Genomic cartography of varicella–zoster virus: A complete genome-based analysis of strain variability with implications for attenuation and phenotypic differences

Abstract

In order to gain a better perspective on the true variability of varicella-zoster virus (VZV) and to catalogue the location and number of differences, 11 new complete genome sequences were compared with those previously in the public domain (18 complete genomes in total). Three of the newly sequenced genomes were derived from a single strain in order to assess variations that can occur during serial passage in cell culture. The analysis revealed that while VZV is relatively stable genetically it does posses a certain degree of variability. The reiteration regions, origins of replication and intergenic homopolymer regions were all found to be variable between strains as well as within a given strain. In addition, the terminal viral sequences were found to vary within and between strains specifically at the 3' end of the genome. Analysis of single nucleotide polymorphisms (SNPs) identified a total of 557 variable sites, 451 of which were found in coding regions and resulted in 187 different in amino acid substitutions. A comparison of the SNPs present in the two gE mutant strains, VZV-MSP and VZV-BC, suggested that the missense mutation in gE was primarily responsible for the accelerated cell spread phenotype. Some of the variations noted with high passage in cell culture are consistent with variations seen in the IE62 gene of the vaccine strains (S628G, R958G and I1260V) that may help in pinpointing variations essential for attenuation. Although VZV has been considered to be one of the most genetically stable human herpesviruses, this initial assessment of genomic VZV cartography provides insight into ORFs with previously unreported variations.

Characterization of the Repeat Sequences of Varicella-Zoster Virus

“…The consensus sequence of the 9 bp element was GC/tCCGC/ tG/cCA/g (lower case stands for minor deviation of the consensus). The number of repetition (n) varied tremendously among the strains as noted by Tyler et al (11). In fact, the CV (coefficient of variation) value of R3 was calculated to 1.33, largest among the CVs of 5 R sequences (Table 1).…”

“…Original Article among the strains but within a strain (11,12). Not much is known about the functions of R sequences.…”

“…A basic motif of tandem TA repeats followed by tandem GA repeats is flanked by 30 bp at 5' and 22 bp at 3'. The numbers of TA and GA repeats are varied among the VZV strains (11). Reverse complementary sequence of ORI is repeated in TRS, between ORF70 and ORF71.…”

The Attenuated Genotype of Varicella-Zoster Virus Includes an ORF0 Transitional Stop Codon Mutation

“…We first postulated that high numbers of passages may lead invariably to mutations in ORF0, but that was proven untrue by inspection of the sequence of passage 72 of VZV 32, which lacks a mutation in the ORF0 stop codon (Tables 1 and 2) (34). On the other hand, VZV 32-P72 IE62 has a mutation at base 105356 (as does vOka), but this mutation was not found in VZV Ellen.…”

“…The prototype VZV Dumas had previously been sequenced in 1986 (6). Shortly after publication of these sequences plus an additional 11 whole-genome VZV sequences, there were attempts to define the determinants of attenuation (15,26,34). The largest number of SNPs in vOka were found in the viral regulatory gene called open reading frame 62 (ORF62); the IE62 protein is the homolog of herpes simplex virus (HSV) ICP4.…”