A discrete SIS epidemic system with disease incubation period and saturated contact rate is formulated and studied. The qualitative properties of both the disease-free and endemic equilibria in hyperbolic and non-hyperbolic cases are analysed. All potential local bifurcations of the two equilibria are explored. The direction, stability, and explicit approximate expressions for each type of bifurcation are derived. All possible rational rotation numbers on the family of closed-invariant curves generated through the Neimark–Sacker bifurcation are derived and arranged based on the five-level Farey sequence tree. The 1:5 weak resonance on the invariant curve is analysed. By the study of contact bifurcation, the global dynamic behaviour is discussed. Based on the epidemiological background, the significance of each bifurcation is explained. A large number of numerical simulation and numerical continuation examples support the theoretical analyses. At last, the model is used to fit the number of Hepatitis A infections in Guangdong Province, China, from 2018 to 2024. After analysing the residuals, conducting goodness-of-fit test, Student's t-test and Overfitting test, short-term forecasting for the number of infections is carried out.
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