Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

Malboeuf, Christine M.; Yang, Xiao; Charlebois, Patrick; Qu, James; Berlin, Aaron M.; Casali, Monica; Pesko, Kendra N.; Boutwell, Christian L.; DeVincenzo, John P.; Ebel, Gregory D.; Allen, Todd M.; Zody, Michael C.; Henn, Matthew R.; Levin, Joshua Z.

To determine the origin of the Illumina reads, we aligned reads to host, rRNA, and viral references. For the HIV clone samples, the majority of the reads (51-69%) aligned to the HIV reference and less than 6% of reads aligned to host (Table 1 and Supplementary Table S2 ). For the HIV clinical samples, the percent of HIV aligning reads was significantly lower (0.4-7.1%) while the majority of the reads (30-65%) aligned to host (Table 1 and Supplementary Table S2 ). The percent of reads aligning to HIV was higher in the version 1 than version 2 samples (Table 1 and Supplementary Table S2 ). This resulted in a higher average of coverage for the CDS for version 1 than version 2, 2830-fold versus 442-fold, respectively (Table 1 and Supplementary Table S2 ). For WNV clone samples, 13-31% of the reads align to WNV reference and 48-60% aligned to host (Table 1 and Supplementary Table S2 ).