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

Informazioni relative al progetto

ERVE

ID dell’accordo di sovvenzione: 646891

DOI 10.3030/646891

Progetto chiuso

Data della firma CE 17 Agosto 2015

Data di avvio 1 Settembre 2015

Data di completamento 31 Agosto 2021

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale € 1 780 000,00

Contributo UE € 1 780 000,00

Coordinato da

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

Pubblicazioni

Peer reviewed articles (31)

Discovery of three RNA viruses using ant transcriptomic datasets

Autori: Eleni Kleanthous, Ingrida Olendraite, Nina I. Lukhovitskaya, Andrew E. Firth
Pubblicato in: Archives of Virology, Numero 164/2, 2019, Pagina/e 643-647, ISSN 0304-8608
Editore: 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.

Autori: Dinan, Adam M; Lukhovitskaya, Nina; Olendraite, Ingrida; Firth, Andrew
Pubblicato in: Virus Evolution, Numero 1, 2020, Pagina/e veaa007, ISSN 2057-1577
Editore: 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

Autori: Jermilia Charles, Chandra S. Tangudu, Stefanie L. Hurt, Charlotte Tumescheit, Andrew E. Firth, Julian E. Garcia-Rejon, Carlos Machain-Williams, Bradley J. Blitvich
Pubblicato in: Journal of General Virology, Numero 99/12, 2018, Pagina/e 1729-1738, ISSN 0022-1317
Editore: Society for General Microbiology
DOI: 10.1099/jgv.0.001165

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

Autori: Yanhua Li, Andrew E. Firth, Ian Brierley, Yingyun Cai, Sawsan Napthine, Tao Wang, Xingyu Yan, Jens H. Kuhn, Ying Fang
Pubblicato in: Journal of Virology, Numero 93/16, 2019, Pagina/e e00370-19, ISSN 0022-538X
Editore: American Society for Microbiology
DOI: 10.1128/JVI.00370-19

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

Autori: 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
Pubblicato in: Cell, Numero 181/7, 2020, Pagina/e 1502-1517.e23, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2020.05.035

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

Autori: Hazel Stewart, Allan Olspert, Benjamin G. Butt, Andrew E. Firth
Pubblicato in: Journal of General Virology, Numero 100/2, 2019, Pagina/e 199-205, ISSN 0022-1317
Editore: Society for General Microbiology
DOI: 10.1099/jgv.0.001189

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

Autori: 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
Pubblicato in: Journal of Virology, Numero 95, 2021, Pagina/e e0066321, ISSN 0022-538X
Editore: American Society for Microbiology
DOI: 10.1128/jvi.00663-21

A hidden gene in astroviruses encodes a viroporin

Autori: Valeria Lulla, Andrew E. Firth
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-17906-x

Enterovirus Competition Assay to Assess Replication Fitness

Autori: Valeria Lulla, Andrew Firth
Pubblicato in: BIO-PROTOCOL, Numero 9/10, 2019, ISSN 2331-8325
Editore: bio-protocol
DOI: 10.21769/bioprotoc.3233

Complete genome sequences of two insect-specific flaviviruses

Autori: Jermilia Charles, Chandra S. Tangudu, Andrew E. Firth, Bradley J. Blitvich
Pubblicato in: Archives of Virology, Numero 162/12, 2017, Pagina/e 3913-3917, ISSN 0304-8608
Editore: 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?

Autori: Adam M. Dinan, John F. Atkins, Andrew E. Firth
Pubblicato in: Biology Direct, Numero 12/1, 2017, ISSN 1745-6150
Editore: BioMed Central
DOI: 10.1186/s13062-017-0195-0

A Review of Flaviviruses that Have No Known Arthropod Vector

Autori: Bradley Blitvich, Andrew Firth
Pubblicato in: Viruses, Numero 9/6, 2017, Pagina/e 154, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v9060154

Avoidance of reporter assay distortions from fused dual reporters

Autori: Gary Loughran, Michael T. Howard, Andrew E. Firth, John F. Atkins
Pubblicato in: RNA, Numero 23/8, 2017, Pagina/e 1285-1289, ISSN 1355-8382
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.061051.117

Ribosome profiling of the retrovirus murine leukemia virus

Autori: Nerea Irigoyen, Adam M. Dinan, Ian Brierley, Andrew E. Firth
Pubblicato in: Retrovirology, Numero 15/1, 2018, ISSN 1742-4690
Editore: BioMed Central
DOI: 10.1186/s12977-018-0394-5

Protein-directed ribosomal frameshifting temporally regulates gene expression

Autori: Sawsan Napthine, Roger Ling, Leanne K. Finch, Joshua D. Jones, Susanne Bell, Ian Brierley, Andrew E. Firth
Pubblicato in: Nature Communications, Numero 8, 2017, Pagina/e 15582, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/ncomms15582

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

Autori: Roger Ling, Andrew E. Firth
Pubblicato in: Journal of General Virology, Numero 98/8, 2017, Pagina/e 2100-2105, ISSN 0022-1317
Editore: Society for General Microbiology
DOI: 10.1099/jgv.0.000888

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

Autori: Ingrida Olendraite, Nina I. Lukhovitskaya, Sanford D. Porter, Steven M. Valles, Andrew E. Firth
Pubblicato in: Journal of General Virology, Numero 98/9, 2017, Pagina/e 2368-2378, ISSN 0022-1317
Editore: Society for General Microbiology
DOI: 10.1099/jgv.0.000902

Transcriptional and Translational Landscape of Equine Torovirus

Autori: Hazel Stewart, Katherine Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Pubblicato in: Journal of Virology, Numero 92/17, 2018, ISSN 0022-538X
Editore: 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

Autori: Steven M. Valles, David H. Oi, James J. Becnel, James K. Wetterer, John S. LaPolla, Andrew E. Firth
Pubblicato in: Virology, Numero 496, 2016, Pagina/e 244-254, ISSN 0042-6822
Editore: Academic Press
DOI: 10.1016/j.virol.2016.06.014

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

Autori: John F. Atkins, Gary Loughran, Pramod R. Bhatt, Andrew E. Firth, Pavel V. Baranov
Pubblicato in: Nucleic Acids Research, 2016, Pagina/e gkw530, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkw530

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

Autori: Nerea Irigoyen, Andrew E. Firth, Joshua D. Jones, Betty Y.-W. Chung, Stuart G. Siddell, Ian Brierley
Pubblicato in: PLOS Pathogens, Numero 12/2, 2016, Pagina/e e1005473, ISSN 1553-7374
Editore: 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

Autori: Allan Olspert, John P. Carr, Andrew E. Firth
Pubblicato in: Nucleic Acids Research, Numero 44/16, 2016, Pagina/e 7618-7629, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkw441

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

Autori: Sawsan Napthine, Susanne Bell, Chris H Hill, Ian Brierley, Andrew E Firth
Pubblicato in: Nucleic Acids Research, Numero 47/15, 2019, Pagina/e 8207-8223, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz503

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

Autori: Jermilia Charles, Chandra S. Tangudu, Stefanie L. Hurt, Charlotte Tumescheit, Andrew E. Firth, Julian E. Garcia-Rejon, Carlos Machain-Williams, Bradley J. Blitvich
Pubblicato in: Archives of Virology, Numero 164/2, 2019, Pagina/e 649-652, ISSN 0304-8608
Editore: Springer Verlag
DOI: 10.1007/s00705-018-4098-x

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

Autori: 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
Pubblicato in: PLoS Pathogens, Numero 17, 2021, Pagina/e e1009644, ISSN 1553-7374
Editore: Public Library of Science
DOI: 10.1371/journal.ppat.1009644

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

Autori: Andrew E. Firth
Pubblicato in: Journal of General Virology, 2020, ISSN 0022-1317
Editore: Society for General Microbiology
DOI: 10.1099/jgv.0.001469

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

Autori: 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
Pubblicato in: Nature Microbiology, Numero 4/2, 2019, Pagina/e 280-292, ISSN 2058-5276
Editore: Nature Research
DOI: 10.1038/s41564-018-0297-1

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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 47/17, 2019, Pagina/e 9386-9399, ISSN 0305-1048
Editore: 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

Autori: Adam M. Dinan, Sarah Keep, Erica Bickerton, Paul Britton, Andrew E. Firth, Ian Brierley
Pubblicato in: Journal of Virology, Numero 93/18, 2019, ISSN 0022-538X
Editore: American Society for Microbiology
DOI: 10.1128/JVI.00714-19

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

Autori: Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I
Pubblicato in: Nucleic Acids Research, Numero 49, 2021, Pagina/e 11938-11958, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkab969

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

Autori: Hill CH, Pekarek L, Napthine S, Kibe A, Firth AE, Graham SC, Caliskan N, Brierley I
Pubblicato in: Nature Communications, Numero 12, 2021, Pagina/e 7166, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27400-7