Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes

Aedes aegypti exhibits a distinctive mode of late ovarian development

(2023) Heng Zhang et al.   BMC BIOLOGY

Characterization of dengue virus 3’UTR RNA binding proteins in mosquitoes reveals that AeStaufen reduces subgenomic flaviviral RNA in saliva

(2022) Shih-Chia Yeh et al.   PLoS Pathogens

A tetravalent live attenuated dengue virus vaccine stimulates balanced immunity to multiple serotypes in humans

(2021) Usha K. Nivarthi et al.   Nature Communications

A single-dose live attenuated chimeric vaccine candidate against Zika virus

(2021) Wei-Xin Chin et al.   npj Vaccines

The continued threat of emerging flaviviruses

(2020) Theodore C. Pierson et al.   Nature Microbiology

Structure mapping of dengue and Zika viruses reveals functional long-range interactions

(2019) Roland G. Huber et al.   Nature Communications

Attenuation of a dengue virus replicon by codon deoptimization of nonstructural genes

(2019) Gayathri Manokaran et al.   VACCINE

Circularization of flavivirus genomic RNA inhibits de novo translation initiation

(2019) Thomas J Sanford et al.   NUCLEIC ACIDS RESEARCH

ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics

(2019) Marco Cacciabue et al.   PeerJ

Antiviral activity of ST081006 against the dengue virus

(2019) Jing Kai Lee et al.   ANTIVIRAL RESEARCH

Optimization of the codon-pair usage of human respiratory syncytial virus paradoxically resulted in reduced viral replication in vivo and reduced immunogenicity

(2019) Cyril Le Nouën et al.   JOURNAL OF VIROLOGY

Extensive genomic recoding by codon-pair deoptimization selective for mammals is a flexible tool to generate attenuated vaccine candidates for dengue virus 2

(2019) Charles B. Stauft et al.   VIROLOGY

Extensive recoding of dengue virus type 2 specifically reduces replication in primate cells without gain-of-function in Aedes aegypti mosquitoes

(2018) Charles B. Stauft et al.   PLoS One

Pervasive tertiary structure in the dengue virus RNA genome

(2018) Elizabeth A. Dethoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

(2017) Yutong Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

(2017) Steven Busan et al.   RNA

Synonymous Virus Genome Recoding as a Tool to Impact Viral Fitness

(2016) Miguel Angel Martínez et al.   TRENDS IN MICROBIOLOGY

Molecular determinants of plaque size as an indicator of dengue virus attenuation

(2016) Kenneth Choon Meng Goh et al.   Scientific Reports

Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization

(2016) Zhong-Yu Liu et al.   eLife

Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection

(2016) Eleanor Gaunt et al.   eLife

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished

(2015) Bruce Futcher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference

(2015) Sam H. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies: Table 1.

(2015) Peter Simmonds et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA shapes studio

(2014) S. Janssen et al.   BIOINFORMATICS

AUF1 p45 Promotes West Nile Virus Replication by an RNA Chaperone Activity That Supports Cyclization of the Viral Genome

(2014) S. Friedrich et al.   JOURNAL OF VIROLOGY

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

A review of successful flavivirus vaccines and the problems with those flaviviruses for which vaccines are not yet available

(2014) Tomohiro Ishikawa et al.   VACCINE

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

(2014) Fiona Tulloch et al.   eLife

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

(2013) Z.-Y. Liu et al.   JOURNAL OF VIROLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global distribution and burden of dengue

(2013) Samir Bhatt et al.   NATURE

Genetic and Phenotypic Characterization of Manufacturing Seeds for a Tetravalent Dengue Vaccine (DENVax)

(2013) Claire Y.-H. Huang et al.   PLoS Neglected Tropical Diseases

The Helical Domains of the Stem Region of Dengue Virus Envelope Protein Are Involved in both Virus Assembly and Entry

(2011) S.-R. Lin et al.   JOURNAL OF VIROLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Functional RNA Elements in the Dengue Virus Genome

(2011) Leopoldo G. Gebhard et al.   Viruses-Basel

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

A new bioinformatics analysis tools framework at EMBL-EBI

(2010) M. Goujon et al.   NUCLEIC ACIDS RESEARCH

A balance between circular and linear forms of the dengue virus genome is crucial for viral replication

(2010) S. M. Villordo et al.   RNA

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

(2009) Yanga Byun et al.   BIOINFORMATICS

Poly(A)-binding protein binds to the non-polyadenylated 3' untranslated region of dengue virus and modulates translation efficiency

(2009) C. Polacek et al.   JOURNAL OF GENERAL VIROLOGY

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

Functional analysis of dengue virus cyclization sequences located at the 5′ and 3′UTRs

(2008) Diego E. Alvarez et al.   VIROLOGY

The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis

(2008) Karen Clyde et al.   VIROLOGY