Smallpox in the New World:

African slaves were used on the sugar plantation of the West Indies, and with them came smallpox. In 1495, fifty-seven to eighty percent of the native population of Santa Domingo and in 1515, two-thirds of the Indians of Puerto Rico were wiped out by smallpox. Ten years after Cortez arrived in Mexico, the native population had been reduced from twenty-five million to six million five hundred thousand a reduction of seventy-four percent. Even the most conservative estimates place the deaths from smallpox above sixty-five percent (Bray).

Smallpox reached what was to become the United States either from Canada or the West Indies. The first major outbreak of an infectious disease recorded on the northeastern Atlantic coast was 1616-19. The Massachusetts and other Algonquin tribes in the area were reduced from an estimated thirty thousand to three hundred (Bray). When the Pilgrims landed a year later in 1620, there was few Indians left to greet them. Many observers believe this infectious disease was smallpox.

By the end of the sixteen hundreds, smallpox had spread up and down the eastern seaboard and as far west as the Great Lakes. Stearn and Stearn estimated there were approximately one million one hundred and fifty thousand Indians living north of the Rio Grande in the early sixteenth-century, but by 1907, there were less than four hundred thousand (Bray). This decline was not due to smallpox alone. Other diseases played a role, as did warfare between various Indian tribes and with the United States.

It was inevitable that when Europeans came to America that European diseases were going to run rampant through Native American populations. American Indians had no immunities, or genetic tolerance, to any of the European diseases, and not all white Americans had immunities to them either. There is a common misconception that syphilis spread from Native Americans to Europeans. This is not true. Like every other disease, Europeans brought syphilis to America.

With the exception of man's oldest disease, Malaria, the scourges of mankind have resulted from dense populations living in small compact areas…overcrowded cities with little or no sanitation.  Before the arrival of the white man, the Plains Indians as primarily hunter-gatherers were free of communicable diseases.

Smallpox passes through the air in droplets discharged from the nose and mouth. It spreads from the lungs of an infected person into the lungs of a susceptible person. Smallpox can survive years on the clothing and bedding used by smallpox victims. In the early seventeen hundreds, a smallpox outbreak in Quebec resulted in many deaths.  In 1854, a pipeline laid through where the victims had been buried resulted in another smallpox outbreak.

Indian Genocide:

One of the most controversial issues on the internet ... is Indian genocide. Genocide and Holocaust are words that are easy to throw around, often to grab a reader's attention, but proving them is something else. What one group calls genocide, another group may call progress. I challenge anyone to offer documented proof, except for the two blankets given out by Captain Ecuyer at Fort Pitt, of smallpox infected blankets being deliberately given to Indians as a means of spreading smallpox. Letters by General Amherst and Colonel Bouquet mentioning spreading smallpox to Indians does not mean that this was ever carried out. Assumptions derived from letters and oral traditions are not proof of anything.

In a letter (1763) to Colonel Bouquet, Lord Amherst wrote, "Could it not be contrived to send the Small Pox among those disaffected tribes of Indians? We must on this occasion use every stratagem in our power to reduce them".

Bouquet replied that he would try and use infected blankets as a means of introducing the disease among the Indians, but was wary of the effects that it would have on his own men ... at least twenty-five percent or more of Bouquet's soldiers would have been susceptible to the smallpox virus.  

The Amherst letter has been used to support the proposition of germ warfare or genocide against native populations. Amherst may have discussed it in correspondence with Bouquet, but there is no evidence that Colonel Bouquet carried it out. As he mentioned in his reply, Bouquet was afraid of what it would do to his own men and with good reason. 1763 was twenty-three years before Jenner’s work on vaccination, and one hundred years before Pasteur advanced his germ theory. The only thing known about smallpox in 1763 was (a) age, color of skin, and social status meant nothing to the smallpox virus, and (b) an infected person died or, if lucky enough to survive, was often disfigured for life. No matter how bad Amherst may have wanted to be rid of the Indians, it seems doubtful that he would unleash a disease on his soldiers that had already killed millions of his own countrymen.

There is no evidence that Col. Bouquet took any action on Amherst's letter, but there is evidence that Captain Ecuyer at Fort Pitt did.

"Out of our regard for them  (two Indian chiefs) we gave them two blankets and a handkerchief out of the smallpox hospital. I hope it will have the desired effect (William Trent)."

The incident with Captain Ecuyer occurred during the Pontiac Rebellion. There is also evidence that Ecuyer tried to control the spread of smallpox, at least from his own men.

In a letter to Bouquet, Captain Ecuyer writes that Fort Pitt is in good state of defense against all attempts from Savages, who are daily firing upon the Fort; unluckily the Small Pox has broken out in the garrison, for which he has built an Hospital under the Draw Bridge to prevent the Spreading of that distemper (Peter d'Errico, nativeweb.org).

In 1763, Fort Pitt was under siege by Indian forces under the command of Chief Pontiac (Pontiac's Rebellion). With smallpox in the garrison at Fort Pitt and Indians attacking the fort, two blankets would have had little to do with the spread of smallpox among the Indians. A far greater source for spreading the smallpox virus would have been infected blood from mutilated soldier and settler bodies, scalps, clothing, and in some cases cannibalism, which occurred during the Pontiac Rebellion. Every warrior that returned from Fort Pitt with smallpox infected war trophies to Indian villages up and down the East coast carried the smallpox virus with them.

* * *

The smallpox virus reeked havoc all over the world for hundreds of years, but for a one- or two-year period, influenza killed as many people as any known virus. The influenza outbreak of 1918-1919 killed approximately forty million people. An estimated six hundred and seventy-five thousand Americans, including Native Americans, died of influenza. This was ten times as many Americans as were killed during World War I. Of the U. S. soldiers who died in Europe, half of them fell to the influenza virus, not to the enemy (http://www.stanford.edu/group/virus/uda/) ... Nobody claims this was genocide.

Smallpox and the Plains Indians:

The smallpox outbreak of 1780-82 followed the distribution and trade route of the Indian horse (Haines). The outbreak in 1800-02 spread from the Plains Indians to the Indians along the Pacific coast. Despite heavy losses during these periods, the most devastating outbreak of smallpox was yet to come.

In 1832, the first steamboat, a small side-wheeler named, Yellow Stone, reached Fort Union at the mouth of the Yellowstone River. The use of steamboats on the Missouri allowed large quantities of trade goods to move up and down the river. The buffalo hide trade now became more important than the trade in furs. Remote Indian villages brought their buffalo hides to the American Fur Company posts. This set the stage for the ensuing disaster.

In June of 1837, the St. Peter arrived at Fort Clark, 60 miles north of present day Bismarck, North Dakota. Knowing there were men aboard the boat with smallpox, F. A. Chardon and others of the American Fur Company tried to keep the Mandans away from the boat, but to no avail. The two Mandan villages that had provided aid to Lewis and Clark during the winter of 1804-05 were devastated. Thirty-one Mandans out of a population of sixteen hundred survived the epidemic.

The 1837 smallpox outbreaks were initially confined to the Indian tribes that lived by, or had come to trade at, the upper Missouri River trading posts. The Mandan, Blackfeet, and the Assiniboine nations suffered the highest number of deaths. The 1837-40 smallpox outbreaks were said to have a ninety-eight percent death rate among those infected (Bray).

Despite warnings from the traders, Hidatsa, Arikara, and Sioux warriors raided the empty Mandan villages and carried smallpox back to their people. Hundreds of [empty] lodges ... stood as mute testimony to the devastation of smallpox. As one writer wrote, “No language can picture the scene of desolation which the country presents. In whatever direction we go we see nothing but melancholy wrecks of human life. The tents are still standing on every hill, but no rising smoke announces the presence of human beings, and no sounds, but the croaking of the raven and the howling of the wolf interrupts the fearful silence (Chittenden).”  

The St. Peters continued on to Fort Union arriving there on June 24, 1837. The only Indians at the post were the Indian wives of thirty employees. Hoping to control the infection before the Assiniboine arrived for the September trade, Larpentuer noted that, “prompt measures were adopted to prevent an epidemic.” The measures taken were to vaccinate the Indian women. According to Larpentuer, “their systems were prepared according to Dr. Thomas’ Medical Book and they were vaccinated from Halsey himself…the operation proved fatal to most of our patients.”

Larpentuer goes on to say, "About fifteen days afterwards there was such a stench in the fort that it could be smelt at a distance of 300 yards. It was awful--the scene in the fort where some went crazy, and others were half eatin [sic] by maggots before they died." This was during the hottest part of the summer (Chittenden). Jacob Halsey was in charge of Fort Union, and had been infected coming upriver on the boat. Five months later, he claimed only four died from the attempted vaccination. Halsey's statement is in contrast to Larpentuer's comments, and his account seems highly unlikely based on the virulence of the smallpox virus. 

The Assiniboine started arriving at the post while the “controlled infection” was in full force. Infected Assiniboine carried smallpox back into Canada. From Fort Union smallpox spread by boat to Fort McKenzie near the junction of the Marias and the Missouri rivers.

Basically, the same story was repeated with the Blackfeet. There is no way to know how many Indians of the upper Missouri and the Plains of Canada were infected with smallpox. Estimates on the number killed range from sixty thousand to one hundred and fifty thousand. The most conservative estimate puts the number at more than 15,000 deaths (Chittenden).

The American Fur Company traders can certainly be criticized for the handling of the 1837 smallpox outbreak, especially the vaccination of the Indian women. However at the time and under the prevailing circumstances, the traders did the best they could. Even though the Indians were repeatedly warned to stay away from the posts, they insisted on trading their goods. It is hard to believe there was any malicious intent on the part of the fur traders when the fur company’s economic survival depended on the Indian trade.

The Indian Culture played a part in the high death rate. The use of the sweat lodge-cold water plunge may well have doubled the fatalities among the Plains tribes (Haines). This is not meant as criticism of the Sweat Lodge which was, and is, extremely important in the Indian Culture, but to point out that the Plains Indians had little or no concept of the dangers involved with the white-man diseases.

source: http://www.thefurtrapper.com/indian_smallpox.htm