Low-bias RNA sequencing of the HIV-2 genome from blood plamsa

Abstract

ABSTRACTAccurate determination of the genetic diversity present in the HIV quasi-species is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second strain of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection is associated with slower HIV-1 disease progression in co-infected subjects. The majority of traditional and next generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population. Additionally, target-enrichment through PCR requiresa priorisequence knowledge, which is lacking for HIV-2. Therefore, a target enrichment free method of library preparation would be valuable for the field. We applied an RNA shotgun sequencing (RNA-Seq) method without PCR amplification to cultured viral stocks and patient plasma samples from HIV-2 infected individuals. Libraries generated from total plasma RNA were analysed with a two-step pipeline: (1)de novogenome assembly, followed by (2) read re-mapping. By this approach, whole genome sequences were generated with a 28x-67x mean depth of coverage. Assembled reads showed a low level of GC-bias and comparison of the genome diversity on the intra-host level showed low diversity in the accessory genevpxin all patients. Our study demonstrates that RNA-Seq is a feasible full-genomede novosequencing method for blood plasma samples collected from HIV-2 infected individuals.IMPORTANCEAn accurate picture of viral genetic diversity is critical for the development of a globally effective HIV vaccine. However, sequencing strategies are often complicated by target enrichment prior to sequencing, introducing biases that can distort variant frequencies, which are not easily corrected for in downstream analyses. Additionally, detaileda priorisequence knowledge is needed to inform robust primer design when employing PCR amplification, a factor that is often lacking when working with tropical diseases localised in developing countries. Previous work has demonstrated that direct RNA shotgun sequencing (RNA-Seq) can be used to circumvent these issues for HCV and Norovirus. We applied shotgun RNA sequencing (RNA-Seq) to total RNA extracted from HIV-2 blood plasma samples, demonstrating the applicability of this technique to HIV-2 and allowing us to generate a dynamic picture of genetic diversity over the whole genome of HIV-2 in the context of low-bias sequencing.