Unbiased optical mapping of telomere-integrated endogenous human herpesvirus 6

Significance Low-complexity and repetitive elements are difficult to study using existing sequencing technologies. Determination of the boundaries and structures of the termini of inherited chromosomally integrated HHV-6 (iciHHV-6) genomes is particularly challenging, as it integrates into highly repetitive human telomeres. We therefore developed a genome imaging approach that revealed the chromosomal location of the virus, its orientation, the presence of long internal telomeres at the host−virus junction, and the lengths of the distal telomeres capping the integrated virus genome. This genome imaging approach has wide applications for mapping transposable elements or large viruses that integrate into low-complexity regions of host genomes.
Next-generation sequencing technologies allowed sequencing of thousands of genomes. However, there are genomic regions that remain difficult to characterize, including telomeres, centromeres, and other low-complexity regions, as well as transposable elements and endogenous viruses. Human herpesvirus 6A and 6B (HHV-6A and HHV-6B) are closely related viruses that infect most humans and can integrate their genomes into the telomeres of infected cells. Integration also occurs in germ cells, meaning that the virus can be inherited and result in individuals harboring the virus in every cell of their body. The integrated virus can reactivate and cause disease in humans. While it is well established that the virus resides in the telomere region, the integration locus is poorly defined due to the low sequence complexity (TTAGGG)n of telomeres that cannot be easily resolved through sequencing. We therefore employed genome imaging of the integrated HHV-6A and HHV-6B genomes using whole-genome optical site mapping technology. Using this technology, we identified which chromosome arm harbors the virus genome and obtained a high-resolution map of the integration loci of multiple patients. Surprisingly, this revealed long telomere sequences at the virus−subtelomere junction that were previously missed using PCR-based approaches. Contrary to what was previously thought, our technique revealed that the telomere lengths of chromosomes harboring the integrated virus genome were comparable to the other chromosomes. Taken together, our data shed light on the genetic structure of the HHV-6A and HHV-6B integration locus, demonstrating the utility of optical mapping for the analysis of genomic regions that are difficult to sequence.