Neutral red (NR) is a dye that must be actively imported into the cell, and, therefore, the dye has been used for decades to selectively stain living cells. In addition, NR can also be incorporated into virus particles, although the mechanism behind this is poorly understood. Once encapsulated into the virion, NR, a light sensitive dye, can be photoactivated to inactivate the virus. The proposed mechanism explaining this observation is that activation of NR allows the dye to cross-link viral genome to viral capsid and thus preventing viral uncoating and infection. To study the early events of murine norovirus (MNV)-host interaction, light-sensitive NR-containing MNV is used to distinguish between input virus (i.e., NR-containing virus) and replicated virus (i.e., NR-free virus). This protocol describes the incorporation of NR into MNV capsids and the use of these virions for detection of viral replication in a mouse and in tissue culture by standard plaque assay. The same technique is also used for study of poliovirus replication (1-3). Thus, there is the potential that this technique can be used for additional non-enveloped viruses. However, this has to be tested on a case-by-case basis as unpublished data on feline calicivirus suggests not all viruses may be able to stably incorporate NR into their capsid (J. Parker, personal communication).