Deep sequencing reads matching to viral sequences.

*Viral reads were identified by comparison to viral nucleotide and amino acid databases using the SNAP [29] and RAPSearch [30] aligners, respectively. Viral hits were confirmed to be true by BLASTn alignment to LSV or the closest viral genus or species in GenBank using an E-value cutoff of 1×10−8. Out of 15,134,328 total reads, 40,489 reads (0.27%) were identified as viral by SNAP and/or RAPSearch. Out of these 40,489 viral hits, 37,322 (92.2%) corresponded to LSV. The actual number of LSV reads in the dataset is 142,941 (0.94% of the total reads); thus, only 26.1% (37,322 of 142,941) of the actual number of LSV reads was detected.