Mouse Rotavirus

It is a virus that infects the intestinal tract and causes symptoms in mice 4 to 14 days old.

The virus primarily infects the cell lining the small intestine (epithelial cells), most of which are absorptive cells (enterocytes). It may also infect the large intestine in a similar manner. This damages the cells and causes the pups to:

"lack a full complement of enzymes for digestion and absorption, resulting in diarrhoea due to maldigestion and malabsorption."
Viral Infections of Laboratory Mice

It is also sometimes called Murine Rotavirus A (MuRV-A).

Primary rotavirus symptoms in infant mice:

• Yellow "mustard-like" diarrhea

• Swollen distended abdomen

• Inflamed or irritated vent

In more severe cases:

• Weight loss and dehydration

• Wavy or sparse coat from malnutrition

• Death due to dehydration and/or malnutrition

Since the main damage caused by the virus is done to the intestinal lining, it causes yellow diarrhea and malnutrition in pups 4 - 14 days old. How severe the symptoms are depends on the immune system of the individual mouse, and if the doe nursing them is immune. While it is common for infected pups to show symtoms, it is not likely that they will die due to it.

"Clinical symptoms following MuRV-A/EDIM infection range from inapparent or mild to severe, sometimes fatal, diarrhoea. ‘Epizootic diarrhoea of infant mice’ describes the clinical syndrome associated with natural or experimental infection by MuRV-A/EDIM during the first 2 weeks of life [8, 36, 291, 391, 392]. Diarrhoea usually begins around 48 h after infection and persists for about 1 week. Affected suckling mice have soft, yellow faeces that wet and stain the perianal region (Figure 3.2.8). In severe instances, the mice may be stunted, have dry scaly skin, or are virtually covered with faecal material. Morbidity is very high but mortality is usually low."
Viral Infections of Laboratory Mice 

Typically mice under 2 weeks of age are going to be the only ones showing symptoms. Mice of any age can become infected, but the virus will not replicate much and they don't get diarrhea. "Pups suckling from immune dams are protected against EDIM during their period of disease susceptibility."

"Susceptibility to EDIM depends on the age of the host and peaks between 4 and 14 days of age [8, 36, 291, 391, 392]. Mice older than about 2 weeks can still be infected with MuRV-A/EDIM, but small numbers of enterocytes become infected, there is little replication of virus and diarrhoea does not occur. The exact reason for this age-related resistance to disease is unknown. Pups suckling from immune dams are protected against EDIM during their period of disease susceptibility [396]. In general, the infection is self-limiting and resolves within days. Successful viral control and clearance is promoted by an intact immune response [396–399], and some immunodeficient mice (e.g. Prkdcscid and Rag2tm1Fwa mice) may shed virus for extended periods or become persistently infected [400, 401]. Protection against MuRV-A/EDIM reinfection is primarily mediated by antibodies [396, 397]."
Viral Infections of Laboratory Mice 

Yes and no. The baseline immune system that the mouse has is going to be a major component in how severe the illness will get. This is not something that can be changed at an individual level, as genetic health should be managed at a mousery level. That said, a dam nursing her pups is going to pass on antibodies that will help keep her offspring healthy. If a doe is immune to rotavirus, she can protect her litter from ever showing symptoms.

There is a vaccine for the human version of rotavirus, but we don't have access to that for our mice. Rotavirus itself does not kill pups, but the damage to the intestines has the potential to. If a particular litter is starting to look quite bad and malnutrition is obvious, you may be able to foster them to another litter with healthy pups so they can get antibodies from that doe instead. Whether or not you feel comfortable breeding those pups later on is up to you. 

"Pups suckling from immune dams are protected against EDIM during their period of disease susceptibility [396]. In general, the infection is self-limiting and resolves within days. Successful viral control and clearance is promoted by an intact immune response [396–399], and some immunodeficient mice ... may shed virus for extended periods or become persistently infected [400, 401]. Protection against MuRV-A/EDIM reinfection is primarily mediated by antibodies [396, 397]."
Viral Infections of Laboratory Mice 

Either from the droppings of wild mice in the vicinity, or from other contaminated materials such as bedding or dust.

"Transmission Rotavirus is shed in large amounts in feces, and fecal oral transmission is the normal route of transmission. Spread throughout an animal room is through fecally contaminated bedding, dust, or other materials. Vertical transmission has not been noted."
Charles River - Mouse Rotavirus 

"Murine rotavirus-A/EDIM is highly contagious and transmitted by the faecal–oral route [8, 291, 391]. Dissemination of the virus occurs through direct contact or contaminated fomites and aerosols and is facilitated by the general property of rotaviruses that they remain infectious outside the body..."
Viral Infections of Laboratory Mice 

This is my personal opinion as a mouse breeder of 7 years. I am not a professional. This page is only based on information I have been able to pull from various articles.

From what I have read, your best option is a 8-12 week breeding cessation along with sanitizing bins with cleaners “containing phenols, chlorine or ethanol”. Mice that are immunocompetent (good genetic health) should be fine after 8-10 weeks after getting the virus. Immunodeficient (poor genetic health) should not be bred for 12 weeks after getting it.

Or, you can euthanize your colony, sanitize, and restart, but the virus is incredibly common in both wild mice AND labs. In 2006, 30% of labs either had the virus, or their colonies had antibodies for it. If even labs with their strict biosecurity policies struggle to keep free of it, I'm not sure we can hope to do that as hobbyists with much fewer resources.

"MuRV-A/EDIM infection remains prevalent in contemporary mouse colonies and appears to occur worldwide. Large commercial laboratories found 0.6% to 9% of mouse sera from North American and European facilities to be positive for antibodies against MuRV-A/EDIM [11, 12, 14, 15], and up to 30% of mouse colonies in the USA were identified as affected in a survey performed in 2006 [13]."
Viral Infections of Laboratory Mice 

As of 2015, mouse rotavirus (EDIM) is not considered to be zoonotic.
An Overview of Typical Infections of Research Mice: Health Monitoring and Prevention of Infection