Literature DB >> 28613146

Revisiting the genotyping scheme for varicella-zoster viruses based on whole-genome comparisons.

Nancy J Jensen1, Pierre Rivailler1, Hung Fu Tseng2, Mark L Quinlivan1,3, Kay Radford1, Jennifer Folster1, Rafael Harpaz1, Philip LaRussa4, Steven Jacobsen2, D Scott Schmid1.   

Abstract

We report whole-genome sequences (WGSs) for four varicella-zoster virus (VZV) samples from a shingles study conducted by Kaiser Permanente of Southern California. Comparative genomics and phylogenetic analysis of all published VZV WGSs revealed that strain KY037798 is in clade IX, which shall henceforth be designated clade 9. Previously published single nucleotide polymorphisms (SNP)-based genotyping schemes fail to discriminate between clades 6 and VIII and employ positions that are not clade-specific. We provide an updated list of clade-specific positions that supersedes the list determined at the 2008 VZV nomenclature meeting. Finally, we propose a new targeted genotyping scheme that will discriminate the circulating VZV clades with at least a twofold redundancy. Genotyping strategies using a limited set of targeted SNPs will continue to provide an efficient 'first pass' method for VZV strain surveillance as vaccination programmes for varicella and zoster influence the dynamics of VZV transmission.

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Year:  2017        PMID： 28613146      PMCID： PMC5721928          DOI： 10.1099/jgv.0.000772

Source DB:  PubMed          Journal:  J Gen Virol        ISSN： 0022-1317            Impact factor:   3.891


  14 in total

1.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

Authors:  Kazutaka Katoh; Kazuharu Misawa; Kei-ichi Kuma; Takashi Miyata
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2.  MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors:  Robert C Edgar
Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

3.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Authors:  Koichiro Tamura; Glen Stecher; Daniel Peterson; Alan Filipski; Sudhir Kumar
Journal:  Mol Biol Evol       Date:  2013-10-16       Impact factor: 16.240

4.  Global distribution of measles genotypes and measles molecular epidemiology.

Authors:  Paul A Rota; Kevin Brown; Annette Mankertz; Sabine Santibanez; Sergey Shulga; Claude P Muller; Judith M Hübschen; Marilda Siqueira; Jennifer Beirnes; Hinda Ahmed; Henda Triki; Suleiman Al-Busaidy; Annick Dosseh; Charles Byabamazima; Sheilagh Smit; Chantal Akoua-Koffi; Josephine Bwogi; Henry Bukenya; Niteen Wairagkar; Nalini Ramamurty; Patcha Incomserb; Sirima Pattamadilok; Youngmee Jee; Wilina Lim; Wenbo Xu; Katsuhiro Komase; Makoto Takeda; Thomas Tran; Carlos Castillo-Solorzano; Paul Chenoweth; David Brown; Mick N Mulders; William J Bellini; David Featherstone
Journal:  J Infect Dis       Date:  2011-07       Impact factor: 5.226

5.  The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Authors:  N Saitou; M Nei
Journal:  Mol Biol Evol       Date:  1987-07       Impact factor: 16.240

6.  Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination.

Authors:  Roland Zell; Stefan Taudien; Florian Pfaff; Peter Wutzler; Matthias Platzer; Andreas Sauerbrei
Journal:  J Virol       Date:  2011-11-30       Impact factor: 5.103

7.  Prevention of herpes zoster: recommendations of the Advisory Committee on Immunization Practices (ACIP).

Authors:  Rafael Harpaz; Ismael R Ortega-Sanchez; Jane F Seward
Journal:  MMWR Recomm Rep       Date:  2008-06-06

8.  Transmission of a newly characterized strain of varicella-zoster virus from a patient with herpes zoster in a long-term-care facility, West Virginia, 2004.

Authors:  Adriana S Lopez; Andrea Burnett-Hartman; Ram Nambiar; Linda Ritz; Patricia Owens; Vladimir N Loparev; Dalya Guris; D Scott Schmid
Journal:  J Infect Dis       Date:  2008-03-01       Impact factor: 5.226

9.  Recombination of Globally Circulating Varicella-Zoster Virus.

Authors:  Peter Norberg; Daniel P Depledge; Samit Kundu; Claire Atkinson; Julianne Brown; Tanzina Haque; Yusuf Hussaini; Eithne MacMahon; Pamela Molyneaux; Vassiliki Papaevangelou; Nitu Sengupta; Evelyn S C Koay; Julian W Tang; Gillian S Underhill; Anna Grahn; Marie Studahl; Judith Breuer; Tomas Bergström
Journal:  J Virol       Date:  2015-07       Impact factor: 6.549

Review 10.  A proposal for a common nomenclature for viral clades that form the species varicella-zoster virus: summary of VZV Nomenclature Meeting 2008, Barts and the London School of Medicine and Dentistry, 24-25 July 2008.

Authors:  Judith Breuer; Charles Grose; Peter Norberg; Graham Tipples; D Scott Schmid
Journal:  J Gen Virol       Date:  2010-01-13       Impact factor: 3.891
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  6 in total

1.  Varicella in Tshuapa Province, Democratic Republic of Congo, 2009-2014.

Authors:  Jessica Leung; Andrea M McCollum; Kay Radford; Christine Hughes; Adriana S Lopez; Sarah Anne J Guagliardo; Beatrice Nguete; Toutou Likafi; Joelle Kabamba; Jean Malekani; Robert Shongo Lushima; Elisabeth Pukuta; Stomy Karhemere; Jean Jacques Muyembe Tamfum; Mary G Reynolds; Emile Wemakoy Okitolonda; D Scott Schmid; Mona Marin
Journal:  Trop Med Int Health       Date:  2019-05-22       Impact factor: 2.622

2.  Vaccine Strain and Wild-Type Clades of Varicella-Zoster Virus in Central Nervous System and Non-CNS Disease, New York State, 2004-2019.

Authors:  Patrick Bryant; Tugba Yildirim; Sara B Griesemer; Kara Shaw; Dylan Ehrbar; Kirsten St George
Journal:  J Clin Microbiol       Date:  2022-03-24       Impact factor: 11.677

3.  Analysis of the reiteration regions (R1 to R5) of varicella-zoster virus.

Authors:  Nancy J Jensen; Daniel P Depledge; Terry Fei Fan Ng; Jessica Leung; Mark Quinlivan; Kay W Radford; Jennifer Folster; Hung-Fu Tseng; Philip LaRussa; Steven J Jacobsen; Judith Breuer; D Scott Schmid
Journal:  Virology       Date:  2020-04-04       Impact factor: 3.513

Review 4.  Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution.

Authors:  Daniel W Renner; Moriah L Szpara
Journal:  J Virol       Date:  2017-12-14       Impact factor: 5.103

Review 5.  Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion.

Authors:  Charlotte J Houldcroft
Journal:  Pathogens       Date:  2019-10-12

6.  Genetic characterization of varicella-zoster and HIV-1 viruses from the cerebrospinal fluid of a co-infected encephalitic patient, Ghana.

Authors:  Philip El-Duah; Augustina Angelina Sylverken; Michael Owusu; Yaw Ampem Amoako; Richmond Yeboah; Richmond Gorman; Emmanuella Nyarko-Afriyie; Julia Schneider; Terry C Jones; Joseph Bonney; Titus Adade; Eric Smart Yeboah; Tabea Binger; Victor Max Corman; Christian Drosten; Richard Odame Phillips
Journal:  Virol J       Date:  2022-07-26       Impact factor: 5.913
  6 in total

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