The presence of previously unidentified diseases or new variants of diseases is another way diseases can arise in an area where they were not known to previously exist. Each year new strains of pathogens are discovered, and occasionally completely novel pathogens are recognized. The Transmissible Spongiform Encephalopathies (TSEs) are examples of a novel pathogen type that has emerged into several forms over the last few decades.

Bovine Spongiform Encephalopathy (BSE), commonly referred to as Mad Cow Disease, is one of several TSEs recognized in humans and animals. The agents of TSEs have not been completely characterized, but the pathogen appears to be smaller than a virus. Three major theories have been put forth to describe the causative agents of TSEs: (1) the agent is a virus with unusual characteristics, (2) the agent is a prion with an exclusively host-coded protein that is modified to a partially protease-resistant form after infection, or (3) the agent is a small, noncoding regulatory nucleic acid coated with a host-derived protective protein.

Affected animals develop progressive neurologic degeneration and exhibit incoordination, ataxia, nervousness or aggression, and decreased production despite continued appetite.

BSE was first diagnosed in Great Britain in 1986 and the number of cases escalated each year to peak in 1993. Epidemiological evidence suggests that development of this disease in British cattle occurred when cattle consumed feed that used contaminated meat and bone meal as a protein source. The relationship of BSE to other TSEs is not fully understood, but cases of new variant Creutzfeldt Jakob disease (vCJD), a human TSE, have been causally linked to exposure to BSE. The use of mammalian meat-and-bone meal in feed for all food-producing animals is now prohibited; in addition, because older animals are more likely to be infected, carcasses from animals more than 30 months of age are no longer allowed to be used as domestic animal or human food.