Literature DB >> 23363820

Sequencing-based genotyping of mixed human papillomavirus infections by use of RipSeq software.

Keith D Tardif1, Keith E Simmon, Oyvind Kommedal, Michael T Pyne, Robert Schlaberg.   

Abstract

Sequencing-based pathogen identification directly from clinical specimens requires time-consuming interpretation, especially with mixed chromatograms when multiple microorganisms are detected. We assessed RipSeq Mixed software for human papillomavirus (HPV) genotyping by comparison to the linear array HPV genotyping assay. RipSeq Mixed provided rapid, sequencing-based HPV typing for single-type infections and coinfections with 2 types.

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Year:  2013        PMID： 23363820      PMCID： PMC3666769          DOI： 10.1128/JCM.00091-13

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


  23 in total

1.  Enhanced detection and typing of human papillomavirus (HPV) DNA in anogenital samples with PGMY primers and the Linear array HPV genotyping test.

Authors:  François Coutlée; Danielle Rouleau; Patrick Petignat; Georges Ghattas; Janet R Kornegay; Peter Schlag; Sean Boyle; Catherine Hankins; Sylvie Vézina; Pierre Coté; John Macleod; Hélène Voyer; Pierre Forest; Sharon Walmsley; Eduardo Franco
Journal:  J Clin Microbiol       Date:  2006-06       Impact factor: 5.948

2.  A sensitive in-house RT-PCR genotyping system for combined detection of plasma HIV-1 and assessment of drug resistance.

Authors:  Kim Steegen; Els Demecheleer; Nancy De Cabooter; Dieudonné Nges; Marleen Temmerman; Peter Ndumbe; Kishor Mandaliya; Jean Plum; Chris Verhofstede
Journal:  J Virol Methods       Date:  2005-12-20       Impact factor: 2.014

3.  The use of general primers GP5 and GP6 elongated at their 3' ends with adjacent highly conserved sequences improves human papillomavirus detection by PCR.

Authors:  A M de Roda Husman; J M Walboomers; A J van den Brule; C J Meijer; P J Snijders
Journal:  J Gen Virol       Date:  1995-04       Impact factor: 3.891

4.  Genotyping of human papillomavirus in cervical lesions by L1 consensus PCR and the Luminex xMAP system.

Authors:  Han-Liang Jiang; Hai-Hong Zhu; Lin-Fu Zhou; Feng Chen; Zhi Chen
Journal:  J Med Microbiol       Date:  2006-06       Impact factor: 2.472

5.  Determination of hepatitis C virus genotype by direct sequence analysis of products generated with the Amplicor HCV test.

Authors:  J J Germer; P N Rys; J N Thorvilson; D H Persing
Journal:  J Clin Microbiol       Date:  1999-08       Impact factor: 5.948

6.  Development and clinical evaluation of a highly sensitive PCR-reverse hybridization line probe assay for detection and identification of anogenital human papillomavirus.

Authors:  B Kleter; L J van Doorn; L Schrauwen; A Molijn; S Sastrowijoto; J ter Schegget; J Lindeman; B ter Harmsel; M Burger; W Quint
Journal:  J Clin Microbiol       Date:  1999-08       Impact factor: 5.948

7.  Human papillomavirus (HPV) study of 2916 cytological samples by PCR and DNA sequencing: genotype spectrum of patients from the west German area.

Authors:  Norbert Speich; Christoph Schmitt; Reinhard Bollmann; Magdolna Bollmann
Journal:  J Med Microbiol       Date:  2004-02       Impact factor: 2.472

8.  Phylogenetic classification of human papillomaviruses: correlation with clinical manifestations.

Authors:  M Van Ranst; J B Kaplan; R D Burk
Journal:  J Gen Virol       Date:  1992-10       Impact factor: 3.891

Review 9.  Classification of papillomaviruses.

Authors:  Ethel-Michele de Villiers; Claude Fauquet; Thomas R Broker; Hans-Ulrich Bernard; Harald zur Hausen
Journal:  Virology       Date:  2004-06-20       Impact factor: 3.616

10.  Direct 16S rRNA gene sequencing from clinical specimens, with special focus on polybacterial samples and interpretation of mixed DNA chromatograms.

Authors:  Oyvind Kommedal; Kristine Kvello; Rune Skjåstad; Nina Langeland; Harald G Wiker
Journal:  J Clin Microbiol       Date:  2009-09-09       Impact factor: 5.948
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  1 in total

1.  An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

Authors:  Nathan D Grubaugh; Karthik Gangavarapu; Joshua Quick; Nathaniel L Matteson; Jaqueline Goes De Jesus; Bradley J Main; Amanda L Tan; Lauren M Paul; Doug E Brackney; Saran Grewal; Nikos Gurfield; Koen K A Van Rompay; Sharon Isern; Scott F Michael; Lark L Coffey; Nicholas J Loman; Kristian G Andersen
Journal:  Genome Biol       Date:  2019-01-08       Impact factor: 13.583
  1 in total

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