had 23 matching whole-transcriptome samples and 22 of these were identified to be positive for HBV by CaPSID (filtering criteria used: maximum gene coverage ≥50%, read percentage identity ≥89% and PMER ≥ 1.0). By combining WGS and RNA-seq tumor samples, 47 out of 50 samples tested positive for HBV when analyzed by CaPSID.

40Using VERSE, virus integration sites were detected in 28 out of 47 (60%) of these. This result indicates that for a subset of viral integration events, VERSE might be a more stringent approach compared to previously used methods. This can be explained by the fact that VERSE requires both the presence of paired-end chimeric and soft clipped reads whereas the previously described method relied only on paired-end reads. To explore these results further, we compared integration sites obtained with VERSE and those described previously with an overlapping window of 10 bp. Our analysis indicates that among 23 integration sites identified by VERSE in RNA-seq data and that overlap with the previously published results, 91% were classified with high confidence hits and only 9% with low (N total overlap = 23, high = 21 (91%) and low = 2 (9%)). However, a similar result was not observed for integration events found using WGS data (N total overlap = 14, high = 6 (43%), low = 8 (57%)), for which the proportion of integration events classified as high and low was similar.

41Thus, our analysis indicates that one important factor for improving the agreement between these two datasets is the confidence level assigned by VERSE to each candidate integration site—but only in the case when integration sites are detected using RNA-seq data. To reduce the potential number of false-positive hits, we decided to use all integration sites predicted by VERSE when these were obtained using WGS data and only high-confidence calls when using RNA-seq data.

42On the basis of the presence of vector sequences in the contig assembled by P-DiP and the background model from CaPSID, we could identify which virus hits originated from common laboratory contaminants or were due to sequence similarities to the human genome. In addition, we filtered known contaminants (see below). For P-DiP, we filtered all hits that did not have more target reads than any artificial sequence (excluding artificial viruses) on an individual contig region. Hits caused by vector and other artificial sequences were identified by analyzing the assembled contigs for combined hits to viral pathogens and artificial sequences. Checking viral hits that occurred at least 40 times in such a contig, we could clearly separate contaminants from viral pathogens.

43The gammaretrovirus hits (NCBI taxonomy ID 153135; species, murine leukemia virus) were also marked as artifacts, on the basis of the additional BLAST hits of the corresponding contigs to the Mus musculus genome by P-DiP as well as the background model of the CaPSID pipeline, which was designed to limit the number of spurious hits. Most of the frequent virus hits prone to contamination by artificial sequences were lambdalikevirus, alphabaculovirus, microvirus, simplexvirus, hepacivirus, CMV, orthopoxvirus and punalikevirus. However, restricting to at least 1 PMER for the potential virus hit contaminants reduced these to one CMV case.

44We filtered all Microviridae (taxonomy ID 10841) because of the phix174 spike-in used during sequencing. Caudovirales (taxonomy ID 28883), tailed bacteriophages, were removed as they typically infect bacterial hosts. Baculoviridae were filtered because these infect insect cells and are commonly used in the laboratory. The virus coverage was analyzed by aligning the potentially pathogenic reads with BWA-mem to the human hg19 reference genome after adding the respective virus reference sequence that was most frequently detected within the genus. Coverage was thereafter calculated base specific using BEDTools coverage. As we identified EBV in all 14 normal blood controls from ovarian cancer that were EBV immortalized, these were removed from the virus hits.

45We tested for mutual exclusivity, for example, between virus detections and driver gene mutations by applying DISCOVER. On the basis of the gene expression data, immune-cell proportions were analyzed by CIBERSORT. For survival analysis, Cox proportional hazards analysis was performed using R libraries ‘survival’ and ‘survminer’ for the figures. The optimal cut points were identified by maxstat using a previously described method (library maxstat).

46The viral load in relation to the human genome equivalents was calculated based on the human bases sequenced (read length × number of reads mapped to the human genomes), tumor sample purity (if available or 100% otherwise) assuming a ploidy of two and using a human genome size of 2,897,310,462 bases (the mappable part of the human genome). This number of human genome equivalents was then related to the viral genome equivalents that were calculated based on the number of identified viral reads, read length and virus genome size.

47The ethics oversight for the PCAWG protocol was undertaken by the TCGA Program Office and the Ethics and Governance Committee of the ICGC. Each individual ICGC and TCGA project that contributed data to PCAWG had its own local arrangements for ethics oversight and regulatory alignment.

48If not specified otherwise, we used two-sided Wilcoxon rank-sum tests for groups with n > 3. Further details can be found in the Nature Research Reporting Summary.

49Further information on research design is available in the Nature Research Reporting Summary linked to this article.

50Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41588-019-0558-9.