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New diseases continue to emerge in both human and animal populations, and the importance of animals, as reservoirs for viruses that can cause zoonoses are evident. Thus, an increased knowledge of the viral flora in animals, both in healthy and diseased individuals, is important both for animal and human health. Viral metagenomics is a culture-independent approach that is used to investigate the complete viral genetic populations of a sample. This review describes and discusses the different possible steps of a viral metagenomic study utilizing sequence-independent amplification, high-throughput sequencing, and bioinformatics to identify viruses. With this technology, multiple viruses can be detected simultaneously and novel and highly divergent viruses can be discovered and genetically characterized for the first time. This review also briefly discusses the applications of viral metagenomics in veterinary …