In genome analysis, it is often important to identify variants from a reference genome. However, identifying variants that occur with low frequency can be challenging, as it is computationally intensive to do so accurately. LoFreq is a widely used program that is adept at identifying low frequency variants. This paper presents an FPGA-based accelerator for LoFreq. In particular, this accelerator is targeted at virus analysis, which is particularly challenging, compared to human genome analysis, as the characteristics of the data to be analyzed are fundamentally different. This accelerator can achieve up to 120X speedups on the core computation of LoFreq and speedups of up to 32.4X across the entire program.