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The animals were used to attract the virus in the hopes that if it (the virus) were present, they'd be able to isolate and study its origin.
The monkeys and guinea pigs were sentinel animals, like canaries in a coal mine: they would be placed in cages inside and near Kitum Cave in the hope that some of them would break with Marburg virus. There are no instruments that can detect a virus. The best way to find a virus in the wild, at the present time, is to place a sentinel animal at the suspected location of the virus and hope the animal gets sick. Johnson figured that if any of his monkeys or guinea pigs crashed, he would be able to isolate the virus from the sick animals and would perhaps be able to discover how the animals had caught it.
Preston, Richard (2012-03-14). The Hot Zone: The Terrifying True Story of the Origins of the Ebola Virus (p. 143). Knopf Doubleday Publishing Group. Kindle Edition.