Viral genomics is an interesting and challenging field of science. The vast amount of data, coupled with the intrinsic variability of viruses, demands robust data management and computational methods that support domain experts in studying this complex domain. This Chapter addresses the demand for data and knowledge integration as a way to analyse and discover new insights on SARS-CoV-2 and other viruses, even through artificial intelligence. Finally, a novel method for detecting recombination events in RNA viruses is presented. This method offers significant advantages over existing approaches and represents a valuable resource for public health preparedness. Overall, this work contributes significantly to viral genomics by addressing important challenges in data integration, knowledge modeling, and recombination detection.