Date Published: April 8, 2019
Publisher: Springer Berlin Heidelberg
Author(s): Cedric Chih Shen Tan, Sebastian Maurer-Stroh, Yue Wan, October Michael Sessions, Paola Florez de Sessions.
Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for characterizing properties innate to RNA strands such as secondary structure, RNA–RNA interactions, and also for nanopore direct RNA sequencing involving the sequencing of native RNA strands. The latter strategy, ultracentrifugation, causes loss in genomic information due to its inability to retrieve unassembled viral RNA. To address this, we developed a novel application of current nucleic acid hybridization technologies for direct characterization of RNA. In particular, we modified a current enrichment protocol to capture whole viral native RNA genomes for downstream RNA assays to circumvent the abovementioned problems. This technique involves hybridization of biotinylated baits at 500 nucleotides (nt) intervals, stringent washes and release of free native RNA strands using DNase I treatment, with a turnaround time of about 6 h 15 min. RT-qPCR was used as the primary proof of concept that capture-based purification indeed removes host background. Subsequently, capture-based purification was applied to direct RNA sequencing as proof of concept that capture-based purification can be coupled with downstream RNA assays. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold. We also report that application of this protocol to direct RNA sequencing yielded a reduction in human host RNA background by 1580-fold, a 99.91% recovery of viral genome with at least 15× coverage, and a mean coverage across the genome of 120×. This report is, to the best of our knowledge, the first description of a capture-based purification method for assays that involve direct manipulation or characterisation of native RNA. This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes.
Viruses with RNA genomes are the cause of many infectious diseases with serious consequences to human health and mortality such as flaviviruses, HIV-1, SARS-coronavirus, HTLV-1 and influenza virus (Cantara et al. 2014). It has been shown that RNA–RNA interactions (Romero-López and Berzal-Herranz 2009) and intramolecular structure (Witteveldt et al. 2014) of viral RNA genomes play an important role in viral replication. However, extraction of viral RNA directly from culture often yields viral RNA with high host RNA background (Marston et al. 2013).