Systematic discovery of functional elements in RNA virus genomes: an Encyclopedia of RNA Virus Elements

Project Information

ERVE

Grant agreement ID: 646891

DOI 10.3030/646891

Project closed

EC signature date 17 August 2015

Start date 1 September 2015

End date 31 August 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 780 000,00

EU contribution € 1 780 000,00

Coordinated by

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom

Publications

Peer reviewed articles (31)

Discovery of three RNA viruses using ant transcriptomic datasets

Author(s): Eleni Kleanthous, Ingrida Olendraite, Nina I. Lukhovitskaya, Andrew E. Firth
Published in: Archives of Virology, Issue 164/2, 2019, Page(s) 643-647, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-018-4093-2

A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.

Author(s): Dinan, Adam M; Lukhovitskaya, Nina; Olendraite, Ingrida; Firth, Andrew
Published in: Virus Evolution, Issue 1, 2020, Page(s) veaa007, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/veaa007

Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges

Author(s): Jermilia Charles, Chandra S. Tangudu, Stefanie L. Hurt, Charlotte Tumescheit, Andrew E. Firth, Julian E. Garcia-Rejon, Carlos Machain-Williams, Bradley J. Blitvich
Published in: Journal of General Virology, Issue 99/12, 2018, Page(s) 1729-1738, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.001165

Programmed −2/−1 Ribosomal Frameshifting in Simarteriviruses: an Evolutionarily Conserved Mechanism

Author(s): Yanhua Li, Andrew E. Firth, Ian Brierley, Yingyun Cai, Sawsan Napthine, Tao Wang, Xingyu Yan, Jens H. Kuhn, Ying Fang
Published in: Journal of Virology, Issue 93/16, 2019, Page(s) e00370-19, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00370-19

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

Author(s): Jessica Sook Yuin Ho, Matthew Angel, Yixuan Ma, Elizabeth Sloan, Guojun Wang, Carles Martinez-Romero, Marta Alenquer, Vladimir Roudko, Liliane Chung, Simin Zheng, Max Chang, Yesai Fstkchyan, Sara Clohisey, Adam M. Dinan, James Gibbs, Robert Gifford, Rong Shen, Quan Gu, Nerea Irigoyen, Laura Campisi, Cheng Huang, Nan Zhao, Joshua D. Jones, Ingeborg van Knippenberg, Zeyu Zhu, Natasha Moshkina, Léa
Published in: Cell, Issue 181/7, 2020, Page(s) 1502-1517.e23, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.05.035

Propensity of a picornavirus polymerase to slip on potyvirus-derived transcriptional slippage sites

Author(s): Hazel Stewart, Allan Olspert, Benjamin G. Butt, Andrew E. Firth
Published in: Journal of General Virology, Issue 100/2, 2019, Page(s) 199-205, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.001189

Targeting the Conserved Stem Loop 2 Motif in the SARS-CoV-2 Genome

Author(s): Lulla V, Wandel MP, Bandyra KJ, Ulferts R, Wu M, Dendooven T, Yang X, Doyle N, Oerum S, Beale R, O'Rourke SM, Randow F, Maier HJ, Scott W, Ding Y, Firth AE, Bloznelyte K, Luisi BF
Published in: Journal of Virology, Issue 95, 2021, Page(s) e0066321, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/jvi.00663-21

A hidden gene in astroviruses encodes a viroporin

Author(s): Valeria Lulla, Andrew E. Firth
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17906-x

Enterovirus Competition Assay to Assess Replication Fitness

Author(s): Valeria Lulla, Andrew Firth
Published in: BIO-PROTOCOL, Issue 9/10, 2019, ISSN 2331-8325
Publisher: bio-protocol
DOI: 10.21769/bioprotoc.3233

Complete genome sequences of two insect-specific flaviviruses

Author(s): Jermilia Charles, Chandra S. Tangudu, Andrew E. Firth, Bradley J. Blitvich
Published in: Archives of Virology, Issue 162/12, 2017, Page(s) 3913-3917, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-017-3552-5

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?

Author(s): Adam M. Dinan, John F. Atkins, Andrew E. Firth
Published in: Biology Direct, Issue 12/1, 2017, ISSN 1745-6150
Publisher: BioMed Central
DOI: 10.1186/s13062-017-0195-0

A Review of Flaviviruses that Have No Known Arthropod Vector

Author(s): Bradley Blitvich, Andrew Firth
Published in: Viruses, Issue 9/6, 2017, Page(s) 154, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v9060154

Avoidance of reporter assay distortions from fused dual reporters

Author(s): Gary Loughran, Michael T. Howard, Andrew E. Firth, John F. Atkins
Published in: RNA, Issue 23/8, 2017, Page(s) 1285-1289, ISSN 1355-8382
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.061051.117

Ribosome profiling of the retrovirus murine leukemia virus

Author(s): Nerea Irigoyen, Adam M. Dinan, Ian Brierley, Andrew E. Firth
Published in: Retrovirology, Issue 15/1, 2018, ISSN 1742-4690
Publisher: BioMed Central
DOI: 10.1186/s12977-018-0394-5

Protein-directed ribosomal frameshifting temporally regulates gene expression

Author(s): Sawsan Napthine, Roger Ling, Leanne K. Finch, Joshua D. Jones, Susanne Bell, Ian Brierley, Andrew E. Firth
Published in: Nature Communications, Issue 8, 2017, Page(s) 15582, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms15582

An analysis by metabolic labelling of the encephalomyocarditis virus ribosomal frameshifting efficiency and stimulators

Author(s): Roger Ling, Andrew E. Firth
Published in: Journal of General Virology, Issue 98/8, 2017, Page(s) 2100-2105, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.000888

Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses

Author(s): Ingrida Olendraite, Nina I. Lukhovitskaya, Sanford D. Porter, Steven M. Valles, Andrew E. Firth
Published in: Journal of General Virology, Issue 98/9, 2017, Page(s) 2368-2378, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.000902

Transcriptional and Translational Landscape of Equine Torovirus

Author(s): Hazel Stewart, Katherine Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Published in: Journal of Virology, Issue 92/17, 2018, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00589-18

Isolation and characterization of Nylanderia fulva virus 1, a positive-sense, single-stranded RNA virus infecting the tawny crazy ant, Nylanderia fulva

Author(s): Steven M. Valles, David H. Oi, James J. Becnel, James K. Wetterer, John S. LaPolla, Andrew E. Firth
Published in: Virology, Issue 496, 2016, Page(s) 244-254, ISSN 0042-6822
Publisher: Academic Press
DOI: 10.1016/j.virol.2016.06.014

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Author(s): John F. Atkins, Gary Loughran, Pramod R. Bhatt, Andrew E. Firth, Pavel V. Baranov
Published in: Nucleic Acids Research, 2016, Page(s) gkw530, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkw530

High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling

Author(s): Nerea Irigoyen, Andrew E. Firth, Joshua D. Jones, Betty Y.-W. Chung, Stuart G. Siddell, Ian Brierley
Published in: PLOS Pathogens, Issue 12/2, 2016, Page(s) e1005473, ISSN 1553-7374
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1005473

Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins

Author(s): Allan Olspert, John P. Carr, Andrew E. Firth
Published in: Nucleic Acids Research, Issue 44/16, 2016, Page(s) 7618-7629, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkw441

Characterization of the stimulators of protein-directed ribosomal frameshifting in Theiler's murine encephalomyelitis virus

Author(s): Sawsan Napthine, Susanne Bell, Chris H Hill, Ian Brierley, Andrew E Firth
Published in: Nucleic Acids Research, Issue 47/15, 2019, Page(s) 8207-8223, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz503

Discovery of a novel Tymoviridae-like virus in mosquitoes from Mexico

Author(s): Jermilia Charles, Chandra S. Tangudu, Stefanie L. Hurt, Charlotte Tumescheit, Andrew E. Firth, Julian E. Garcia-Rejon, Carlos Machain-Williams, Bradley J. Blitvich
Published in: Archives of Virology, Issue 164/2, 2019, Page(s) 649-652, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-018-4098-x

Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection

Author(s): Echavarría-Consuegra L, Cook GM, Busnadiego I, Lefèvre C, Keep S, Brown K, Doyle N, Dowgier G, Franaszek K, Moore NA, Siddell SG, Bickerton E, Hale BG, Firth AE, Brierley I, Irigoyen N
Published in: PLoS Pathogens, Issue 17, 2021, Page(s) e1009644, ISSN 1553-7374
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1009644

A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a

Author(s): Andrew E. Firth
Published in: Journal of General Virology, 2020, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.001469

An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells

Author(s): Valeria Lulla, Adam M. Dinan, Myra Hosmillo, Yasmin Chaudhry, Lee Sherry, Nerea Irigoyen, Komal M. Nayak, Nicola J. Stonehouse, Matthias Zilbauer, Ian Goodfellow, Andrew E. Firth
Published in: Nature Microbiology, Issue 4/2, 2019, Page(s) 280-292, ISSN 2058-5276
Publisher: Nature Research
DOI: 10.1038/s41564-018-0297-1

C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis

Author(s): Shreekara Gopalakrishna, Sarah F Pearce, Adam M Dinan, Florian A Schober, Miriam Cipullo, Henrik Spåhr, Anas Khawaja, Camilla Maffezzini, Christoph Freyer, Anna Wredenberg, Ilian Atanassov, Andrew E Firth, Joanna Rorbach
Published in: Nucleic Acids Research, Issue 47/17, 2019, Page(s) 9386-9399, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz684

Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution

Author(s): Adam M. Dinan, Sarah Keep, Erica Bickerton, Paul Britton, Andrew E. Firth, Ian Brierley
Published in: Journal of Virology, Issue 93/18, 2019, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00714-19

Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus

Author(s): Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I
Published in: Nucleic Acids Research, Issue 49, 2021, Page(s) 11938-11958, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab969

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Author(s): Hill CH, Pekarek L, Napthine S, Kibe A, Firth AE, Graham SC, Caliskan N, Brierley I
Published in: Nature Communications, Issue 12, 2021, Page(s) 7166, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27400-7