As I’ve mentioned before, I’m currently working with the missionary diaries of an Elder Joseph Brooks who served in Southeast Texas from 1899 to 1902. Elder Brooks’ description of a smallpox outbreak strikes me as interesting. He wrote (19 Jan 1900):
We did not think it wise to hold any meetings there as there was a disease among the people that had been pronounced Small Pox by some of the Doctors. So we did not try to get a house to preach in. We distributed some tracts among the people in places where we thought there was the least danger of coming in contact with the disease. We left the town and went into the country.
On 24 Jan he noted that they “had decided to leave that settlement as there seemed to be very little interest and besides it was sickly times.” A week later, 02 Feb 1900, they had to change boarding plans:
We went on with the expectation of stopping with a friend we had made the trip before but he had a sick child. He said she had that breaking out that was called small pox. So we did not want to come in contact with the disease. We were not afraid of it ourselves but we were afraid we might be the means of scattering it.
The disease was probably Variola minor or “pseudo-smallpox,” an outbreak of which began in Florida in 1896 and spread over the whole country. Unlike the often fatal V. major, V. minor was only occasionally fatal and often mild enough to pass as chickenpox or measles.  The diagnostic ambiguity might be why Elder Brooks specified that “some” of the doctors called it smallpox.
Most striking to me is Brooks’ assertion that “we were not afraid of it ourselves.” So far, I’ve come up with five possible (non-exclusive) sources for their confidence: youthful bravado, disdain for a mild disease, and confidence in divine protection, vaccination, or some way to avoid contraction. I find the first two unlikely. Elder Brooks had already seen plenty of sick missionaries. Over the course of his mission, he or his companion were ill or injured about one of every five days—hardly a lifestyle conducive to bravado about disease.  It is possible the Elders simply weren’t impressed by V. minor‘s relatively mild symptoms, but who scoffs at chicken pox, “mild” or not?
The third possibility is more plausible: Mormon scriptures and preaching suggest that missionaries receive protection against harm and disease.  However, the Elders’ own experience with illness, the measured expectations they placed on faith-based healing, their reliance on medicine, and their concern about becoming disease vectors indicate a non-fundamentalist approach to divine protection.  Though they might have expected to avoid the worst of some conditions, they did not expect to be spared every suffering.
Alternately, it is possible they thought they knew how to avoid smallpox infection but not transmission, though Elder Brooks doesn’t say so. It seems most likely that the Elders had been vaccinated. Smallpox immunization and/or containment policies were implemented in Mormon colonies as early as the 1850s and became more aggressive in the late 1890s (though were still voluntary) so the Elders had ample opportunity for immunization. The programs became far more vigorous after the 1899-1900 outbreak in Utah.  At some point after Elder Brooks’ mission, vaccinations became standard. A 1926 announcement noted that “it is now the custom for missionaries to be vaccinated for smallpox and innoculated (sic) for typhoid fever before entering the mission field. This has been done at the Missionary Home, but it is considered advisable to request missionaries to have this attended to at home before reporting here.”
I was reminded of this episode by SC Taysom’s post on exorcism last week.
 Donald R. Hopkins, Princes and Peasants: Smallpox in History (Chicago: University of Chicago Press, 1983), p. 287-290. See also, for example, “A Smallpox Epidemic in Texas,” New York Times, 19 Jan 1900, p. 2.
 I count 119 days out of the 591 days 30 Oct 99 – 11 June 01 when one or both of the companions were ill or injured. There were 15 other days Elder Brooks felt poorly but worked. I’ll forbear on a more detailed description of the counting criteria. For comparison, in the 1970s the average illness/injury loss rate was between 4 and 6 days per capita per year (1 – 2% of days per companionship versus Elder Brooks’ 20%; missionaries who returned home early were not counted after they went home). Susan Jensen, “Health Problems of Selected LDS Missionaries Throughout the World” (Master’s Thesis, Brigham Young University, 1981).
 For example, Matt. 6:25-34, Mark 16:17-18, 1 Nephi 22:17, Mosiah 13:2-8, D&C 84:65-73. I haven’t chased down contemporary sources about missionary protection, but I think the point is well attested.
 Elder Brooks describes multiple administrations to the sick but not at the expense of temporal care. He also does not seem theologically distraught when healings are not immediate.
 That is, when the 1896 Florida epidemic reached Utah. Eric L. Bluth, “Pus, Pox, Propaganda and Progress: The Compulsory Smallpox Vaccination Controversy in Utah, 1899-1901” (Masters Thesis, Brigham Young University, 1993), p. 19-28.
 Heber J. Grant, 20 Sep 1926 in James R. Clark, Messages of the First Presidency of the Church of Jesus Christ of Latter-day Saints, 1833-1964 (Salt Lake City: Bookcraft, 1966-1971), Vol. 5, p. 248-249. The Mission Home was created in the early 1920s.