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 whether our method captured the entire target region (CDS), reads were aligned to the CDS of the viral references using the Mosaik alignment tool. For both HIV clone and clinical samples, reproducible coverage of the entire CDS was obtained ( Figure 1A ). In all 13 cases, complete coverage was obtained (Supplementary Figure S1 ). As previous reports using this system utilized only the version 1 system (39), we compared the coverage pattern between version 1 and version 2 systems for HIV clone and clinical samples ( Figure 1B) . For both HIV clone and clinical samples, version 2 had more even coverage than version 1 ( Figure 1B ) based on a lower coefficient of variation (CV) (Supplementary Table S3 ). More even coverage is highly desirable for sequencing viral samples and other applications; therefore the version 2 system would be the preferred system.