LOW-BIAS RNA SEQUENCING OF THE HIV-2 GENOME FROM BLOOD PLASMA.

摘要: Accurate determination of the genetic diversity present in HIV quasispecies is critical for development a preventative vaccine: particular, little known about viral second type HIV, HIV-2. A better understanding HIV-2 biology relevant to vaccine field because substantial proportion infected people experience long-term control, and prior infection has been associated with slower HIV-1 disease progression coinfected subjects. The majority traditional next-generation sequencing methods have relied on target amplification sequencing, introducing biases that may obscure true signals population. Additionally, enrichment through PCR requires priori sequence knowledge, which lacking Therefore, free method library preparation would be valuable field. We applied an RNA shotgun (RNA-Seq) without cultured stocks patient plasma samples from HIV-2-infected individuals. Libraries generated total were analyzed two-step pipeline: (i) de novo genome assembly, followed by (ii) read remapping. By this approach, whole-genome sequences 28× 67× mean depth coverage. Assembled reads showed low level GC bias, comparison diversities at intrahost accessory gene vpx all patients. Our study demonstrates RNA-Seq feasible full-genome blood collected individuals.IMPORTANCE An accurate picture globally effective vaccine. However, strategies are often complicated can distort variant frequencies, not easily corrected downstream analyses. detailed knowledge needed inform robust primer design when employing amplification, factor working tropical diseases localized developing countries. Previous work demonstrated direct used circumvent these issues hepatitis C virus (HCV) norovirus. extracted samples, demonstrating applicability technique allowing us generate dynamic over whole context low-bias sequencing.