Literature DB >> 19729846

RNA virus genomics: a world of possibilities.

Edward C Holmes1.   

Abstract

The increasing availability of complete genome sequences of RNA viruses has the potential to shed new light on fundamental aspects of their biology. Here, I use case studies of 3 RNA viruses to explore the impact of genomic sequence data, with particular emphasis on influenza A virus. Notably, the studies of RNA virus genomics undertaken to date largely focused on issues of evolution and epidemiology, and they have given these disciplines new impetus. However, genomic data have so far made fewer inroads into areas of more direct importance for disease, prevention, and control; thus, harnessing their full potential remains an important goal.

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Year:  2009        PMID: 19729846      PMCID: PMC2735898          DOI: 10.1172/JCI38050

Source DB:  PubMed          Journal:  J Clin Invest        ISSN: 0021-9738            Impact factor:   14.808


  88 in total

1.  Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman.

Authors:  Astrid K N Iversen; Gerald H Learn; Peter Skinhøj; James I Mullins; Andrew J McMichael; Andrew Rambaut
Journal:  AIDS       Date:  2005-06-10       Impact factor: 4.177

Review 2.  Evolution and ecology of influenza A viruses.

Authors:  R G Webster; W J Bean; O T Gorman; T M Chambers; Y Kawaoka
Journal:  Microbiol Rev       Date:  1992-03

3.  Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.

Authors:  Elodie Ghedin; Naomi A Sengamalay; Martin Shumway; Jennifer Zaborsky; Tamara Feldblyum; Vik Subbu; David J Spiro; Jeff Sitz; Hean Koo; Pavel Bolotov; Dmitry Dernovoy; Tatiana Tatusova; Yiming Bao; Kirsten St George; Jill Taylor; David J Lipman; Claire M Fraser; Jeffery K Taubenberger; Steven L Salzberg
Journal:  Nature       Date:  2005-10-05       Impact factor: 49.962

4.  Subtype C Is associated with increased vaginal shedding of HIV-1.

Authors:  Grace C John-Stewart; Ruth W Nduati; Christine M Rousseau; Dorothy A Mbori-Ngacha; Barbra A Richardson; Stephanie Rainwater; Dana D Panteleeff; Julie Overbaugh
Journal:  J Infect Dis       Date:  2005-06-23       Impact factor: 5.226

Review 5.  The evolution of epidemic influenza.

Authors:  Martha I Nelson; Edward C Holmes
Journal:  Nat Rev Genet       Date:  2007-01-30       Impact factor: 53.242

6.  The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies.

Authors:  P Farci; A Shimoda; A Coiana; G Diaz; G Peddis; J C Melpolder; A Strazzera; D Y Chien; S J Munoz; A Balestrieri; R H Purcell; H J Alter
Journal:  Science       Date:  2000-04-14       Impact factor: 47.728

7.  Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase.

Authors:  L M Mansky; H M Temin
Journal:  J Virol       Date:  1995-08       Impact factor: 5.103

8.  The emergence of HIV/AIDS in the Americas and beyond.

Authors:  M Thomas P Gilbert; Andrew Rambaut; Gabriela Wlasiuk; Thomas J Spira; Arthur E Pitchenik; Michael Worobey
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-31       Impact factor: 11.205

9.  Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period.

Authors:  V Wittke; T E Robb; H M Thu; A Nisalak; S Nimmannitya; S Kalayanrooj; D W Vaughn; T P Endy; E C Holmes; J G Aaskov
Journal:  Virology       Date:  2002-09-15       Impact factor: 3.616

10.  Stochastic processes are key determinants of short-term evolution in influenza a virus.

Authors:  Martha I Nelson; Lone Simonsen; Cecile Viboud; Mark A Miller; Jill Taylor; Kirsten St George; Sara B Griesemer; Elodie Ghedin; Elodie Ghedi; Naomi A Sengamalay; David J Spiro; Igor Volkov; Bryan T Grenfell; David J Lipman; Jeffery K Taubenberger; Edward C Holmes
Journal:  PLoS Pathog       Date:  2006-12       Impact factor: 6.823

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  32 in total

1.  Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs.

Authors:  Benjamin Bolduc; Daniel P Shaughnessy; Yuri I Wolf; Eugene V Koonin; Francisco F Roberto; Mark Young
Journal:  J Virol       Date:  2012-02-29       Impact factor: 5.103

Review 2.  Viral quasispecies evolution.

Authors:  Esteban Domingo; Julie Sheldon; Celia Perales
Journal:  Microbiol Mol Biol Rev       Date:  2012-06       Impact factor: 11.056

3.  Tales from the gene pool: a genomic view of infectious disease.

Authors:  Karen Honey
Journal:  J Clin Invest       Date:  2009-09-01       Impact factor: 14.808

4.  Genomic characterization of Zika virus isolated from Indonesia.

Authors:  Frilasita A Yudhaputri; Hidayat Trimarsanto; Aditya Perkasa; Benediktus Yohan; Sotianingsih Haryanto; Ageng Wiyatno; Amin Soebandrio; Khin Saw Myint; Jeremy P Ledermann; Ronald Rosenberg; Ann M Powers; R Tedjo Sasmono
Journal:  Virology       Date:  2017-07-26       Impact factor: 3.616

5.  A Novel Taxon of Monosegmented Double-Stranded RNA Viruses Endemic to Triclad Flatworms.

Authors:  Jeffrey T A Burrows; Delphine Depierreux; Max L Nibert; Bret J Pearson
Journal:  J Virol       Date:  2020-10-27       Impact factor: 5.103

6.  Molecular epidemiology of autochthonous dengue virus strains circulating in Mexico.

Authors:  Pilar Rivera-Osorio; Gilberto Vaughan; Jose Ernesto Ramírez-González; Salvador Fonseca-Coronado; Karina Ruíz-Tovar; Mayra Yolanda Cruz-Rivera; Juan Alberto Ruíz-Pacheco; Mauricio Vázquez-Pichardo; Juan Carlos Carpio-Pedroza; Fernando Cázares; Alejandro Escobar-Gutiérrez
Journal:  J Clin Microbiol       Date:  2011-07-20       Impact factor: 5.948

7.  Determination of spontaneous mutation frequencies in measles virus under nonselective conditions.

Authors:  Xiaomeng Zhang; Linda J Rennick; W Paul Duprex; Bert K Rima
Journal:  J Virol       Date:  2012-12-19       Impact factor: 5.103

Review 8.  Ensuring privacy in the study of pathogen genetics.

Authors:  Sanjay R Mehta; Staal A Vinterbo; Susan J Little
Journal:  Lancet Infect Dis       Date:  2014-04-07       Impact factor: 25.071

9.  Genomic analysis of dengue virus serotype 1 (DENV-1) genotypes from Surabaya, Indonesia.

Authors:  Benediktus Yohan; Puspa Wardhani; Hidayat Trimarsanto; A Aryati; R Tedjo Sasmono
Journal:  Virus Genes       Date:  2018-04-03       Impact factor: 2.332

10.  The molecular and clinical features of dengue during outbreak in Jambi, Indonesia in 2015.

Authors:  Sotianingsih Haryanto; Rahma F Hayati; Benediktus Yohan; Lanceria Sijabat; Ifo F Sihite; Sukmal Fahri; Febrina Meutiawati; Jonathan A N Halim; Stefanie N Halim; Amin Soebandrio; R Tedjo Sasmono
Journal:  Pathog Glob Health       Date:  2016-05-23       Impact factor: 2.894

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