The use of orphans in the early smallpox vaccinations is well documented.
The Balmis Expedition in the early 1800s under Dr. Francisco de Balmis, used about fifty orphaned children in total; they were initially "recruited" from the 'Casa de Expósitos;orphanage in A Coruña in Galacia but more were obtained in the Americas.
Charles Maitland, who work preceded that of Jenner, experimented (under royal license) in the 1720s on prisoners in Newgate and later on orphaned children, before variolating the daughters of the Princess of Wales.
In the twentieth century orphanages were useful in the development of polio vaccines; John Kolmer tested his attenuated poliovirus vaccine on about 10,000 children in the United States and Canada (most of them in schools and orphanages).
At least twenty died and more were paralysed.
His vaccine used an attenuated strain of polio, where animals were infected and mutated and (hopefully) harmless virus particles harvested.
When he presented his results at 1935 annual meeting of the American Public Health Association the reception was, to put it mildly, poor; there were numerous objections to his research and one delegate called Kolmer a murderer to his face. His poor experiment design, without a control group to compare infection rates, also made deductions from his research difficult.
Curiously Kolmer’s
bio at the AAI does not mention his polio research.
The real tragedy was that Kolmer was not the only person to be presenting on polio vaccine research that day in Milwaukee. Immediately after him there was a presentation by Dr. Maurice Brodie about his work on a polio vaccine, based on an inactivated (dead, killed by formaldehyde) form of the polio virus and initially tested on monkeys
Brodie's research was of far higher quality and his vaccine safer (he'd tested it initially on himself and his fellow researchers). Brodie was fired and died three years later while Kolmer, an established researcher whose vaccine was unsafe and probably ineffective, kept his job and receiveda second appointment as professor of medicine at Temple University.
Unfortunately the hostility generated by Kolmer killed off research into a polio vaccine for almost fifteen years; Salk's work in 1952 was on similar lines to that of Brodie.