Sequencing of 21 Varicella-Zoster Virus Genomes Reveals Two Novel Genotypes and Evidence of Recombination

Abstract

Genotyping of 21 varicella-zoster virus (VZV) strains using a scattered single nucleotide polymorphism (SNP) method revealed ambiguous SNPs and two nontypeable isolates. For a further genetic characterization, the genomes of all strains were sequenced using the 454 technology. Almost-complete genome sequences were assembled, and most remaining gaps were closed with V aricella-zoster virus (VZV) is a member of the genus Varicellovirus within the subfamily Alphaherpesvirinae, family Herpesviridae (8). The alphaherpesviruses are characterized by their short reproduction cycle, fast spreading, efficient destruction of infected cells, and persistence in sensory ganglia. VZV replication is limited exclusively to cells of human and simian origins. The VZV genome consists of double-stranded DNA with a size of 125 kb and comprises 73 genes, 70 of which are unique and 3 of which are duplicated (9). The virus genome includes two main coding regions, unique long (U L ) and unique short (U S ), and flanking inverted repeats, termed terminal and internal repeats long (TR L , IR L ) and short (TR S , IR S ). In addition to these repeats, there are five genomic regions with tandem reiterations, designated R1 to R5.Primary infection with VZV causes varicella (chickenpox), a condition characterized by fever and exanthema with small blisters. Virus uptake occurs via the mucous membranes of the respiratory tract, with primary replication seen in the regional lymph nodes. During a short phase of primary cell-associated viremia, the virus infects peripheral blood mononuclear cells. In a secondary viremia, the virus spreads to cutaneous epithelial cells, where it induces rash. Usually, the virus is spread by excretion of aerosolized virus particles from the respiratory tract and highly infectious vesicle fluid from rash (2). After primary infection, VZV establishes a lifelong latency in trigeminal and dorsal root ganglia. Endogenous viral reactivation, e.g., after decline of VZV-specific cell-mediated immunity, may lead to viral replication and inflammation in the ganglion. Then, progeny virus migrates along the axons of neurons and is released in the skin, where it causes herpes zoster (shingles). Zoster is characterized by a unilateral vesicular rash within a single cutaneous dermatome. In most cases, the thoracic region is involved.Genetic characterization of VZV DNA is achieved by analysis of restriction fragment length polymorphism (RFLP), single nucleotide polymorphisms (SNPs), and full-genome sequencing. Early RFLP analyses revealed both interstrain variations among wild-type isolates and differences between wild-and vaccine-type viruses. The most commonly used RFLP markers of VZV included the polymorphism of open reading frames (ORFs) 38 (PstI), 54 (BglI), and 62 (SmaI) (19,23,45). These markers allowed the majority of wild-type strains in North America and Europe to be typed as PstI ϩ BglI Ϫ , whereas African and Asian strains were BglI ϩ and Japanese Oka-like wild-type strains were PstI ϩ /PstI Ϫ BglI ϩ SmaI Ϫ ; the Oka vacc...

Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1

“…It is possible that EHV-1 recombination events may have occurred but were not able to be detected at the required level of statistical significance, because an insufficient number of SNPs specific for the parental viruses were transferred to the recombinant viruses. However, evidence of frequent, natural recombination has been readily detected in VZV, which also has a highly conserved genome (approximately 30-200 SNP differences between any two strains), using similar methods to those in this study (Norberg et al, 2015(Norberg et al, , 2006Zell et al, 2012).…”

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

“…High‐throughput genome sequencing has provided evidence of recombination between strains in other herpesviruses, namely HSV‐2, VZV, Marek's disease virus, HSV‐1, pseudorabies virus, human cytomegalovirus and infectious laryngotracheitis virus (Hughes & Rivailler, 2007; Kolb, Larsen, Cuellar, & Brandt, 2015; Lee et al., 2013; Norberg et al., 2011, 2015; Sijmons et al., 2015; Szpara et al., 2014; Szpara, Tafuri, et al., 2011; Zell et al., 2012). In the present study, network analysis suggested that recombination has also occurred between EHV‐1 strains.…”

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

“…Only a single, fully sequenced clade 9 isolate (JN704710) had been previously identified and described in the literature [4]. The complete genome sequence for the KPSC study isolate (KY037798) identified in this study fulfilled the requirement for redesignating provisional clade IX as established clade 9.…”

“…All 102 publicly available VZV WGSs (or nearly complete genomic sequences) were downloaded from GenBank (search 10 May 2016). The WGSs were analysed using the analysis scheme developed by Zell and coworkers [4], specifically, limiting analyses to unique sequences. The genome sequence was divided into eight distinct regions (A to H), as illustrated in Fig.…”

“…VZV nomenclature currently recognizes nine clades, six established clades designated by Arabic numerals 1 to 6, and three provisional clades designated by the Roman numerals VII, VIII and IX [3,4]. In accordance with the nomenclature system proposed in 2008, two WGSs are needed to redesignate a provisional clade as established.…”