Direct RNA nanopore sequencing of full-length coron-avirus genomes provides novel insights into structural variants and enables modification analysis, bioRxiv, 2018-12-01

ABSTRACTSequence analyses of RNA virus genomes remain challenging due to the exceptional genetic plasticity of these viruses. Because of high mutation and recombination rates, genome replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses that are generally referred to as ‘quasispecies’. Although standard (short-read) sequencing technologies allow to readily determine consensus sequences for these ‘quasispecies’, it is far more difficult to reconstruct large numbers of full-length haplotypes of (i) RNA virus genomes and (ii) subgenome-length (sg) RNAs comprised of noncontiguous genome regions that may be present in these virus populations. Here, we used a full-length, direct RNA sequencing (DRS) approach without any amplification step to characterize viral RNAs produced in cells infected with a human coronavirus representing one of the largest RNA virus genomes known to date.Using DRS, we were able to map the longest (~26 kb) contiguous read to the viral reference genome. By combining Illumina and nanopore sequencing, a highly accurate consensus sequence of the human coronavirus (HCoV) 229E genome (27.3 kb) was reconstructed. Furthermore, using long reads that did not require an assembly step, we were able to identify, in infected cells, diverse and novel HCoV-229E sg RNAs that remain to be characterized. Also, the DRS approach, which does not require reverse transcription and amplification of RNA, allowed us to detect methylation sites in viral RNAs. Our work paves the way for haplotype-based analyses of viral quasispecies by demonstrating the feasibility of intra-sample haplotype separation. We also show how supplementary short-read sequencing (Illumina) can be used to reduce the error rate of nanopore sequencing.Even though a number of technical challenges remain to be addressed to fully exploit the potential of the nanopore technology, our work illustrates that direct RNA sequencing may significantly advance genomic studies of complex virus populations, including predictions on long-range interactions in individual full-length viral RNA haplotypes.

biorxiv genomics 100-200-users 2018

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis, bioRxiv, 2018-12-01

Sequence analyses of RNA virus genomes remain challenging due to the exceptionalgenetic plasticity of these viruses. Because of high mutation and recombinationrates, genome replication by viral RNA-dependent RNA polymerases leads topopulations of closely related viruses, so-called 'quasispecies'. Standard(short-read) sequencing technologies are ill-suited to reconstruct large numbersof full-length haplotypes of (i) RNA virus genomes and (ii) subgenome-length(sg) RNAs comprised of noncontiguous genome regions. Here, we used afull-length, direct RNA sequencing (DRS) approach based on nanopores tocharacterize viral RNAs produced in cells infected with a human coronavirus.Using DRS, we were able to map the longest (~26 kb) contiguous read to theviral reference genome. By combining Illumina and nanopore sequencing, wereconstructed a highly accurate consensus sequence of the human coronavirus(HCoV) 229E genome (27.3 kb). Furthermore, using long reads that did notrequire an assembly step, we were able to identify, in infected cells, diverseand novel HCoV-229E sg RNAs that remain to be characterized. Also, the DRSapproach, which circumvents reverse transcription and amplification of RNA,allowed us to detect methylation sites in viral RNAs. Our work paves the way forhaplotype-based analyses of viral quasispecies by demonstrating the feasibilityof intra-sample haplotype separation.Even though several technical challenges remain to be addressed to exploit thepotential of the nanopore technology fully, our work illustrates that direct RNAsequencing may significantly advance genomic studies of complex viruspopulations, including predictions on long-range interactions in individualfull-length viral RNA haplotypes.

biorxiv genomics 100-200-users 2018

 

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