Viral DNA integration: Many bacterial and animal viruses lie dormant in the infected cell, and their DNA may be integrated into the DNA of the host cell chromosome. The integrated viral DNA replicates as the cell genome replicates. Several diseases are closely associated with virus integration, for example AIDS and liver cancer.

We developed HIVID, a detection method for integration sites in the human genome of a new generation of viruses based on viral sequence capture. For the first time, HIVID uses virus probe capture technology to enrich virus DNA fragments, while also making innovative improvements in bioinformatics algorithms. Compared to traditional methods that use whole-genome sequencing to detect viral integration, HIVID greatly reduces costs and improves efficiency. Not only can high frequency virus integration be detected, but also very low frequency virus integration events can be detected. Then we applied the HIVID method to detect the integration of HPV virus in cervical cancer cells, discovered new recurrent integration genes, and proposed the micro-homologous integration mechanism of the virus and human genome for the first time. Subsequently, we applied the HIVID method to the study of the distribution of integration sites of HBV virus DNA in the liver cancer cell genome and found multiple new recurrent integration genes. The successful implementation of these two projects is of great significance for the clinical treatment of cervical cancer and liver cancer. For example, it can use newly discovered integrated hotspot genes to design diagnostic kits and new drugs.

Key words: Virus integration; host genome; sequencing; cancer