Disclosed herein are methods and systems for determining an origin of viral sequence reads detected in a sample (e.g., a liquid biopsy sample) from an individual. The sample may contain cfDNA fragments of varying fragment lengths. Embodiments of the present disclosure can receive sequence read data associated with the sample, which may be a liquid biopsy sample. The sequence read data can be used to determine if one or more viral sequence reads are detected in the sample. If the viral sequence reads are detected, the system can determine one or more fragmentomic features based on the sequence read data. The system can then generate an output indicative of the origin of the viral sequence reads by inputting the fragmentomic features into a statistical model including, for example, a trained machine-learning model. Based on the output, the system can then determine whether the viral sequence reads originate from a tumor.