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A Year of Wonders by Geraldine Brooks: "This gripping historical novel is based on the true story of Eyam, the "Plague Village", in the rugged mountain spine of England. In 1666, a tainted bolt of cloth from London carries bubonic infection to this isolated settlement of shepherds and lead miners. A visionary young preacher convinces the villagers to seal themselves off in a deadly quarantine to prevent the spread of disease. The story is told through the eyes of eighteen-year-old Anna Frith, the vicar's maid, as she confronts the loss of her family, the disintegration of her community, and the lure of a dangerous and illicit love. As the death toll rises and people turn from prayers and herbal cures to sorcery and murderous witch-hunting, Anna emerges as an unlikely and courageous heroine in the village's desperate fight to save itself."
If you like A Year of Wonders by Geraldine Brooks, you may like these books as well:
Divining Women by Kaye Gibbons
In this enveloping tale of marital strife and female resilience, Gibbons considers conflicts between blacks and whites and men and women within the context of the First World War and the Spanish influenza epidemic. (Booklist)
Doomsday Book by Connie Willis
Kivrin, a history student at Oxford in 2048, travels back in time to a 14th-century English village, despite a host of misgivings on the part of her unofficial tutor. When the technician responsible for the procedure falls prey to a 21st-century epidemic, he accidentally sends Kivrin back not to 1320 but to 1348--right into the path of the Black Death. (Publisher's Weekly)
Fever, 1793 by Laurie Halse Anderson
(This is a Young adult book, but very good)
In 1793 Philadelphia, sixteen-year-old Matilda Cook, separated from her sick mother, learns about perseverance and self-reliance when she is forced to cope with the horrors of a yellow fever epidemic. (Catalog Summary)
Magnolia Creek by Jill Marie Landis
On the eve of the Civil War, Sara Collier marries the dashing Dru Talbot, just before he rides off to join the Confederate Army. Later, hearing that he has been killed, Sara rises above her grief and makes one wrong choice--which the battle-scarred surgeon must deal with when he returns to start over with his bride. (Catalog summary)
A Plague on Both Your Houses by Susanna Gregory
The corpse of a man clad in black robes is found pinioned to a waterwheel, one of many inexplicable deaths for physician Matthew Bartholomew to decipher. Amidst a complex tangle of lies and intrigue, the Black Death arrives in his town, and his theories of a dark and sinister conspiracy are quickly replaced by a struggle for personal survival. (Catalog Summary)
The Plague Tales by Ann Benson
What happens when the bubonic plague, long absent from the modern world, is let loose into twenty-first-century society? The Plague Tales weaves together two parallel stories in this work of fiction. (catalog summary)
There are also many books that take place in modern times that talk about plagues, epidemics and so on. They are mostly thrillers though, rather than historical fiction.
The First Horseman by John Case
The Spanish Flu killed forty million people worldwide in 1918. Now, with history threatening to repeat itself, a scientific expedition speeds toward a remote island in the Arctic Sea to recover strains of the lethal virus preserved under layers of ice. For Washington Post reporter Frank Daly, it is the story of a lifetime. But his plan to join the expedition is ruined by a ferocious storm that delays him. And when he meets up with the ship upon its return to port in Norway, it is clear that something has gone terribly wrong...
Blood Heat by Steve R. Pieczenik
"Orestes Bradley, youthful director of the National Insitute for Infectious Diseases in Washington, is puzzled by three unconnected patients who all display symptoms of bubonic plague; and he himself has been infected. When the patients disappear, Bradley turns detective. More plague cases occur, clustered near U.S. military bases, and Bradley begins to suspect a germ warfare experiment run amok and a conspiracy between the Army and an international pharmaceutical company." (Library Journal Review)
The Cobra Event by Richard Preston
"What happens when one crazed scientist takes it upon himself to develop and release a new biological weapon that will "thin out" the human race? A doctor working for the Centers for Disease Control first notices some strange evidence in a young girl's death. Soon other bodies are arriving at the morgue in similar condition. The police, the FBI, and national medical and science personnel become involved in trying to get to the bottom of the deadly disease that is attacking New York City. Though the details in this novel are fictional, they are based on the history of biological weapons and the advanced genetic engineering and biotechnology that is available today..." (School Library Journal Review)