Amplification of the complete SARS-CoV-2 genome: PrimeSTAR GXL emerges as a pivotal component

As experts gear up for the Oxford Global NextGen Omics 2023 conference in London in November, we are always on the lookout for exciting ways researchers are applying great products to breakthrough technologies in next-gen sequencing. One of these technologies from Oxford Nanopore—long-read nanopore DNA and RNA sequencing—has gained recent traction due to its relatively low cost, scalability, and delivery of real-time sequencing data. It was used during the COVID-19 pandemic to rapidly sequence the genomes of SARS-CoV-2 and identify variants in order to combat spread of the virus.

Here we shine the spotlight on the work of Dr. Redmond Smyth, who has published a protocol in Nature Methods. The protocol uses this popular technology to characterize viral RNA structures, including SARS-CoV-2, with the help of Takara Bio’s PrimeSTAR GXL DNA Polymerase.

Dr. Smyth is an RNA biochemist and virologist working at the Helmholtz Institute of RNA-based Infection Research (HIRI) in Germany. His research investigates the mechanistic role of RNA structure in the replication and evolution of RNA viruses, such as HIV-1, influenza, and SARS-CoV-2. Originally from Ireland, Dr. Smyth pursued his undergraduate degree in Natural Sciences at the University of Cambridge, UK, where he specialized in Virology and Immunology. He completed his PhD at the Burnet Institute in Melbourne, Australia, where he investigated mechanisms underpinning genetic diversity in HIV-1. He then undertook a postdoctoral position at the IBMC in Strasbourg, France, where he received training in RNA biochemistry. During this time, he worked to gain a deeper understanding of how the HIV-1 genomic RNA is incorporated into viral particles. In 2015, he was recruited as a chargé de recherché (CR2) by the CNRS, France. Since 2018, he heads his own research group at the Helmholtz Institute.

Dr. Redmond Smyth

Read on to learn more about Dr. Smyth’s work, and how other labs can use these same products and protocols as they explore this exciting sequencing technology.

Can you tell us about your team and the research focus of your lab? How does it align with the theme of the institute?

Our team comprises dedicated scientists with a profound interest in RNA biology and virology, with a special focus on RNA viruses. RNA viruses are a significant threat to human health and a key class of emerging infectious diseases, responsible for millions of deaths annually. A defining feature of these viruses is their RNA genome, which encodes all the proteins necessary for hijacking host cells.

Traditionally, infectious disease research has focused on developing drugs that bind to viral proteins to disrupt their function, but viral RNA genomes play a crucial role in regulating infection through their ability to fold into complex three-dimensional structures. These RNA structures interact with other molecules within the host cell to influence vital processes such as splicing, translation, immune evasion, and viral evolution. Due to their essential nature, viral RNA structure represents a novel and extremely attractive target for antiviral intervention.

Our research projects are focused on uncovering novel functional RNA structures present in RNA virus genomes. By studying these structures, we can gain valuable insights into how they impact viral replication and evolution. Some RNA structures function by binding to proteins or other nucleic acids, and our team is dedicated to investigating these complex interactions. Additionally, RNA structure may exist as alternative folds, each with its unique biological function. We address these issues by developing and applying innovative experimental techniques. Our ultimate goal is to identify novel, conserved and potentially druggable antiviral targets, which would open up completely new avenues for prevention and treatment of viral diseases.

Our lab is housed within the Helmholtz Institute for RNA-based Infection Research (HIRI), which is one of the few institutes in the world to focus on RNA and Infection. The HIRI mission is to better understand the role of RNA in infection processes and to harness this knowledge in the design of novel anti-infective strategies. Our mechanistic studies are a key part of the institute’s mission.

You recently published a novel method known as nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP). How does the application of nanopore sequencing enhance the DMS-MaP workflow?

Our recent scientific breakthrough, Nano-DMS-MaP, marks a significant advancement in our methodological arsenal for probing RNA structures. The technique amalgamates two powerful tools—long-read nanopore sequencing and dimethylsulfate (DMS) mutational profiling—allowing us to achieve unprecedented resolution in structural analysis.

This advance is important because within cellular environments, RNA isoforms are expressed with sequence variations, often arising from phenomena like alternative splicing and diverse transcription start sites. Consequently, these seemingly minor differences in RNA sequences can significantly impact their folding patterns, leading to distinct functional outcomes.

Nanopore sequencing plays a transformative role in our approach. Unlike conventional short-read Illumina sequencing, which struggles with unambiguous assignment to specific transcript isoforms, nanopore sequencing offers long reads that can be uniquely mapped to individual RNA isoforms. This breakthrough capability enables us to deconvolute the structural intricacies of various RNA isoforms, providing a more comprehensive and precise understanding of their functions.

By harnessing the power of Nano-DMS-MaP, we recently made a notable discovery concerning the HIV-1 genome, where the folding patterns significantly diverge between spliced and unspliced RNAs, shedding light on how HIV-1 discriminates between these RNA types during viral assembly.

What were the primary challenges encountered during the development of this method? How did PrimeSTAR GXL assist in overcoming these hurdles?

The development of Nano-DMS-MaP presented its share of challenges. One of the major obstacles involved obtaining DNA molecules that sufficiently covered all potential splice junctions, thereby facilitating precise RNA isoform identification. To tackle this, we adopted the ultra-processive reverse transcriptase known as MarathonRT, which efficiently generated the requisite cDNA. Moreover, we confronted the challenge of amplifying diverse and complex cDNA into double-stranded DNA for sequencing. After extensive testing of various enzymes, PrimeSTAR GXL emerged as a pivotal component in overcoming this hurdle.

Your lab has a history of employing PrimeSTAR GXL in previous publications. What standout results have you achieved with this polymerase?

Indeed, our lab has utilized PrimeSTAR GXL in past investigations, and its consistent performance has been a mainstay of our work. In our ongoing endeavors to characterize the RNA structures of influenza viruses using Nano-DMS-MaP, PrimeSTAR GXL has repeatedly demonstrated its utility in rescuing experiments that that did not amplify with other enzymes.

Using PrimeSTAR GXL, we were also able to amplify the entire 30 kb SARS-CoV-2 sequence—something I still find remarkable.

This method has shown promising results in the study of HIV; how do you envision other scientists utilizing this protocol? What broad impact could this work have on the field of infectious diseases?

Nano-DMS-MaP's potential applications extend far beyond our laboratory. We anticipate that other researchers in the field of RNA biology will eagerly adopt this protocol for their investigations. With its versatility, straightforward workflow, and the ability to uncover high-resolution structural information at the isoform level, we hope Nano-DMS-MaP will become the gold standard for studying RNA structural variations.

In the realm of infectious disease research, this method opens a gateway to uncover novel RNA-regulatory mechanisms that were previously concealed. Pathogens often exploit RNA isoforms to code for different proteins. By applying Nano-DMS-MaP, researchers can now unveil specific RNA structures harbored within these transcripts and discover novel functional determinants that could serve as potential targets for innovative anti-viral strategies.

What are your lab's next major research goals?

Looking ahead, we aim to delve deeper into RNA folding by elucidating the mechanisms through which multiple RNA molecules interact to form inter-molecular complexes with distinct functions crucial to viral replication. Exploring the influence of cellular localization on viral RNA structure and function represents an additional exciting avenue for our research.

References

Bohn, P. et al. Nano-DMS-MaP allows isoform-specific RNA structure determination. Nature Methods, 20, 849–859 (2023).