High-throughput sequencing techniques are beginning to be used in many fields, both in science and industry. These techniques make it possible to analyze the biological composition of a given sample without the need to know the studied sequences, as is the case with classical molecular biology techniques in which primers and probes of known sequences are required. Shotgun or untargeted metagenomic approaches enable the simultaneous identification of viral sequences from a sample, referred to as ‘virome’, which is a diverse community of mainly eukaryotic RNA and DNA eukaryotic viruses and bacteriophages. Virome characterization provides a potential solution to the challenges associated with the traditional surveillance of viruses. Additionally, the use of targeted sequencing allows us to study the population composition of a determined virus or viral group to analyze its diversity. Targeted sequencing allows us to detect new variants as well as to know the dynamics of the virus in the environment.