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

Total Cost €


EC-Contrib. €






Project "ERVE" data sheet

The following table provides information about the project.


Organization address
postcode: CB2 1TN

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Project website
 Total cost 1˙780˙000 €
 EC max contribution 1˙780˙000 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-CoG
 Funding Scheme ERC-COG
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2021-08-31


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 


 Project objective

Identification of the full complement of genes and other functional elements in any virus is crucial to fully understand its molecular biology and guide the development of effective control strategies. Our recent discoveries of new 'hidden' genes in the potyviruses, alphaviruses, arteriviruses, flaviviruses and influenza A virus have demonstrated that, even in the most well-studied and economically-important viruses, small overlapping genes can remain undetected throughout decades of research. Comparative computational analyses can be used to efficiently identify hidden features and target experimental analyses, thus saving time and cost, and minimizing animal experiments. With the rapid increase in sequencing data, for the first time it is now possible to map out at high resolution functional elements genome-wide in hundreds of important virus species.

Our research involves the development of powerful new tools for virus comparative genomics, and the application of these tools to uncover hidden genes and other functional elements in RNA virus and retrovirus genomes. Hidden genes are often translated via non-canonical mechanisms, such as programmed ribosomal frameshifting, and we are particularly interested in discovering and characterizing new types of non-canonical translation. Deciphering these 'exceptions-to-the-rule' enhances our understanding of the mechanics of protein synthesis. Further, these novel mechanisms may also be relevant to cellular gene expression.

The goals of this project are:

1) To computationally identify all 'hidden' genes and major functional non-coding elements in the genomes of RNA viruses and retroviruses of medical, veterinary and agricultural importance.

2) To experimentally characterize the most interesting new features.

3) To characterize novel translation mechanisms utilized by RNA viruses.

4) To develop web interfaces to our software and an interactive RNA virus comparative genomics database.


year authors and title journal last update
List of publications.
2018 Hazel Stewart, Katherine Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Transcriptional and Translational Landscape of Equine Torovirus
published pages: , ISSN: 0022-538X, DOI: 10.1128/JVI.00589-18
Journal of Virology 92/17 2020-02-12
2016 John F. Atkins, Gary Loughran, Pramod R. Bhatt, Andrew E. Firth, Pavel V. Baranov
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
published pages: gkw530, ISSN: 0305-1048, DOI: 10.1093/nar/gkw530
Nucleic Acids Research 2020-02-12
2016 Steven M. Valles, David H. Oi, James J. Becnel, James K. Wetterer, John S. LaPolla, Andrew E. Firth
Isolation and characterization of Nylanderia fulva virus 1, a positive-sense, single-stranded RNA virus infecting the tawny crazy ant, Nylanderia fulva
published pages: 244-254, ISSN: 0042-6822, DOI: 10.1016/j.virol.2016.06.014
Virology 496 2020-02-12
2017 Roger Ling, Andrew E. Firth
An analysis by metabolic labelling of the encephalomyocarditis virus ribosomal frameshifting efficiency and stimulators
published pages: 2100-2105, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000888
Journal of General Virology 98/8 2020-02-12
2017 Ingrida Olendraite, Nina I. Lukhovitskaya, Sanford D. Porter, Steven M. Valles, Andrew E. Firth
Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses
published pages: 2368-2378, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000902
Journal of General Virology 98/9 2020-02-12
2017 Sawsan Napthine, Roger Ling, Leanne K. Finch, Joshua D. Jones, Susanne Bell, Ian Brierley, Andrew E. Firth
Protein-directed ribosomal frameshifting temporally regulates gene expression
published pages: 15582, ISSN: 2041-1723, DOI: 10.1038/ncomms15582
Nature Communications 8 2020-02-12
2017 Bradley Blitvich, Andrew Firth
A Review of Flaviviruses that Have No Known Arthropod Vector
published pages: 154, ISSN: 1999-4915, DOI: 10.3390/v9060154
Viruses 9/6 2020-02-12
2017 Jermilia Charles, Chandra S. Tangudu, Andrew E. Firth, Bradley J. Blitvich
Complete genome sequences of two insect-specific flaviviruses
published pages: 3913-3917, ISSN: 0304-8608, DOI: 10.1007/s00705-017-3552-5
Archives of Virology 162/12 2020-02-12
2018 Nerea Irigoyen, Adam M. Dinan, Ian Brierley, Andrew E. Firth
Ribosome profiling of the retrovirus murine leukemia virus
published pages: , ISSN: 1742-4690, DOI: 10.1186/s12977-018-0394-5
Retrovirology 15/1 2020-02-12
2017 Adam M. Dinan, John F. Atkins, Andrew E. Firth
ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
published pages: , ISSN: 1745-6150, DOI: 10.1186/s13062-017-0195-0
Biology Direct 12/1 2020-02-12
2016 Allan Olspert, John P. Carr, Andrew E. Firth
Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins
published pages: 7618-7629, ISSN: 0305-1048, DOI: 10.1093/nar/gkw441
Nucleic Acids Research 44/16 2020-02-12
2016 Nerea Irigoyen, Andrew E. Firth, Joshua D. Jones, Betty Y.-W. Chung, Stuart G. Siddell, Ian Brierley
High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling
published pages: e1005473, ISSN: 1553-7374, DOI: 10.1371/journal.ppat.1005473
PLOS Pathogens 12/2 2020-02-12
2017 Gary Loughran, Michael T. Howard, Andrew E. Firth, John F. Atkins
Avoidance of reporter assay distortions from fused dual reporters
published pages: 1285-1289, ISSN: 1355-8382, DOI: 10.1261/rna.061051.117
RNA 23/8 2020-02-12

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