Journal article
Bioinformatics of varicella-zoster virus: Single nucleotide polymorphisms define clades and attenuated vaccine genotypes
Infection, genetics and evolution, Vol.18, pp.351-356
08/2013
DOI: 10.1016/j.meegid.2012.11.008
PMCID: PMC3594394
PMID: 23183312
Abstract
Varicella zoster virus (VZV) is one of the human herpesviruses. To date, over 40 complete VZV genomes have been sequenced and analyzed. The VZV genome contains around 125,000 base pairs including 70 open reading frames (ORFs). Enumeration of single nucleotide polymorphisms (SNPs) has determined that the following ORFs are the most variable (in descending order): 62, 22, 29, 28, 37, 21, 54, 31, 1 and 55. ORF 62 is the major immediate early regulatory VZV gene. Further SNP analysis across the entire genome has led to the observation that VZV strains can be broadly grouped into clades within a phylogenetic tree. VZV strains collected in Singapore provided important sequence data for construction of the phylogenetic tree. Currently five VZV clades are recognized; they have been designated clades 1 through 5. Clades 1 and 3 include European/North American strains; clade 2 includes Asian strains, especially from Japan; and clade 5 includes strains from India. Clade 4 includes some strains from Europe, but its geographic origins need further documentation. Within clade 1, five variant viruses have been isolated with a missense mutation in the gE (ORF 68) glycoprotein; these strains have an altered increased cell spread phenotype. Bioinformatics analyses of the attenuated vaccine strains have also been performed, with a subsequent discovery of a stop-codon SNP in ORFO as a likely attenuation determinant. Taken together, these VZV bioinformatics analyses have provided enormous insights into VZV phylogenetics as well as VZV SNPs associated with attenuation.
Details
- Title: Subtitle
- Bioinformatics of varicella-zoster virus: Single nucleotide polymorphisms define clades and attenuated vaccine genotypes
- Creators
- Vincent T Chow - Department of Microbiology, National University of Singapore, SingaporeGraham A Tipples - Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, CanadaCharles Grose - Virology Laboratory, Children’s Hospital, University of Iowa, Iowa City, IA, USA
- Resource Type
- Journal article
- Publication Details
- Infection, genetics and evolution, Vol.18, pp.351-356
- DOI
- 10.1016/j.meegid.2012.11.008
- PMID
- 23183312
- PMCID
- PMC3594394
- NLM abbreviation
- Infect Genet Evol
- ISSN
- 1567-1348
- eISSN
- 1567-7257
- Publisher
- Elsevier B.V
- Grant note
- name: Institute for Mathematical Sciences at the National University of Singapore; name: NIH, award: AI89716
- Language
- English
- Date published
- 08/2013
- Academic Unit
- Stead Family Department of Pediatrics; Infectious Disease (Pediatrics)
- Record Identifier
- 9984093233402771
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