Prices remained high in Dawson and supply fluctuated according to the season. During the winter of 1897 salt became worth its weight in gold, while nails, vital for construction work, rose in price to $28  per lb . Cans of butter sold for $5  each. The only eight horses in Dawson were slaughtered for dog food as they could not be kept alive over the winter. The first fresh goods arriving in the spring of 1898 sold for record prices, eggs reaching $3  each and apples $1 . Under these conditions scurvy, a potentially fatal illness caused by the lack of vitamin C, proved a major problem in Dawson City, particularly during the winter where supply of fresh food was not available. English prospectors gave it the local name of "Canadian black leg", on account of the unpleasant effects of the condition. It struck, among others, writer Jack London and, although not fatal in his case, brought an end to his mining career. Dysentery and malaria were also common in Dawson, and an epidemic of typhoid broke out in July and ran rampant throughout the summer. Up to 140 patients were taken into the newly constructed St Mary's Hospital and thousands were affected. Measures were taken by the following year to prevent further outbreaks, including the introduction of better sewage management and the piping in of water from further upstream. These gave improvements in 1899, although typhoid remained a problem. The new Hän reserve, however, lay downstream from Dawson City, and here the badly contaminated river continued to contribute to epidemics of typhoid and diphtheria throughout the gold rush.

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