'great plague', until deaths from the plague of 1665 surpassed it. these official figures are likely to under-report actual numbers. early days rattus rattus, the black rat. smaller than rattus norvegicus, the brown rat, which later supplanted it, it is also keener to live near humankind. timber houses and overcrowded slums provided excellent homes. the link between the rat as reservoir of infection and host to fleas which could transfer to man was not understood. efforts were made to eliminate cats and dogs: if anything, this encouraged the rats. body lice were also important plague vectors. plague was sufficiently uncommon that medical practitioners might have had no personal experience of seeing the disease; medical training varied from those who had attended the college of physicians, to apothecaries who also acted as doctors, to charlatans. other diseases abounded, such as an outbreak of smallpox the year before, and these uncertainties all added to difficulties identifying the true start of the epidemic. contemporary accounts suggest cases of plague occurred through the winter of 1664–65, some of which were fatal but a number of which did not display the virulence of the later epidemic. the winter was cold, the ground frozen from december to march, river traffic on the thames twice blocked by ice, and it may be that the cold weather held back its spread. this outbreak of bubonic plague in england is thought to have spread from the netherlands, where the disease had been occurring intermittently since 1599. it is unclear exactly where the disease first struck but the initial contagion may have arrived with dutch trading ships carrying bales of cotton from amsterdam, which was ravaged by the disease in 1663–64, with a mortality given of 50,000. the first areas to be struck are believed to be the dock areas just outside london, and the parish of st giles. in both of these localities, poor workers were crowded into ill-kept structures. two suspicious deaths were recorded in st giles parish in 1664 and another in february 1665. these did not appear as plague deaths on the bills of mortality, so no control measures were taken by the authorities, but the total number of people dying in london during the first four months of 1665 showed a marked increase. by the end of april, only four plague deaths had been recorded, two in the parish of st. giles, but total deaths per week had risen from around 290 to 398. there had been three official cases in april, a level of plague which in earlier years had not induced any official response, but the privy council now acted to introduce household quarantine. justices of the peace in middlesex were instructed to investigate any suspected cases and to shut up the house if it was confirmed. shortly after, a similar order was issued by the king's bench to the city and liberties. a riot broke out in st. giles when the first house was sealed up; the crowd broke down the door and released the inhabitants. rioters caught were punished severely. instructions were given to build pest-houses, which were essentially isolation hospitals built away from other people where the sick could be cared for (or stay until they died). this official activity suggests that despite the few recorded cases, the government was already aware that this was a serious outbreak of plague. two men discovering a dead woman in the street with the arrival of warmer weather, the disease began to take a firmer hold. in the week 2–9 may, there were three recorded deaths in the parish of st giles, four in neighbouring st clement danes and one each in st andrew holborn and st mary woolchurch haw. only the last was actually inside the city walls. a privy council committee was formed to investigate methods to best prevent the spread of plague, and measures were introduced to close some of the ale houses in affected areas and limit the number of lodgers allowed in a household. in the city, the lord mayor issued a proclamation that all householders must diligently clean the streets outside their property, which was a householder's responsibility, not a state one (the city employed scavengers and rakers to remove the worst of the mess). matters just became worse, and aldermen were instructed to find and punish those failing their duty. as cases in st. giles began to rise, an attempt was made to quarantine the area and constables were instructed to inspect everyone wishing to travel and contain inside vagrants or suspect persons. people began to be alarmed. samuel pepys, who had an important position at the admiralty, stayed in london and provided a contemporary account of the plague through his diary. on 30 april he wrote: "great fears of the sickness here in the city it being said that two or three houses are already shut up. god preserve us all!" another source of information on the time is a journal of the plague year, which was written by daniel defoe and published in 1722. he had been only six when the plague struck but made use of his family's recollections (his uncle was a saddler in east london and his father a butcher in cripplegate), interviews with survivors and sight of such official records as were available. the onset of the disease was recalled two years later by puritan minister thomas vincent:it was in the month of may that the plague was first taken notice of; our bill of mortality did let us know but of three which died of the disease in the whole year before; but in the beginning of may the bill tells us of nine...fear quickly begins to creep upon peoples hearts; great thoughts and discourse there is in town about the plague, and they cast in their minds whether they should go if the plague should increase. yet when the next weeks bill signifieth to them the disease from nine to three their minds are something appeased; discourse of that subject cools; fears are hushed, and hopes take place, that the black cloud did but threaten, and give a few drops; but the wind would drive it away. but when in the next bill the number of the dead by the plague is mounted from three to fourteen, and in the next to seventeen, and in the next to forty-three, and the disease begins so much to increase, and disperse. now secure sinners begin to be startled, and those who would have slept at quiet still in their nests, are unwillingly awakened. exodus from the city scenes in london during the plague by july 1665, plague was rampant in the city of london. the rich ran away, including king charles ii of england, his family and his court, who left the city for salisbury, moving on to oxford in september when some cases of plague occurred in salisbury. the aldermen and most of the other city authorities opted to stay at their posts. the lord mayor of london, sir john lawrence, also decided to stay in the city. businesses were closed when merchants and professionals fled. defoe wrote "nothing was to be seen but wagons and carts, with goods, women, servants, children, coaches filled with people of the better sort, and horsemen attending them, and all hurrying away". as the plague raged throughout the summer, only a small number of clergymen, physicians and apothecaries remained to cope with an increasingly large number of victims. ellen cotes, author of london's dreadful visitation, expressed the hope that "neither the physicians of our souls or bodies may hereafter in such great numbers forsake us". the poorer people were also alarmed by the contagion and some left the city, but it was not easy for them to abandon their accommodation and livelihoods for an uncertain future elsewhere. before exiting through the city gates, they were required to possess a certificate of good health signed by the lord mayor and these became increasingly difficult to obtain. as time went by and the numbers of plague victims rose, people living in the villages outside london began to resent this exodus and were no longer prepared to accept townsfolk from london, with or without a certificate. the refugees were turned back, were not allowed to pass through towns and had to travel across country, and were forced to live rough on what they could steal or scavenge from the fields. many died in wretched circumstances of starvation and dehydration in the hot summer that was to follow. height of the epidemic a bill of mortality for the plague in 1665 in the last week of july, the london bill of mortality showed 3,014 deaths, of which 2,020 had died from the plague. the number of deaths as a result of plague may have been underestimated, as deaths in other years in the same period were much lower, at around 300. as the number of victims affected mounted up, burial grounds became overfull, and pits were dug to accommodate the dead. drivers of dead-carts travelled the streets calling "bring out your dead" and carted away piles of bodies. the authorities became concerned that the number of deaths might cause public alarm and ordered that body removal and interment should take place only at night. as time went on, there were too many victims, and too few drivers, to remove the bodies which began to be stacked up against the walls of houses. daytime collection was resumed and the plague pits became mounds of decomposing corpses. in the parish of aldgate, a great hole was dug near the churchyard, fifty feet long and twenty feet wide. digging was continued by labourers at one end while the dead-carts tipped in corpses at the other. when there was no room for further extension it was dug deeper until ground water was reached at twenty feet. when finally covered with earth it housed 1,114 corpses. plague doctors traversed the streets diagnosing victims, many of them without formal medical training. several public health efforts were attempted. physicians were hired by city officials and burial details were carefully organized, but panic spread through the city and, out of the fear of contagion, bodies were hastily buried in overcrowded pits. the means of transmission of the disease were not known but thinking they might be linked to the animals, the city corporation ordered a cull of dogs and cats. this decision may have affected the length of the epidemic since those animals could have helped keep in check the rat population carrying the fleas which transmitted the disease. thinking bad air was involved in transmission, the authorities ordered giant bonfires to be burned in the streets and house fires to be kept burning night and day, in the hope that the air would be cleansed. tobacco was thought to be a prophylactic and it was later said that no london tobacconist had died from the plague during the epidemic. two women lying dead in a london street trade and business had dried up, and the streets were empty of people except for the dead-carts and the dying victims, as witnessed and recorded by samuel pepys in his diary: "lord! how empty the streets are and how melancholy, so many poor sick people in the streets full of sores… in westminster, there is never a physician and but one apothecary left, all being dead." that people did not starve was down to the foresight of sir john lawrence and the corporation of london who arranged for a commission of one farthing to be paid above the normal price for every quarter of corn landed in the port of london. another food source was the villages around london which, denied of their usual sales in the capital, left vegetables in specified market areas, negotiated their sale by shouting, and collected their payment after the money had been left submerged in a bucket of vinegar to "disinfect" the coins. records state that plague deaths in london and the suburbs crept up over the summer from 2,000 people per week to over 7,000 per week in september. these figures are likely to be a considerable underestimate. many of the sextons and parish clerks who kept the records themselves died. quakers refused to co-operate and many of