Metagenomic analysis enables more systemic detection of both known and novel viral pathogens [9] [10] [11] [12] and is approached through a variety of microarray and sequencing strategies [13, 14] . The Virochip is a pan-viral microarray platform that has been previously utilized in the detection and discovery of viruses from both human and animal samples [15] [16] [17] [18] [19] . Deep sequencing and shotgun sequencing of human clinical samples has been used for viral detection [20] [21] [22] [23] , novel virus discovery [24] [25] [26] [27] , and divergent virus genome recovery [28] . Viral metagenomic approaches have also been employed as a diagnostic supplement to pathogen detection as part of public health monitoring systems [22] , but have been limited to shotgun sequencing of viral-enriched libraries and have yet to utilize deep sequencing data. Currently available sequencing platforms can generate millions to billions of sequencing reads per run, far exceeding large-scale shotgun sequencing [13] . Deep sequencing of clinical samples, in which hundreds of thousands to millions of sequencing reads are generated per sample, can be incorporated into stepwise virus detection pipelines [29] . Database searches using Basic Local Alignment Search Tool (BLAST) and other alignment tools [30] can be used to identify sequences in samples that correspond to known and novel viruses, including those present at low concentrations or deriving from viruses that may be too divergent to be detected with PCR or microarray methods. Deep sequencing represents an unbiased, highly sensitive method for identifying viral nucleic acid in clinical samples.