Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma

Intra-host tumor virus variants may influence the pathogenesis and treatment responses of some virally-associated cancers. However, intra-host variability Kaposi sarcoma-associated herpesvirus (KSHV), etiologic agent sarcoma (KS), has to date been explored with sequencing technologies that possibly introduce more errors than which occurs in viral population, these studies have only studied variable regions. Here, full-length KSHV genomes tumors and/or oral swabs from 9 Ugandan adults HIV-associated KS were characterized. Furthermore, we used deep, short-read using duplex unique molecular identifiers (dUMI)–random double-stranded oligonucleotides barcode individual DNA molecules before library amplification. This allowed suppression PCR ~10 ?9 /base as well afforded accurate determination genome numbers sequenced each sample. assembled de novo , rearrangements observed confirmed by Sanger sequencing. 131-kb sequences, excluding major repeat regions, successfully obtained 23 clinical specimens, averaging 2.3x10 4 reads/base. Strikingly, virtually identical within individuals at point mutational level. The heterogeneity was confined tumor-associated mutations rearrangements, all impacting protein-coding sequences. Although it is unclear whether changes important tumorigenesis or occurred a result genomic instability tumors, similar across individuals. These included inactivation K8.1 gene 3 retention region around first internal (IR1) instances deletions rearrangements. Notably, same breakpoint junctions found distinct single individuals, suggesting metastatic spread rearranged genomes. findings define vivo greater precision possible past suggest possibility aberrant contribute aspects tumorigenesis. study use dUMI provides proof concept for utilizing this technique detailed other populations vivo.