Persecution of Jews during the Black Death

The Black Death persecutions and massacres were a series of violent attacks on Jewish communities falsely blamed for outbreaks of the Black Death in Europe from 1348 to 1351.
History of persecutions.
The official church policy at the time was to protect Jews because Jesus was Jewish. In practice, however, Jews were often targets of Christian loathing. As the plague swept across Europe in the mid-14th century, annihilating nearly half the population, people had little scientific understanding of the disease and were looking for an explanation.
Jews were often taken as scapegoats and accusations spread that they had caused the disease by deliberately poisoning wells. This is likely because they were affected less than other people, 
since many Jews chose not to use the common wells of towns and cities. Jews were also sometimes coerced through torture to confess to poisoning wells. 
The first massacres directly related to the plague took place in April 1348 in Toulon, Provence where the Jewish quarter was sacked, and forty Jews were murdered in their homes; the next occurred in Barcelona. In 1349, massacres and persecution spread across Europe, including the Erfurt massacre, the Basel massacre, massacres in Aragon, and Flanders. 2,000 Jews were burnt alive on 14 February 1349 in the "Valentine's Day" Strasbourg massacre, where the plague had not yet affected the city. While the ashes smouldered, Christian residents of Strasbourg sifted through and collected the valuable possessions of Jews not burnt by the fires. Many hundreds of Jewish communities were destroyed in this period. Within the 510 Jewish communities destroyed in this period, some members killed themselves to avoid the persecutions. In the spring of 1349 the Jewish community in Frankfurt am Main was annihilated. This was followed by the destruction of Jewish communities in Mainz and Cologne. The 3,000 strong Jewish population of Mainz initially defended themselves and managed to hold off the Christian attackers. But the Christians managed to overwhelm the Jewish ghetto in the end and killed all of its Jews.
At Speyer, Jewish corpses were disposed in wine casks and cast into the Rhine. By the close of 1349 the worst of the pogroms had ended in Rhineland. But around this time the massacres of Jews started rising near the Hansa townships of the Baltic Coast and in Eastern Europe. By 1351 there had been 350 incidents of anti-Jewish pogroms and 60 major and 150 minor Jewish communities had been exterminated. All of this caused the eastward movement of Northern Europe's Jewry to Poland and Lithuania, where they remained for the next six centuries. King Casimir III of Poland enthusiastically gave refuge and protection to the Jews. This is consistent with his previous edicts vis-a-vis Jews. On 9 October 1334, Casimir confirmed the privileges granted to Jews in 1264 by Bolesław V the Chaste. Under penalty of death, he prohibited the kidnapping of Jewish children for the purpose of enforced Christian baptism, and he inflicted heavy punishment for the desecration of Jewish cemeteries. The king had therefore been previously well-disposed to Jews. He was also interested in tapping the economic potential of the Jews.
Perceived Jewish immunity.
There are many possible reasons why Jews were accused to be the cause for the plague. One reason was because there was a general sense of anti-Semitism in the 14th century. Jews were also isolated in the ghettos, which meant in some places that Jews were less affected. Additionally, there are many Jewish laws that promote cleanliness: a Jew must wash his or her hands before eating bread and after using the bathroom, it was customary for Jews to bathe once a week before the Sabbath, a corpse must be washed before burial, and so on.
Government responses.
In many cities the civil authorities either did little to protect the Jewish communities or actually abetted the rioters. 
Pope Clement VI (the French-born Benedictine, Pierre Roger) tried to protect the Jewish communities, issuing two papal bulls in 1348, on 6 July and 26 September, saying that those who blamed the plague on the Jews had been "seduced by that liar, the Devil". He went on to emphasize that “It cannot be true that the Jews, by such a heinous crime, are the cause or occasion of the plague, because through many parts of the world the same plague, by the hidden judgment of God, has afflicted and afflicts the Jews themselves and many other races who have never lived alongside them.” He urged clergy to take action to protect Jews and offered them papal protection in the city of Avignon. In this, Clement was aided by the research of his personal physician Guy de Chauliac, who argued from his own treatment of the infected that the Jews were not to blame. 
Clement's efforts were in part undone by the newly elected Charles IV, Holy Roman Emperor making property of Jews killed in riots forfeit, giving local authorities a financial incentive to turn a blind eye.
Aftermath.
As the plague waned in 1350, so did the violence against Jewish communities. In 1351, the plague and the immediate persecution was over, though the background level of persecution and discrimination remained. Ziegler (1998) comments that "there was nothing unique about the massacres". 20 years after the Black Death the Brussels massacre (1370) wiped out the Belgian Jewish community.
Jewish tales of the Black Death in the early modern period.
Though told for nearly 350 years, there were no written accounts of the Black Death through Jewish tales until 1696, by Yiftah Yosef ben Naftali Hirts Segal Manzpach in the Mayse Nissim. Yuzpa Shammes, as he frequently was referred to, was a scribe and shammash of the Worms community for several decades. His accounts intend to show that the Jews were not idle but that they took action against inevitably becoming the scapegoat. Despite Yuzpa's assertion that the Jews fought against the massacres, there are contradicting accounts that claim that there was no evidence of "armed resistance". These contradicting tales display the effect of oral tradition being manipulated to fit certain circumstances.