Literature DB >> 19109473

Simple, sensitive, and swift sequencing of complete H5N1 avian influenza virus genomes.

Dirk Höper1, Bernd Hoffmann, Martin Beer.   

Abstract

The spread of highly pathogenic avian influenza A virus (HPAIV) of subtype H5N1 demands fast and reliable methods for in-depth, full-length sequence analysis. For this purpose, we designed a simple and sensitive method for the preparation of sequencing libraries from H5N1 HPAIV diagnostic RNA samples for sequencing with the Genome Sequencer FLX instrument. The method presented seamlessly integrates high-throughput pyrosequencing with the Roche/454 instrument into diagnostics without the need for additional equipment or molecular biological techniques besides standard PCR and the Genome Sequencer FLX sample preparation and sequencing pipeline.

Entities:  

Mesh：

Year:  2008        PMID： 19109473      PMCID： PMC2650901          DOI： 10.1128/JCM.01028-08

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN： 0095-1137            Impact factor:   5.948


  11 in total

1.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

2.  Molecular analysis of highly pathogenic avian influenza virus of subtype H5N1 isolated from wild birds and mammals in northern Germany.

Authors:  Siegfried Weber; Timm Harder; Elke Starick; Martin Beer; Ortrud Werner; Bernd Hoffmann; Thomas C Mettenleiter; Egbert Mundt
Journal:  J Gen Virol       Date:  2007-02       Impact factor: 3.891

3.  NP, PB1, and PB2 viral genes contribute to altered replication of H5N1 avian influenza viruses in chickens.

Authors:  Jamie L Wasilenko; Chang Won Lee; Luciana Sarmento; Erica Spackman; Darrell R Kapczynski; David L Suarez; Mary J Pantin-Jackwood
Journal:  J Virol       Date:  2008-02-27       Impact factor: 5.103

Review 4.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

5.  A universal heterologous internal control system for duplex real-time RT-PCR assays used in a detection system for pestiviruses.

Authors:  B Hoffmann; K Depner; H Schirrmeier; M Beer
Journal:  J Virol Methods       Date:  2006-06-27       Impact factor: 2.014

6.  Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes.

Authors:  Erica Spackman; Dennis A Senne; T J Myers; Leslie L Bulaga; Lindsey P Garber; Michael L Perdue; Kenton Lohman; Luke T Daum; David L Suarez
Journal:  J Clin Microbiol       Date:  2002-09       Impact factor: 5.948

7.  Phylogenetic analyses of highly pathogenic avian influenza virus isolates from Germany in 2006 and 2007 suggest at least three separate introductions of H5N1 virus.

Authors:  E Starick; M Beer; B Hoffmann; C Staubach; O Werner; A Globig; G Strebelow; C Grund; M Durban; F J Conraths; T Mettenleiter; T Harder
Journal:  Vet Microbiol       Date:  2007-10-18       Impact factor: 3.293

8.  Persistent host markers in pandemic and H5N1 influenza viruses.

Authors:  David B Finkelstein; Suraj Mukatira; Perdeep K Mehta; John C Obenauer; Xiaoping Su; Robert G Webster; Clayton W Naeve
Journal:  J Virol       Date:  2007-07-25       Impact factor: 5.103

9.  DNA sequencing with chain-terminating inhibitors.

Authors:  F Sanger; S Nicklen; A R Coulson
Journal:  Proc Natl Acad Sci U S A       Date:  1977-12       Impact factor: 11.205

10.  A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence.

Authors:  Gina M Conenello; Dmitriy Zamarin; Lucy A Perrone; Terrence Tumpey; Peter Palese
Journal:  PLoS Pathog       Date:  2007-10-05       Impact factor: 6.823
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  22 in total

1.  Truncation and sequence shuffling of segment 6 generate replication-competent neuraminidase-negative influenza H5N1 viruses.

Authors:  Donata Kalthoff; Susanne Röhrs; Dirk Höper; Bernd Hoffmann; Jessica Bogs; Jürgen Stech; Martin Beer
Journal:  J Virol       Date:  2013-10-09       Impact factor: 5.103

2.  Divergent Human-Origin Influenza Viruses Detected in Australian Swine Populations.

Authors:  Frank Y K Wong; Celeste Donato; Yi-Mo Deng; Don Teng; Naomi Komadina; Chantal Baas; Joyanta Modak; Mark O'Dea; David W Smith; Paul V Effler; Julie Cooke; Kelly R Davies; Aeron Hurt; Nina Kung; Avram Levy; Richmond Loh; Songhua Shan; Mustaghfira W Shinwari; Vittoria Stevens; Joanne Taylor; David T Williams; James Watson; Debbie Eagles; Sam McCullough; Ian G Barr; Vijaykrishna Dhanasekaran
Journal:  J Virol       Date:  2018-07-31       Impact factor: 5.103

3.  A comprehensive deep sequencing strategy for full-length genomes of influenza A.

Authors:  Dirk Höper; Bernd Hoffmann; Martin Beer
Journal:  PLoS One       Date:  2011-04-29       Impact factor: 3.240

4.  Natural Reassortants of Potentially Zoonotic Avian Influenza Viruses H5N1 and H9N2 from Egypt Display Distinct Pathogenic Phenotypes in Experimentally Infected Chickens and Ferrets.

Authors:  Mahmoud M Naguib; Reiner Ulrich; Elisa Kasbohm; Christine L P Eng; Donata Hoffmann; Christian Grund; Martin Beer; Timm C Harder
Journal:  J Virol       Date:  2017-11-14       Impact factor: 5.103

5.  Highly pathogenic avian influenza virus subtype H5N1 escaping neutralization: more than HA variation.

Authors:  Dirk Höper; Donata Kalthoff; Bernd Hoffmann; Martin Beer
Journal:  J Virol       Date:  2011-11-16       Impact factor: 5.103

Review 6.  Deep sequencing: becoming a critical tool in clinical virology.

Authors:  Miguel E Quiñones-Mateu; Santiago Avila; Gustavo Reyes-Teran; Miguel A Martinez
Journal:  J Clin Virol       Date:  2014-06-24       Impact factor: 3.168

7.  Large-scale sequencing and the natural history of model human RNA viruses.

Authors:  Vivien G Dugan; Kazima Saira; Elodie Ghedin
Journal:  Future Virol       Date:  2012-06-01       Impact factor: 1.831

8.  Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses.

Authors:  Bin Zhou; Yi-Mo Deng; John R Barnes; October M Sessions; Tsui-Wen Chou; Malania Wilson; Thomas J Stark; Michelle Volk; Natalie Spirason; Rebecca A Halpin; Uma Sangumathi Kamaraj; Tao Ding; Timothy B Stockwell; Mirella Salvatore; Elodie Ghedin; Ian G Barr; David E Wentworth
Journal:  J Clin Microbiol       Date:  2017-10-04       Impact factor: 5.948

9.  The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies.

Authors:  Muthannan A Ramakrishnan; Zheng Jin Tu; Sushmita Singh; Ashok K Chockalingam; Marie R Gramer; Ping Wang; Sagar M Goyal; My Yang; David A Halvorson; Srinand Sreevatsan
Journal:  PLoS One       Date:  2009-09-22       Impact factor: 3.240

10.  Feasibility of using 454 pyrosequencing for studying quasispecies of the whole dengue viral genome.

Authors:  Kwanrutai Chin-inmanu; Aroonroong Suttitheptumrong; Duangjai Sangsrakru; Sithichoke Tangphatsornruang; Somvong Tragoonrung; Prida Malasit; Sumalee Tungpradabkul; Prapat Suriyaphol
Journal:  BMC Genomics       Date:  2012-12-13       Impact factor: 3.969
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