We detected virus sequence at concentrations as low as ,2 in 10 6 reads. Virus sequence detected in a clinical sample at vanishingly low copy numbers may reflect several possible hostmicrobe scenarios. The sequence detected may be that of a pathogenic virus capable of causing illness at low copy number or through indirect effects, a ubiquitous non-disease causing microbe, a virus outside of its primary replication site, low-level contamination, an artifact of sample collection timing/processing, or remains of incomplete immune clearance. Additional evidence must be considered in each case to define the host-microbe relationship.