Direct RNA Sequencing of the Complete Influenza A Virus Genome

For the first time, a complete genome of an RNA virus has been sequenced in its original form. Previously, RNA was sequenced by the chemical degradation of radiolabelled RNA, a difficult method that produced only short sequences. Instead, RNA has usually been sequenced indirectly by copying it into cDNA, which is often amplified to dsDNA by PCR and subsequently analyzed using a variety of DNA sequencing methods. We designed an adapter to short highly conserved termini of the influenza virus genome to target the (-) sense RNA into a protein nanopore on the Oxford Nanopore MinION sequencing platform. Utilizing this method and total RNA extracted from the allantoic fluid of infected chicken eggs, we demonstrate successful sequencing of the complete influenza virus genome with 100% nucleotide coverage, 99% consensus identity, and 99% of reads mapped to influenza. By utilizing the same methodology we can redesign the adapter in order to expand the targets to include viral mRNA and (+) sense cRNA, which are essential to the viral life cycle. This has the potential to identify and quantify splice variants and base modifications, which are not practically measurable with current methods.


Introduction
Decades ago, a method was published describing the use of base-specific chemical degradation with chromatographic and autoradiographic resolution as a way of directly sequencing short stretches of RNA 1 . Since then, little progress has been made on directly sequencing RNA. Instead, the elucidation of RNA sequences is typically indirect and primarily requires methods that synthesize cDNA from RNA templates. While these methods are powerful 2 , they suffer from limitations inherent to cDNA synthesis and amplification such as template switching 3 , artifactual splicing 4 , loss of strandedness information 5 , obscuring of base modifications 6 , and propagation of error 7 . In 2009, a method for RNA sequencing was developed on the Helicos Genetic Analysis System where poly(A) mRNA is sequenced by the step-wise synthesis and imaging of nucleotides labeled with an interfering but cleavable fluorescent dye 8 . While the input material requirements for this method are extremely low, the long workflow and short reads are limiting. Nevertheless, these approaches expose two major limitations of RNA sequencing: sequencing by synthesis and short read length. Overall, current technologies for sequencing RNA templates present difficulties in the assessment of base modifications, splice variants, and analysis of single RNA molecules.
Influenza viruses are negative-sense segmented RNA viruses [9][10][11] , and sequencing these viruses has played an important role in their understanding for 40 years 12,13 including the discovery of highly conserved viral RNA termini 14 (Figure 1A). These 3' and 5' termini are 12 and 13 nucleotides in length, respectively, and they are highly conserved across the PB2, PB1, PA, HA, NP, NA, M, and NS genome segments of influenza A viruses, which enabled the development of a universal primer set for influenza A virus genome amplification 15,16 . Even though these conserved vRNA termini have been readily exploited for efficient next generation sequencing (NGS) of influenza virus segments [16][17][18] , current methods retain some of the limitations inherent to cDNA-based techniques [3][4][5][6][7] . A new tool for long read direct RNA sequencing could reduce these biases and greatly aid efforts to directly sequence influenza virus and other RNA viruses.
Oxford Nanopore Technologies (ONT) recently released their direct RNA sequencing protocol. This method involves the sequential ligations of a reverse transcriptase adapter (RTA) and a sequencing adapter 19 . The RTA is a small dsDNA molecule (Figure 1B) that contains a T10 overhang designed to hybridize with poly(A) mRNA and a 5' phosphate (Pi) that ligates to the RNA creating a DNA-RNA hybrid. The RTA also serves as a priming location for reverse transcription of the entire length of the RNA molecule, though the cDNA generated is not sequenced.
The DNA-RNA hybrid is then ligated to the sequencing adapter which directs the RNA strand of the assembled library into the nanopore for sequencing 19 .
We describe direct RNA sequencing of an influenza A virus genome through modification of recently released RNA methods from Oxford Nanopore Technologies 19 ( Figure 1C) by targeting the conserved 3' end of the genome with an adapter to capture it (Figure 1D), rather than a primer to amplify it. The efficacy of the adapter is tested by sequencing the RNA genome of an influenza virus generated by reverse genetics A/Puerto

Nanopore sequencing
First, the RNA calibration strand enolase was directly sequenced on the MinION platform. Three sequencing experiments covered 100% of the 1,314 nucleotide long RNA molecule to an average depth of 122,207 ± 8,126 (sd). Of the 169,041 ± 28,741 reads, 98.6 ± 1.7% mapped to the reference sequence (Table 1), with 100% of the mapped reads in the sense orientation. The direction of the reads and the positive slope of the coverage diagram ( Figure S1) are indicative of directional sequencing of mRNA from the 3' end. The distribution of read lengths ( Figure S2 and Table S1) accurately corresponds to the expected length of 1,314 nucleotides. The read level accuracy was 90.4 ± 0.8%, and the consensus sequence was 99.7% in concordance with the known reference.
Based on available details on the RTA system, it was possible to make further modification to target other RNA species (Figure 1). To adapt this technique for the influenza virus genome, the target sequence of the RTA was changed from an oligo-dT to a sequence complementary to the 12 nucleotides that are conserved at the 3' end of the RNA segments of influenza A viruses (Table S2).
To test the effectiveness of the modified adapter, total RNA from allantoic fluid (crude) harvested from infected chicken eggs was sequenced via MinION. Three sequencing experiments covered 100% of the PB2, PB1, PA, HA, NP, NA, M, and NS gene segments to an average depth of 3,269 ± 1,892 (Figure 2). Although, there is reduced coverage at the extreme termini ( Figure 3) and a heavy coverage bias towards the 3' terminus of the negative sense RNA, since this approach reads from the 3' to 5' end of the molecule. Of the 54,353 ± 15,314 reads, 98.8 ± 0.1% mapped to influenza (Table 1) in a roughly even distribution among the 8 segments ( Figure   S3), with 100% of the mapped reads in the negative-sense orientation. The distribution of read lengths (Figure 4 and Table S1) corresponds well to the expected length of the respective segment. The read level accuracy was 86.3 ± 0.3%, and the consensus sequence was 98.97 ± 0.01% in concordance with consensus sequence generated using our modified version of the multi-segment reverse transcriptase polymerase chain reaction (M-RTPCR) 15,16 , Nextera, and MiSeq approach. The distribution of read lengths ( Figure S5 and Table S1) corresponds to expected lengths of each respective segment. The read level accuracies for the two runs were 85.2 and 83.8%, and the consensus sequences were 98.7 and 98.5% in concordance with consensus sequence generated using our standardized M-RTPCR amplified genome and MiSeq approach.

Illumina MiSeq sequencing
The viral RNA segments from the pure and crude preparation were amplified by M-RTPCR 15,16 , and size fractionation of those amplicons showed the characteristic banding pattern of the amplified influenza virus genome ( Figure S6). Sequencing of the RNA from purified virus or crude virus produced 163,264 and 143,572 reads, respectively, of which 99.9% mapped to influenza A virus ( Table 1). The reads were roughly evenly distributed among the 8 segments (Figures S3). The mapped reads covered 100% of all 8 genome segments (Figures 2 and S4) with reduced coverage at the extreme termini ( Figure S7). The read level accuracy was 99.6% and the consensus sequences, which were used as the reference genome for the nanopore assemblies, were defined as 100% accurate and were 100% identical to each other.

Discussion
We have demonstrated, for the first time, complete 20 sequencing of an RNA virus genome by direct RNA sequencing. Using a method originally designed to sequence mRNA, we adapted the target sequence to bind the 3' sequence conserved among influenza A viruses. The specificity of this adapter allowed efficient sequencing of influenza virus RNA genomic segments from RNA isolated from purified virus particles (control) or from RNA isolated from a crude extract that contains a myriad of viral and host (chicken) RNAs. Using this adapter, 98.8% of reads from the crude RNA preparation mapped to the influenza virus, which is practically as efficient as with purified virus RNA sample (99.3%). This performance on crude virus stocks demonstrates that the sequence directed library preparation is a very effective method to select specific target RNA species among a population of RNAs, as the vast majority of reads were to A/Puerto Rico/8/1934 using 12 ribonucleotides as the target sequence.
The data shows that other modifications to the adapter could target other RNA species such as RNAs from specific pathogens and different RNA species within a particular pathogen. For example, one could compare (+) sense cRNA [replication intermediate of (-) sense vRNAs], (+) sense mRNAs, or (-) sense RNAs present during RNA virus infections (such as for influenza viruses). The data illustrates that the adapter sequence could be modified to target specific viral families, genus, or species by extending the target sequence and or by adding degeneracies. This is an advantage over poly(A) methods that have a reduced signal-to-noise ratio due to host mRNA. Targeting influenza A virus vRNA and cRNA independently may prove difficult as there is complementarity between the two conserved termini of the vRNA segments, and therefore high sequence identity between the 3' termini of the (-) sense vRNA and (+) sense cRNA. Rather, cRNA and vRNA reads can be sorted based on their (+) and (-) polarity, respectively.
In addition to avoiding any of the previously discussed limitations of cDNA synthesis and PCR amplification strategies, the technique developed for direct RNA sequencing is highly amenable to sequencing a variety of non-poly-adenylated RNAs from hosts and pathogens, including untranslated regions (UTRs), without biasing the sequence to the primer. This allows the examination of the UTRs in their native form, which we have done here with influenza A virus. However, direct RNA sequencing of UTRs is limited by read level accuracy and a loss of coverage at the extreme 5' end of the molecule. The extreme 3' termini (Uni-12) of all segments were fully sequenced and matched the expected sequence with the exception of the degeneracy at the +4 position which was not resolved. The sequences for the extreme 5' termini (Uni-13) that were obtained match the expected sequences with the exception of a C to G substitution at the -9 position in the segments PB1 and PB2. The loss of coverage at the extreme 5' end of the molecule is most likely due to unreliable processivity as the last of the molecule passes and resulted in the final nine nucleotides not being sequenced in some of the segments.
The data presented demonstrates the adaptability of the platform and RNA sequencing protocol. The unmodified components were used to target enolase mRNA and could be used to target the variety of mRNA species present in any sample. Specifically, one could dissect viral replication processes as well as host mRNAs activated during an influenza infection at a given point in time. Genomic length and quantitative sequencing of viral mRNA species has the potential to provide direct detection of base modifications, splice variants, and transcriptional changes under different replication conditions, such as viruses used for vaccine production that are transferred between mammalian and avian hosts.
The primary limitations of this technology are the high read level error rate and high input material requirements. Reducing the error rate would enable multiplexing and more accurate consensus sequence determination and is a requirement for understanding nucleotide polymorphisms and genome sub-populations, particularly in viruses such as influenza that have significant intra-host diversity and or base modifications to be identified. There are currently several bioinformatic tools for detecting DNA base modifications such as Tombo, Nanopolish, SignalAlign, and mCaller; however, RNA specific tools have yet to be released 19 . Currently, the RNA input requirements for direct RNA sequencing are high and are not physically achievable with most original clinical samples. Lessening the RNA input requirement of the direct RNA sequencing would take full advantage of the unbiased nature of direct RNA sequencing and allow for the detection and description of the rich diversity intrinsic to influenza and other viruses. Although ONT has continuously improved their basecaller Albacore, there is still demonstrable potential for improvement. The RNA basecaller was likely developed using the very same enolase mRNA used here, which would make it most effective at basecalling enolase mRNA. The marked difference in accuracy between the enolase and influenza virus reads demonstrates that further development of the RNA basecaller can, at a minimum, bring the accuracy of all RNA reads up to that of enolase reads.
Moreover, the DNA basecaller is overall more developed and more accurate than the RNA basecaller (89% versus 85% read level accuracy for influenza samples). The continued effort to advance this technology by ONT will undoubtedly result in higher accuracy reads and greatly improved utility.

Concentration and purification of A/Puerto Rico/8/1934 reassortant virus
A/Puerto Rico/8/1934 reassortant virus was grown in 11 day-old embryonated hen eggs at 35°C for 48 hours. Allantoic fluid was harvested from the chilled eggs and clarified at 5,400 x g, 10 minutes, 4°C, (Sorvall SLA-1500 rotor). The virus was clarified twice more by centrifugation at 15,000 x g, 5 minutes, 4°C (Sorvall SLA-1500 rotor). Virus was pelleted by centrifugation at 39,000 x g, 3 hours at 4°C (Sorvall A621 rotor). Virus pellets were resuspended overnight in PBS and loaded onto a 30%/55% (w/w) density sucrose gradient. The gradient was centrifuged at 90,000 x g for 14 hours at 4°C (Sorvall AH629 rotor). The virus fractions were harvested and sedimented at 131,000 x g (Sorvall AH629 rotor) for 2.5 hours. The resulting virus pellet was resuspended in PBS and aliquoted for future use.

RNA isolation
Enolase II (YHR174W) mRNA is supplied in the ONT materials as the calibration RNA strand (CRS) at a concentration of 50 ng/µL. For influenza virus samples, total RNA was isolated by Invitrogen TM TRIzol® extraction 21 according to manufacturer's instructions with additional considerations for biosafety. The virus was inactivated by the addition of 10 volumes of TRIzol® in a Biosafely Level 2 biosafety cabinet. Following inactivation, a fume hood was used for the chloroform addition and aqueous phase removal steps. RNA pellets were resuspended in 10-40 µL nuclease free water and quantified by Quant-iT TM RiboGreen® RNA Assay Kit. Due to the difficulty in acquiring sucrose-purified material, the pure controls were limited to one MiSeq run and two separate MinION experiments. The availability of crude viral samples allowed it to be sequenced once on MiSeq and three times on MinION from the same RNA preparation.

Nanopore Sequencing
The ONT direct RNA library preparation input material requirement is 500 ng of target molecule in a 9.5 µL volume (Table S4). For mRNA sequencing of the enolase control, the protocol was used according to the manufacturer's instruction. For influenza viral RNA sequencing, modifications were made to the protocol components (Table S2). We altered the supplied reverse transcriptase adapter (RTA) which has a T10 overhang  Alignment read lengths were calculated as matching + inserted bases per read (CIGAR M+I).

Illumina MiSeq Sequencing
The complete influenza genome was amplified with the RNA from both the sucrose purified virus and the allantoic fluid. The MRT-PCR used the Uni/Inf primer set 16 with SuperScript III One-Step RT-PCR with Platinum Taq High Fidelity (Invitrogen). Following amplification, indexed paired-end libraries were generated from 2.5 µl of 0.2 ng/µL using the Nextera XT Sample Preparation Kit (Illumina) following the manufacturer protocol using half-volume tagmentation reactions. Libraries were purified with 0.8X AMPure XP beads (Beckman Coulter, Inc.) and assessed for fragment size (QIAxcel Advanced System, Qiagen) and quantitated using Quant-iT dsDNA High Sensitivity Assay (Invitrogen). Six pmol of pooled libraries were sequenced on the Illumina MiSeq with MiSeq v2 300 cycle kit and 5% PhiX spike-in to increase the sequence diversity. Sequence analysis was performed using IRMA 25 as part of the current Illumina-based pipeline utilized by the Influenza Genomics Team at the Centers for Disease Control and Prevention.