General Rule
Generally, style guides agree that the names of diseases are not routinely capitalized. However, style guides also agree that any part of the name of a disease that is a proper noun in its own right is usually capitalized.
- APA Style Guide advice on the subject is reflected in this blog post at the APA Style Blog site:
... the dictionary tells you whether a word is a proper noun (i.e., a specific person, place, or thing), and proper nouns are capitalized in English and therefore in APA Style (see Publication Manual sections 4.16 and 4.18). Their opposite, regular or “common” nouns (which refer to general persons, places, or things), are lowercase in English and thus in APA Style as well.
(From "Do I Capitalize This Word?", at APA Style Blog.)
- Another source, The Mayfield Handbook of Technical and Scientific Writing, has this to say on the subject:
Do not capitalize medical terms except for any part of a term consisting of a proper noun:
infectious mononucleosis
brachial plexus
Parkinson's disease
(From "Section 9.1: Capitalization" in The Mayfield Handbook of Technical and Scientific Writing.)
- The AP Stylebook gives a terse version of the usual convention:
Capitalize a disease known by name of person or geographical area: Alzheimer’s disease, Parkinson’s disease, Ebola virus.
[From The Associated Press Stylebook, as quoted at Glossophilia in "Capitalizing and pronouncing Ebola (and the naming of other diseases)".]
Other style guides that I consulted, online and off, did not differ substantively from the APA Style Guide, Mayfield Handbook and AP Stylebook with regard to capitalizing disease names.
Note: If the use of a specific style guide is mandated for writing containing the names of diseases, that style guide should be consulted and any rules or exceptions therein should be observed.
Special Cases, Exceptions
- Scientific nomenclature in English: when an organism name (which may also be or contain the name of a disease) is used as a technical (scientific) reference to the organism, this from section 9.1 of the Mayfield Handbook usually applies:
Capitalize and put in italics the phylum, class, order, family, and genus of plants and animals. Do not capitalize the species.
Homo sapiens
Esox lucius
(op. cit.)
These conventions for the scientific names of organisms may apply when the name of a disease is also the name of a family or genus of organisms, as shown by Salmonella in the following excerpt from the Gale Encyclopedia of Medicine:
Such symptoms are most likely due to other organisms such as rotavirus, Salmonella, Shigella, or Escherichia coli.
(Influenza. (n.d.) Gale Encyclopedia of Medicine. (2008). Retrieved November 9 2015 from http://medical-dictionary.thefreedictionary.com/influenza.)
Observe that "rotavirus" is neither italicized nor capitalized. This seeming anomaly is due to "rotavirus" being the name of a virus used generically. A virus is not a species:
Viruses
Italics Use with Virus Names
A virus is not a species; a virus belongs to a species. Italicize species, genus, and family of a virus when used in a taxonomic sense. Note however, that it is fine to not mention taxonomy of a virus, especially one like dengue or polio that is well known.
Do not italicize a virus name when used generically. If you capitalize a virus name (other than one that has a proper name in it so that you must capitalize it), then you need to italicize it.
(From "Scientific Nomenclature", in Emerging Infectious Diseases.)
- Historical events: the names of historical events, or abridgements of such names, are sometimes also used as the names of diseases. This circumstance often results in capitalization that appears to deviate, or actually does deviate, due to scribal error, from the style conventions for disease name capitalization. Two notable examples of the problem area are "Black Death" and "Spanish Flu". Of the two examples, "Spanish Flu" is the more complicated case, yet neither case is a special challenge with regard to conventional capitalization.
Black Death is frequently used as the popular name of bubonic plague. It may, however, refer instead to a historical event, an epidemic of bubonic plague in the Middle Ages, and it is then capitalized according to the convention detailed at, for example, WriteExpress:
Capitalize Historic Periods and Events
The names of historic periods and events are generally capitalized.
(From WriteExpress, "How to Capitalize".)
Spanish Flu, as an abridgement of "1918 Spanish Flu Pandemic", or as an abridgement of any of the various names given to that historical event, observes the usual convention with respect to the capitalization of historical events. When the name is used instead with reference to the disease, then "Spanish", being a specific name (proper noun), retains its capitalization: so, if the reference is not an abridgement of the name of the 1918 Spanish Flu Pandemic event, but rather a reference to a disease only, the conventional capitalization is "Spanish flu".
- Specificity assimilation: Another special case of disease name capitalization arises when proper nouns in the names of diseases become so thoroughly identified with the disease as to no longer depend on the specificity of proper nouns for their meaning.
When this assimilation has occurred may be difficult to ascertain, but generally, as mentioned earlier, a good dictionary will show the term with capitalization as encountered in use. However, the chosen dictionary may also present multiple options for capitalization, and it will remain entirely up to individual writers to discern and choose the most appropriate form.
This perhaps troublesome assimilation of the specificity of proper nouns has at least partly occurred with the name "Black Death". For example, "Black Death" is allowed two forms by the Merriam-Webster online dictionary:
black death
noun, often capitalized B&D
Definition of BLACK DEATH
1 : plague
2 : a severe epidemic of plague and especially bubonic plague that occurred in Asia and Europe in the 14th century.
(From "black death", at Merriam-Webster.)
It can safely be assumed, given the usual conventions for disease names and the names of historical events, that what the dictionary refers to as "often capitalized B&D" is that no capitalization was frequently encountered by lexicographers when the term was used with sense 1, while capitalization of both words was frequently encountered when the term was used with sense 2.
Best Answer
If I were writing about disease stages and I wanted to find a relevant style guide to help me with decisions such as whether to capitalize stage in a term like "Stage I," and whether to capitalize descriptive stage names such as "Clinical Latency," I would obtain and consult the American Medical Association's AMA Manual of Style: A Guide for Authors and Editors, which is now, I believe in its tenth edition. Unfortunately, access to the online AMA Manual of Style requires a subscription—and I have neither a subscription nor a copy of any print edition of the manual.
For what it's worth, The Chicago Manual of Style, fifteenth edition (2003) seems to favor lowercasing stage (and clinical latency) in connection with progressive diseases:
However, as Chicago itself notes (at 8.152), "Medical writers or editors [in the United States] should consult the American Medical Association Manual of Style or Scientific Style and Format [for detailed guidance on style questions in these areas]." If you're writing primarily for a U.S. medical audience, it makes sense to follow the preeminent style guide for that audience. Of course, as in dealing with other type of style question, you are free to take advice from whatever source you like unless you're under strict instructions to follow a particular style.