Elizabeth A. Fenn, Pox Americana: The Great Smallpox Epidemic of 1775-82 (NY: Hill and Wang, 2001), discusses widespread accusations and examples of biological warfare on the American continent:
1. Fear of smallpox in Continental Army
Nothing instilled fear in American soldiers and civilians so much as the prospect that the British might use smallpox as a weapon of war. The concern may seem farfetched and sensational, but it was not without merit. British officers had already demonstrated their willingness to use biological warfare in 1763, when Indians organized under the Ottawa leader Pontiac had threatened the safety of Fort Pitt, on the Pennsylvania frontier. "Out of our regard to them," wrote a trader on the scene, "we gave them two Blankets and an Handkerchief out of the Small Pox Hospital. I hope it will have the desired effect." This act had the sanction of an impressive array of British officers, including Sir Jeffery Amherst, commander in chief at the time, and General Thomas Gage, who replaced Amherst and signed off on reimbursements for the "Sundries" used "to Convey the Smallpox to the Indians." But would the British use germ warfare against their own subjects? Would they use it against individuals of European descent? American colonists seemed to think that they would. It was Gage, after all, who commanded the British army during the first months of the colonists' siege of Boston. Seth Pomeroy was an American officer who had served under Gage during the French and Indian War. "If it is In General Gages power," Pomeroy wrote in May 1775, "I Expect he will Send ye Small pox Into ye Army--but I hope In ye Infinight Mercy of God he will prevent It, as he hath don In Every attempt that he has made yet." Rumors of germ warfare at Boston had circulated as early as March 1775.1
By the year's end, Thomas Gage had turned over his command to Sir William Howe, but talk of germ warfare had failed to subside Instead, the evidence mounted. On December 3, shortly after the British began to force selected citizens to leave Boston, four British deserters arrived at the American headquarters in Cambridge. They brought with them a sinister report. General Howe, they said, had deliberately infected several of the exiles with a design to spread the Small-Pox among the [American] Troops." (pp. 88-89)
2. Smallpox in New Spain
In their quest to reduce the Indians, the missionaries appear to have benefited from the great waves of pestilence that swept New Spain hand in hand with colonial conquest in the sixteenth and seventeeth (sic) centuries. The impact of these epidemics was stunning, particularly in the first century of European contact. From a pre-Columbian population that may have been as high as twenty-five million, the population of central Mexico plummeted to only two million by 1600, rebounding somewhat thereafter. Farther north, a similar pattern emerged, delayed by three-quarters of a century, but dramatic nonetheless. The Pueblo Indians of New Mexico saw their numbers drop from as many as one hundred thousand in 1600 to forty thousand in 1638 and only seventeen thousand in 1680. To the southwest, in the desert province of Sonora, one Jesuit missionary believed that the native population had declined more than 90 percent by 1706.2
These breathtaking numbers represent only the most quantifiable consequence of epidemic disease. Inevitably, the repercussions went far beyond simple statistical decline. Repeated bouts of pestilence shattered native tribal organization, disrupted kinship ties, undermined Indian belief systems, and called into question the skills of traditional medical practitioners. The chaos made many Indians more receptive to the alternative religious and social structures offered by Catholic evangelicals when they moved into disease-ravaged regions.3 (p. 142)
3. Overall significance of smallpox in North America
When Lewis and Clark returned east from their Voyage of Discovery in 1806, they melded the disparate regions of North America into one in the collective Jeffersonian consciousness. But the world the explorers described to the American people was one that had already undergone momentous change. As their own journals indicated, Variola's transit of the continent had preceded them by a full generation. In the years of the American Revolution, long before the two explorers forged a unified continent in the American psyche, converging military, political, social, environmental, and economic upheavals had unwittingly united North Americans far and wide in a common, if horrific, experience. That experience was epidemic smallpox, passed from one human being to another in a chain of connections as terrible as it was stunning. (p. 259)
...
While the American Revolution may have defined the era for history, epidemic smallpox nevertheless defined it for many of the Americans who lived and died in that time.
The American Revolution, the seminal event of the era, was not excluded from Variola's maelstrom. Nor did events stop elsewhere while the revolutionary conflict was waged. The very breadth of Variola's movement redirects our attention to turmoils occurring in places far removed from the well-known fields of battle. The pestilence can teach us the ways in which other upheavals--native warfare, missionization, the fur trade, and the acquisition of horses and guns, all of which enabled Variola to be transmitted--had already reshaped human life on the North American continent. The movement of the virus from one human being to another shows us how people actually lived in the late eighteenth century. For despite the political, social, and racial boundaries of the day, people rubbed elbows: They lived side by side, they talked, they fought, they traveled, they traded, and in these daily transactions, they passed Variola on to one another.
Smallpox moved incrementally through incidental encounters, yet it also seemed to move with a purpose. In a New World environment where acquired immunity was rare, Variola was a virus of empire. It made winners and losers, at once serving the conquerors and determining whom they would be. Smallpox reshaped political and military relations across the continent, even as the Revolution reshaped such relations around the world. In the short term, even such Native American groups as the Sioux and the Blackfeet could benefit from the devastation smallpox left behind, but in the long run, the pestilence seemed invariably to favor the great imperial powers of Europe and the United States. Over the course of the nineteenth century, both the Sioux and the Blackfeet suffered dramatic losses not just to Anglo-American interlopers and the whiskey they brought with them but also to recurring bouts of smallpox and other Old World diseases.4 An unwitting instrument of empire, the pestilence of 1775-82 constitutes another piece in the larger puzzle of Native American population decline as European settlements expanded. It clearly shows that the enormous losses of the early postcontact era were followed by continued losses at a lesser level. Nearly three centuries after Columbus sailed, indigenous depopulation remained farreaching and ongoing. (pp. 275-276)
1. William Trent, "William Trent's Journal at Fort Pitt, 1763," ed. A. T. Volwiler, Mississippi Valley Historical Review 11 (December 1924): 400. For Gage's approval of reimbursements, see Levy, Trent and Company: Account against the Crown, August 13, 1763, in The Papers of Col. Henry Bouquet, ed. Sylvester Kirby Stevens and Donald H. Kent, ser. 21654 (Harrisburg: Department of Public Instruction, Pennsylvania Historical Commission, 1941), 218-19. For more on the Fort Pitt affair, see Elizabeth A. Fenn, "Biological Warfare in Eighteenth-Century America: Beyond Jeffery Amherst," Journal of American History 86 (March 2000): 1552-58. Pomeroy's warning is in Seth Pomeroy to Asahel Pomero Cambridge, May 13, 1775, in Louis Effingham de Forest, ed., The Journals and Papers of Seth Pomeroy (New Haven: Society of Colonial Wars in the State of New York, 1926), 167. For the March 1775 accusations, see Extract of a letter from Boston, author unknown, London Evening Post, March 25--March 28, 1775, in Margaret W. Willard, ed., Letters on the American Revolution, 1774-1776 (Boston and New York: Houghton Mifflin, 1925), 57-58.
2. The statistics for central Mexico, the Pueblos, and Sonora are from Daniel T. Reff, Disease, Depopulation, and Culture Change in Northwestern New Spain, 1518-1764 (Salt Lake City: University of Utah Press, 1991), 228-36; and Peter Gerhard, A Guide to the Historical Geography of New Spain (1972; rev. ed., Norman: University of Oklahoma Press, 1993), 24.
3. This argument is made persuasively in Reff, Disease, chap. 5.
4. On ongoing outbreaks, see James H. Howard, "Dakota Winter Counts as a Source of Plains History," Bulletin 173, Smithsonian Institution Bureau of American Ethnology, Anthropological Papers, no. 61 (Washington, D.C.: U.S. Government Printing Office. 1960): 352; Garrick Mallery Picture-Writing of the American Indians. Tenth Annual Report of the Bureau of Ethnology to the Secretary of the Smithsonian Institution, 1888-'89 (1893; rpt., New York: Dover, n.d.), 1:313, 317; François Marie Perrin du Lac, "Extract from the Travels of Perrin du Lac, 1802," in Nasatir, Before Lewis and Clark, 2:710; Martha Warren Beckwith, "Mythology of the Oglala Sioux," Journal of American Folklore 43 (1930): 356, 361; James H. Howard, "Two Teton Winter Count Texts," North Dakota History 27 (1960): 71, 73; Garrick Mallery, A Calendar of the Dakota Nation (Washington, D.C.: U.S. Government Printing Office, 1877), 11; Edward S. Curtis, The North American Indian, ed. Frederick Webb Hodge (Cambridge. Mass.: University Press, 1908), 3:170, 172, 176, 178; and Ewers, Blackfeet, 64-66, 250, 252, 257-58.