We analyse three viruses, which are biologically and medically different: AAV are single stranded DNA viruses and do not cause any disease, despite of causing chronic infections. They are thus the major platform for gene therapy: There are currently three licensed drugs for treatment of rare genetic diseases available. They are, however, very inefficient meaning that hundreds of viruses are required for infecting a single cell. Likely, inefficiency is caused by inefficient transport of the genome from the cell periphery into the nucleus and not hosts’ innate immune response counteracting infection. The aim of our research is the understanding of the restricting factors by using time-lapse microscopy in combination with genome-wide screening of restricting host factors.
HBV – in contrast to AAVs – are pathogenic and cause acute, fulminant and chronic infections, which are spontaneously cleared with low frequency of c. 1% per year. Chronic infections lead to liver cirrhosis and are the major cause for human hepatocellular carcinoma. HBV also comprises a DNA genome but of partially double stranded nature is - in contrast - extremely efficient. As AAV, it replicates in the nucleus of the cell and the nuclear DNA is very stable and cannot be targeted by current treatments. Our aim is the understanding of virus efficiency and the fate of the genome upon cell division. We address these questions by time-lapse microscopy similar to our studies on AAVs. We further investigate parts of the innate immune response, which may lead to spontaneous clearance of chronic infection. Our focus are deaminations of the viral genome, which may introduce a critical number of mutations, leading to mutated HBV with lower fitness. This is analysed by full-genome deep sequencing of hepadnaviral genomes and correlating the findings with clinical parameters of the patients.
In a similar way, we are analysing the deamination of SARS-CoV-2, which is an RNA virus replicating exclusively in the cytoplasm. We recently showed that increased deamination is correlated with a decreased viral load and with inflammation in the host.