Treatment of human excreta and animal manure (HEAM) is key in controlling the spread of persistent enteric pathogens such as viruses. The extent of virus inactivation during HEAM storage and treatment appeared to vary with virus genome type, though the reasons for this variability are not clear. Here, we investigated the inactivation of viruses of different genome types under conditions representative of HEAM storage or mesophilic digestion. The goals were to characterize the influence of HEAM solution conditions on inactivation and to determine the potential mechanisms involved. Specifically, eight viruses representing the four viral genome types (ssRNA, dsRNA, ssDNA, dsDNA) were exposed to synthetic solutions with well-controlled temperature (20-35°C), pH (8-9) and ammonia concentrations (NH3; 0-40 mmol L-1). DNA and dsRNA viruses were considerably more resistant than ssRNA viruses, resulting in up to 1000-fold longer treatment times to reach a 4 log inactivation. The apparently slower inactivation of DNA viruses was rationalized by the higher stability of DNA compared to ssRNA in HEAM. Pushing the system toward harsher pH (> 9) and temperature (> 35°C) conditions, such as those encountered in thermophilic digestion and alkaline treatments, led to more consistent inactivation kinetics among ssRNA and other viruses. This suggests that the dependence of inactivation on genome type disappeared in favor of protein-mediated inactivation mechanisms common to all viruses. Finally, we recommend the use of MS2 as conservative indicator to assess the inactivation of ssRNA viruses, and the stable ΦX174 or dsDNA phages as indicators for persistent viruses.