Wildlife disease surveillance programs and research studies track infection and identify risk factors for wild populations, humans, and agriculture. Often, several types of samples are collected from individuals to provide more complete information about an animal's infection history. Methods that jointly analyze multiple data streams to study disease emergence and drivers of infection via epidemiological process models remain underdeveloped. Joint-analysis methods can more thoroughly analyze all available data, more precisely quantifying epidemic processes, outbreak status, and risks. We contribute a paired data modeling approach that analyzes multiple samples from individuals. We use "characterization maps" to link paired data to epidemiological processes through a hierarchical statistical observation model. Our approach can provide both Bayesian and frequentist estimates of epidemiological parameters and state. We motivate our approach through the need to use paired pathogen and antibody detection tests to estimate parameters and infection trajectories for the widely applicable susceptible, infectious, recovered (SIR) model. We contribute general formulas to link characterization maps to arbitrary process models and datasets and an extended SIR model that better accommodates paired data. We find via simulation that paired data can more efficiently estimate SIR parameters than unpaired data, requiring samples from 5-10 times fewer individuals. We then study SARS-CoV-2 in wild White-tailed deer (Odocoileus virginianus) from three counties in the United States. Estimates for average infectious times corroborate captive animal studies. Our methods use general statistical theory to let applications extend beyond the SIR model we consider, and to more complicated examples of paired data.

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