Dr Redmond Smyth

Genome Architecture and Evolution of RNA viruses

Our research and approach

The research group led by Redmond Smyth investigates how RNA viruses use RNA structure during their replication and evolution. They seek to exploit knowledge of RNA genomic architecture to advance the development of highly targeted RNA-based therapeutics.

RNA viruses are an important class of emerging infectious diseases. Currently, the majority of antivirals and pharmaceuticals function at protein level. However, RNA structures within viral genomes interact with cellular/viral proteins and nucleic acids to provide a novel surface for pharmaceutical intervention. A detailed understanding of these processes is necessary for the development of novel RNA-based therapeutics.

Redmond Smyth’s group studies RNA-based mechanisms of RNA virus replication and evolution. Their work employs a combination of molecular virology, RNA biochemistry and mathematical modelling. They seek to identify essential RNA structures as new antiviral targets, and to understand how RNA structure regulates viral evolution for better vaccine and pandemic preparedness.

Their current investigations focus on single molecule and single virion analyses using high-throughput, genome-wide chemical probing technologies and mutation based functional screens. They also develop new technologies including RNA-RNA-seq, single molecule RNA structural probing and sequencing coupled microscopy. The group’s overarching goal is to exploit knowledge of RNA virus genome architecture to advance RNA-based therapies.

Team members

Research projects

RNA is a versatile molecule. It is a messenger for protein synthesis, but also a carrier of non-coding elements that regulate cellular activity through specific interactions with proteins, small molecules, and even other nucleic acids. RNA viruses exploit these non-coding RNA elements at almost every stage of their replication cycle, using them to influence splicing, protein translation, evasion of host cell defences, viral evolution and accessibility towards drug binding. Consequently, non-coding RNA represents an extremely attractive target for antiviral intervention, with the potential to revolutionize the treatment of infectious disease.

We use an integrative structural, functional and evolutionary approach to discover and mechanistically characterize non-coding RNA structures involved in viral replication and evolution. As in the protein world, it is often the higher order structure of the RNA, rather than primary sequence, that determines its function. Currently, how RNA structure drives diverse biological functions is not yet fully understood. Moreover, RNA readily undergoes structural changes, allowing it to switch between different functions, between different on/off states, or to adopt specific folds in different environments or in the presence of ligands. RNA dynamics have traditionally frustrated RNA structural characterization by biochemical and biophysical approaches. Our research focuses on unravelling the relationship between RNA structure and function, and we are actively working on new methods to investigate RNA structural dynamics. In the long term, we plan to use this knowledge to rationally develop small molecule drugs that interfere with RNA structure as a novel antiviral strategy.

We are also interested in how RNA structure constrains viral evolution. Retroviruses, such as HIV, package two copies of their RNA genome into each virion leading to recombination (template switching) and the formation of genome chimeras during replication. Another widespread strategy, seen in rotaviruses and influenza viruses, is genome segmentation leading to reassortment. Reassortment and recombination are non-random processes that are known to depend on RNA sequence and structure, but the underlying mechanisms are poorly understood. We study these mechanisms with the goal of improving disease prevention and control strategies. At the population level, we hope to understand the emergence of novel viral strains, such as how potentially pandemic influenza arises from genetic reassortment in humans, pigs or birds. At an individual level, we want to understand how RNA structure leads to immune evasion and the generation of multiple drug resistant viruses. Through our fundamental research we seek to rationally manipulate recombination and reassortment for the development of safer gene therapy vectors, as well as powerful new vaccine platforms.


In focus

HIV: The folding is the key

RNA folds into complex structures which allow it to interact specifically with other molecules in the cell. In HIV-1, minute differences in RNA folding can be crucial in determining whether viral RNA is “packaged” and thus leads to viral replication. This has been discovered by researchers from the Smyth lab by enhancing a method used to study RNA structure with a novel sequencing technology. Their findings could help to design new antivirals and were published in the journal Nature Methods.

Learn more




Isoform-specific RNA structure determination using Nano-DMS-MaP

Gribling-Burrer AS, Bohn P, Smyth RP (2024)

Nature Protocols (Online ahead of print)


Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function

Pekarek L, Zimmer MM, Gribling-Burrer AS, Buck S, Smyth RP, Caliskan N (2023)

Nucleic Acids Research 51 (2): 728–743

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

Schmidt N, Ganskih S, Wei Y, Gabel A, Zielinski S, Keshishian H, Lareau CA, Zimmermann L, Makroczyova J, Pearce C, …, Erhard F, Munschauer M (2023)

Cell 186 (22): 4834-4850.e23

Advanced fluorescence microscopy in respiratory virus cell biology

Xie E, Ahmad S, Smyth RP, Sieben C (2023)

Advances in Virus Research 116: 123-172

Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging

Jakob C, Lovate GL, Desirò D, Gießler L, Smyth RP, Marquet R, Lamkiewicz K, Marz M, Schwemmle M, Bolte H (2023)

Nucleic Acids Research 51 (12): 6479-6494

Nano-DMS-MaP allows isoform-specific RNA structure determination

Bohn P, Gribling-Burrer AS, Ambi UB, Smyth RP (2023)

Nature Methods 20 (6): 849-859


Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging

Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP (2022)

Nature Structural & Molecular Biology 29 (4): 306-319


The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N (2021)

Nature Communications 12 (1): 7193

RNA Structures and Their Role in Selective Genome Packaging

Ye L, Ambi UB, Olguin-Nava M, Gribling-Burrer AS, Ahmad S, Bohn P, Weber MM, Smyth RP (2021)

Viruses 13 (9): 1788


The evolution of RNA structural probing methods: From gels to next-generation sequencing

Mailler E, Paillart J, Marquet R, Smyth RP, Vivet-Boudou V (2019)

Wiley Interdisciplinary Reviews: RNA 10 (2): e1518


In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

Smyth RP, Smith MR, Jousset A, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, …, Kleist M, Marquet R (2018)

Nucleic Acids Research 46 (9): e57

RNA Structure - A Neglected Puppet Master for the Evolution of Virus and Host Immunity

Smyth RP, Negroni M, Lever AM, Mak J, Kenyon JC (2018)

Frontiers in Immunology 9: 2097

Structural and Functional Motifs in Influenza Virus RNAs

Ferhadian D, Contrant M, Printz-Schweigert A, Smyth RP, Paillart J, Marquet R (2018)

Frontiers in Microbiology 9: 559


HIV-1 Pr55Gag binds genomic and spliced RNAs with different affinity and stoichiometry

Bernacchi S, Abd El-Wahab EW, Dubois N, Hijnen M, Smyth RP, Mak J, Marquet R, Paillart J (2017)

RNA Biology 14 (1): 90-103


HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells

Cromer D, Schlub TE, Smyth RP, Grimm AJ, Chopra A, Mallal S, Davenport MP, Mak J (2016)

Viruses 8 (4): 118

A step forward understanding HIV-1 diversity

Smyth RP, Negroni M (2016)

Retrovirology 13: 27

The Life-Cycle of the HIV-1 Gag-RNA Complex

Mailler E, Bernacchi S, Marquet R, Paillart J, Vivet-Boudou V, Smyth RP (2016)

Viruses 8 (9): E248

MIMEAnTo: profiling functional RNA in mutational interference mapping experiments

Smith MR, Smyth RP, Marquet R, Kleist M (2016)

Bioinformatics 32 (21): 3369-3370


Mutational interference mapping experiment (MIME) for studying RNA structure and function

Smyth RP, Despons L, Huili G, Bernacchi S, Hijnen M, Mak J, Jossinet F, Weixi L, Paillart J, Kleist M, Marquet R (2015)

Nature Methods 12 (9): 866-72

Evaluation of anti-HIV-1 mutagenic nucleoside analogues

Vivet-Boudou V, Isel C, El Safadi Y, Smyth RP, Laumond G, Moog C, Paillart J, Marquet R (2015)

The Journal of Biological Chemistry 290 (1): 371-83

Properties of HIV-1 associated cholesterol in addition to raft formation are important for virus infection

Hawkes D, Jones KL, Smyth RP, Pereira CF, Bittman R, Jaworowski A, Mak J (2015)

Virus Research 210: 18-21


Specific recognition of the HIV-1 genomic RNA by the Gag precursor

Abd El-Wahab EW, Smyth RP, Mailler E, Bernacchi S, Vivet-Boudou V, Hijnen M, Jossinet F, Mak J, Paillart J, Marquet R (2014)

Nature Communications 5: 4304

Identifying recombination hot spots in the HIV-1 genome

Smyth RP, Schlub TE, Grimm AJ, Waugh C, Ellenberg P, Chopra A, Mallal S, Cromer D, Mak J, Davenport MP (2014)

Journal of Virology 88 (5): 2891-902

Fifteen to twenty percent of HIV substitution mutations are associated with recombination

Schlub TE, Grimm AJ, Smyth RP, Cromer D, Chopra A, Mallal S, Venturi V, Waugh C, Mak J, Davenport MP (2014)

Journal of Virology 88 (7): 3837-49


Improved quantification of HIV-1-infected CD4+ T cells using an optimised method of intracellular HIV-1 gag p24 antigen detection

Yang H, Yorke E, Hancock G, Clutton G, Sande N, Angus B, Smyth RP, Mak J, Dorrell L (2013)

Journal of Immunological Methods 391 (1-2): 174-8

Intracellular Dynamics of HIV Infection

Petravic J, Ellenberg P, Chan M, Paukovics G, Smyth RP, Mak J, Davenport MP (2013)

Journal of Virology 88 (2): 1113-24

A functional sequence-specific interaction between influenza A virus genomic RNA segments

Gavazzi C, Yver M, Isel C, Smyth RP, Rosa-Calatrava M, Lina B, Moulès V, Marquet R (2013)

PNAS 110 (41): 16604-9


The Origin of Genetic Diversity in HIV-1

Smyth RP, Davenport MP, Mak J (2012)

Virus Research 169 (2): 415-29


8-Modified-2'-deoxyadenosine analogues induce delayed polymerization arrest during HIV-1 reverse transcription

Vivet-Boudou V, Isel C, Sleiman M, Smyth RP, Ben Gaied N, Barhoum P, Laumond G, Bec G, Götte M, Mak J, …, Burger A, Marquet R (2011)

PLOS One 6 (11): e27456

Early events of HIV-1 infection: can signaling be the next therapeutic target?

Jones KL, Smyth RP, Pereira CF, Cameron PU, Lewin SR, Jaworowski A, Mak J (2011)

Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology 6 (2): 269-83

Labeling of multiple HIV-1 proteins with the biarsenical-tetracysteine system

Pereira CF, Ellenberg PC, Jones KL, Fernandez TL, Smyth RP, Hawkes DJ, Hijnen M, Vivet-Boudou V, Marquet R, Johnson I, Mak J (2011)

PLOS One 6 (2): e17016


Accurately measuring recombination between closely related HIV-1 genomes

Schlub TE, Smyth RP, Grimm AJ, Mak J, Davenport MP (2010)

PLOS Computational Biology 6 (4): e1000766

Reducing chimera formation during PCR amplification to ensure accurate genotyping

Smyth RP, Schlub TE, Grimm A, Venturi V, Chopra A, Mallal S, Davenport MP, Mak J (2010)

Gene 469 (1-2): 45-51


The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

Keating CP, Hill MK, Hawkes DJ, Smyth RP, Isel C, Le S, Palmenberg AC, Marshall JA, Marquet R, Nabel GJ, Mak J (2009)

Nucleic Acids Research 37 (3): 945-56