Automatic processing and accurate diagnosis of pathological electrocardiogram (ECG) signals remains a challenge. As long-term ECG recordings continue to increase in prevalence, driven partly by the ease of remote monitoring technology usage, the need to automate ECG analysis continues to grow. In previous studies, a model-based ECG filtering approach to ECG data from healthy subjects has been applied to facilitate accurate online filtering and analysis of physiological signals. We propose an extension of this approach, which models not only normal and ventricular heartbeats, but also morphologies not previously encountered. A switching Kalman filter approach is introduced to enable the automatic selection of the most likely mode (beat type), while simultaneously filtering the signal using appropriate prior knowledge. Novelty detection is also made possible by incorporating a third mode for the detection of unknown (not previously observed) morphologies, and denoted as X-factor. This new approach is compared to state-of-the-art techniques for the ventricular heartbeat classification in the MIT-BIH arrhythmia and Incart databases. F1 scores of 98.3% and 99.5% were found on each database, respectively, which are superior to other published algorithms' results reported on the same databases. Only 3% of all the beats were discarded as X-factor, and the majority of these beats contained high levels of noise. The proposed technique demonstrates accurate beat classification in the presence of previously unseen (and unlearned) morphologies and noise, and provides an automated method for morphological analysis of arbitrary (unknown) ECG leads.