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Journal of Virology, December 2007, p. 12758-12765, Vol. 81, No. 23
0022-538X/07/$08.00+0     doi:10.1128/JVI.01145-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Identification of Five Major and Two Minor Genotypes of Varicella-Zoster Virus Strains: a Practical Two-Amplicon Approach Used To Genotype Clinical Isolates in Australia and New Zealand{triangledown}

Vladimir N. Loparev,1 Elena N. Rubtcova,2 Vanda Bostik,2 Dhwani Govil,1 Christopher J. Birch,3 Julian D. Druce,3 D. Scott Schmid,2* and Margaret C. Croxson4

Centers for Disease Control and Prevention, Coordinating Center for Infectious Diseases, National Center for Preparedness, Detection, and Control of Infectious Diseases, Atlanta, Georgia,1 Centers for Disease Control and Prevention, Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Atlanta, Georgia,2 Victorian Infectious Diseases Reference Laboratory, Melbourne Health, North Melbourne, Victoria, Australia,3 Department of Virology and Immunology, LabPlus, Auckland City Hospital, Auckland, New Zealand4

Received 25 May 2007/ Accepted 13 September 2007

Whole genome phylogenetic analysis in this study resolved a total of five major genotypes among the 22 varicella-zoster virus (VZV) strains or isolates for which complete genomic sequences are available. Consistent with earlier publications we have designated these genotypes European 1 (E1), European 2 (E2), Japanese (J), mosaic 1 (M1), and mosaic 2 (M2). Single nucleotide polymorphism (SNP) analysis performed in a whole-genome alignment revealed that VZV isolates of all five genotypes can be accurately genotyped using SNPs from two amplicons: open reading frame 22 (ORF22) and either ORF21 or ORF50. This modified approach identifies all of the genotypes observed using any of the published genotyping protocols. Of 165 clinical varicella and zoster isolates from Australia and New Zealand typed using this approach, 67 of 127 eastern Australian isolates were E1, 30 were E2, 16 were J, 10 were M1, and 4 were M2; 25 of 38 New Zealand isolates were E1, 8 were E2, and 5 were M1. VZV strain diversity in eastern Australia is thus broader than has been described for any other region, including Europe, Africa, and North America. J strains were far more prevalent than previously observed in countries other than Japan. Two-amplicon typing was in complete accord with genotypes derived using SNP in multiple ORFs (ORFs 1, 21, 22, 38, 50, 54, and 62). Two additional minor genotypes, M3 and M4, could also be resolved using two-amplicon typing.

* Corresponding author. Mailing address: National VZV Laboratory, Centers for Disease Control and Prevention, Mail stop G-18, Room 218, Bldg. 7, Atlanta, GA 30333. Phone: (404) 639-0066. Fax: (404) 639-4056. E-mail: SSchmid{at}cdc.gov

{triangledown} Published ahead of print on 26 September 2007.

Journal of Virology, December 2007, p. 12758-12765, Vol. 81, No. 23
0022-538X/07/$08.00+0     doi:10.1128/JVI.01145-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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