Literature DB >> 26071447

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

Peter Simmonds1, Fiona Tulloch2, David J Evans3, Martin D Ryan2.   

Abstract

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Year:  2015        PMID： 26071447      PMCID： PMC4507241          DOI： 10.1073/pnas.1507339112

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  2 in total

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

Authors:  Sam H Shen; Charles B Stauft; Oleksandr Gorbatsevych; Yutong Song; Charles B Ward; Alisa Yurovsky; Steffen Mueller; Bruce Futcher; Eckard Wimmer
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-30       Impact factor: 11.205

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

Authors:  Fiona Tulloch; Nicky J Atkinson; David J Evans; Martin D Ryan; Peter Simmonds
Journal:  Elife       Date:  2014-12-09       Impact factor: 8.140
  2 in total
  16 in total

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

Authors:  Bruce Futcher; Oleksandr Gorbatsevych; Sam H Shen; Charles B Stauft; Yutong Song; Bingyin Wang; Janet Leatherwood; Justin Gardin; Alisa Yurovsky; Steffen Mueller; Eckard Wimmer
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-12       Impact factor: 11.205

2.  A novel framework for evaluating the performance of codon usage bias metrics.

Authors:  Sophia S Liu; Adam J Hockenberry; Michael C Jewett; Luís A N Amaral
Journal:  J R Soc Interface       Date:  2018-01       Impact factor: 4.118

3.  Synonymous Deoptimization of Foot-and-Mouth Disease Virus Causes Attenuation In Vivo while Inducing a Strong Neutralizing Antibody Response.

Authors:  Fayna Diaz-San Segundo; Gisselle N Medina; Elizabeth Ramirez-Medina; Lauro Velazquez-Salinas; Marla Koster; Marvin J Grubman; Teresa de los Santos
Journal:  J Virol       Date:  2015-11-18       Impact factor: 5.103

4.  Hypervirulent Clostridium difficile ribotypes are CpG depleted.

Authors:  Vinay Kamuju; Santosh Kumar; Wajihul Hasan Khan; Perumal Vivekanandan
Journal:  Virulence       Date:  2018       Impact factor: 5.882

5.  Exploratory re-encoding of yellow fever virus genome: new insights for the design of live-attenuated viruses.

Authors:  R Klitting; T Riziki; G Moureau; G Piorkowski; E A Gould; X de Lamballerie
Journal:  Virus Evol       Date:  2018-07-23

Review 6.  Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns.

Authors:  Nicole R Sexton; Gregory D Ebel
Journal:  Viruses       Date:  2019-07-12       Impact factor: 5.048

7.  The role of ZAP and OAS3/RNAseL pathways in the attenuation of an RNA virus with elevated frequencies of CpG and UpA dinucleotides.

Authors:  Valerie Odon; Jelke J Fros; Niluka Goonawardane; Isabelle Dietrich; Ahmad Ibrahim; Kinda Alshaikhahmed; Dung Nguyen; Peter Simmonds
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 19.160

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

Authors:  Eleanor Gaunt; Helen M Wise; Huayu Zhang; Lian N Lee; Nicky J Atkinson; Marlynne Quigg Nicol; Andrew J Highton; Paul Klenerman; Philippa M Beard; Bernadette M Dutia; Paul Digard; Peter Simmonds
Journal:  Elife       Date:  2016-02-16       Impact factor: 8.140

9.  CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry.

Authors:  Jelke Jan Fros; Isabelle Dietrich; Kinda Alshaikhahmed; Tim Casper Passchier; David John Evans; Peter Simmonds
Journal:  Elife       Date:  2017-09-29       Impact factor: 8.140

10.  mRNA structure regulates protein expression through changes in functional half-life.

Authors:  David M Mauger; B Joseph Cabral; Vladimir Presnyak; Stephen V Su; David W Reid; Brooke Goodman; Kristian Link; Nikhil Khatwani; John Reynders; Melissa J Moore; Iain J McFadyen
Journal:  Proc Natl Acad Sci U S A       Date:  2019-11-11       Impact factor: 11.205
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