Context: CO is an abundant species in comets, creating CO$^+$ ion with emission lines that can be observed in the optical spectral range. A good modeling of its fluorescence spectrum is important for a better measurement of the CO$^+$ abundance. Such a species, if abundant enough, can also be used to measure the $^{12}$C/$^{13}$C isotopic ratio. Aims: This study uses the opportunity of a high CO content observed in the comet C/2016 R2 (PanSTARRS), that created bright CO$^{+}$ emission lines in the optical range, to build and test a new fluorescence model of this species and to measure for the first time the $^{12}$C/$^{13}$C isotopic ratio in this chemical species with ground-based observations. Methods: Thanks to laboratory data and theoretical works available in the scientific literature we developed a new fluorescence model both for $^{12}$CO$^+$ and $^{13}$CO$^+$ ions. The $^{13}$CO$^+$ model can be used for coadding faint emission lines and obtain a sufficient signal-to-noise ratio to detect this isotopologue. Results: Our fluorescence model provides a good modeling of the $^{12}$CO$^+$ emission lines, allowing to publish revised fluorescence efficiencies. Based on similar transition probabilities for $^{12}$CO$^+$ and $^{13}$CO$^+$ we derive a $^{12}$C/$^{13}$C isotopic ratio of 73$\pm$20 for CO$^+$ in comet C/2016 R2. This value is in agreement with the solar system ratio of 89$\pm$2 within the error bars, making the possibility that this comet was an interstellar object unlikely.
Comment: 11 pages, 8 figures