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Non-rocky sub-jovian exoplanets in high irradiation environments are rare. LTT 9979b, also known as TESS Object of Interest (TOI) 193.01, is one of the few such planets discovered to date, and the first example of an ultra-hot Neptune. The planet's bulk density indicates that it has a substantial atmosphere, so to investigate its atmospheric composition and shed further light on its origin, we obtained {\it Spitzer} IRAC secondary eclipse observations of LTT 9979b at 3.6 and 4.5 $μ$m. We combined the {\it Spitzer} observations with a measurement of the secondary eclipse in the {\it TESS} bandpass. The resulting secondary eclipse spectrum strongly prefers a model that includes CO absorption over a blackbody spectrum, incidentally making LTT 9979b the first {\it TESS} exoplanet (and the first ultra-hot Neptune) with evidence of a spectral feature in its atmosphere. We did not find evidence of a thermal inversion, at odds with expectations based on the atmospheres of similarly-irradiated hot Jupiters. We also report a nominal dayside brightness temperature of 2305 $\pm$ 141 K (based on the 3.6 $μ$m secondary eclipse measurement), and we constrained the planet's orbital eccentricity to $e < 0.01$ at the 99.7 \% confidence level. Together with our analysis of LTT 9979b's thermal phase curves reported in a companion paper, our results set the stage for similar investigations of a larger sample of exoplanets discovered in the hot Neptune desert, investigations which are key to uncovering the origin of this population.