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To derive a matched filter for detecting a weak target signal in a hyperspectral image, an estimate of the band-to-band covariance of the target-free background scene is required. We investigate the effects of including some of the target signal in the background scene. Although the covariance is contaminated by the presence of a target signal (there is increased variance in the direction of the target signature), we find that the matched filter is not necessarily affected. In fact, if the variation in plume strength is strictly uncorrelated with the variation in background spectra, the matched filter and its signal-to-clutter ratio (SCR) performance will not be impaired. While there is little a priori reason to expect significant correlation between the plume and the background, there usually is some residual correlation, and this correlation leads to a suppressing effect that limits the SCR obtainable even for strong plumes. These effects are described and quantified analytically, and the crucial role of this correlation is illustrated with some numerical examples using simulated plumes superimposed on real hyperspectral imagery. In one example, we observe an order-of-magnitude loss in SCR for a matched filter based on the contaminated covariance.