Scientific Publications by FDA Staff

J Virol Methods 2006 Sep;136(1-2):8-16

New mosaic subgenotype of varicella-zoster virus in the USA: VZV detection and genotyping by oligonucleotide-microarray.

Sergeev N, Rubtcova E, Chizhikov V, Schmid DS, Loparev VN

Schmid DS, Ctr Dis Control & Prevent, Natl Ctr Infect Dis, Div Viral & Rickettsial Dis, Measles & Herpesvirus Team,Natl VZV Lab, 1600 Clifton Rd,MS G-18, Atlanta, GA 30333 USA Ctr Dis Control & Prevent, Natl Ctr Infect Dis, Div Viral & Rickettsial Dis, Measles & Herpesvirus Team,Natl VZV Lab, Atlanta, GA 30333 USA US FDA, Ctr Devices & Radiol Hlth, Off Sci & Technol, Div Life Sci, Silver Spring, MD 20993 USA US FDA, Ctr Biol Evaluat & Res, Off Vaccines Res & Review, Div Viral Prod, Silver Spring, MD 20993 USA

A rapid and sensitive microarray-based method was used to distinguish the three major circulating genotypes of varicella-zoster virus (VZV). The method analyzes five variable positions located in a 447-nucleotide variable region 1 of open reading frame 22 (ORF 22r1); these single nucleotide polymorphisms (SNP) display in stably occurring patterns specific to each of the VZV genotypes established in previously published studies. Pairs of short oligonucleotide probes (oligoprobes) with sequences corresponding to all of the observed SNP were used to detect specific sequences. Fluorescently labeled ssRNA samples for hybridization with a chip were prepared by in vitro T7 polymerase driven transcription of the amplicons of ORF 22r1, followed by chemical labeling with Cy5 into RNA sample. Ratios between fluorescent hybridization signals from each pair of oligoprobes were used to assess the sequence at each SNP. We evaluated six reference VZV strains and 130 VZV clinical specimens to validate the method. The microarray method accurately identified strains isolated in the US in 2001-2002, representing all major genotypes as determined using more extensive sequence analysis, correctly assigning strains to genotypes E (81.5%), J (3%) and M (15.5%). In addition, a new M variant (M3) was identified.