Divergence of reiterated sequences in a series of genital isolates of herpes simplex virus type 1 from individual patients

Abstract

Both serotypes of herpes simplex virus (HSV), HSV-1 and HSV-2, are aetiological agents of genital herpes, although genital herpes caused by HSV-1 recurs less frequently. The HSV-1 genome contains a number of short, tandemly repeated sequences, and some reiterated sequences can serve as sensitive markers for the differentiation of HSV-1 strains. In the present study, variation in reiterations (assumed to be due to different copy numbers of tandemly repeated sequences) was examined in HSV-1 isolates from genital lesions from the same individual. Six sets (three primaryrecurrence sets and three multiple-recurrence sets) of HSV-1 isolates were analysed: the primaryrecurrence set consisted of two isolates (one isolated at a primary episode and the other at a recurrent episode) from the same individual; the multiple-recurrence set consisted of plural isolates from different episodes of recurrence in the same individual. Variations in length of the major DNA fragment, containing reiteration I (within the a sequence) and/or reiteration IV (within introns of genes US1 and US12), were detected between isolates of each multiple-recurrence set, but not of the primary-recurrence set. Thus, HSV-1 isolates of multiple-recurrence sets are assumed to have diverged more widely within each set than those of primary-recurrence sets, probably because of more rounds of virus DNA replication. This divergence of reiterations seems to indicate a forward step in the division of HSV-1 from a common ancestor into different lineages. INTRODUCTIONHerpes simplex virus (HSV) is a ubiquitous human pathogen which latently infects neural cells of spinal ganglia and is classified into two serotypes, HSV-1 and HSV-2 (Dolan et al., 1998;Everett, 2000;McGeoch et al., 1988;Preston, 2000). HSV-1 is common in general populations and is often acquired non-sexually during childhood years. Although there is evidence that the majority of genital herpes infections are HSV-2-related, an increase in HSV-1 genital infection in at least some countries (e.g. UK, USA and Japan) has been suggested (Hashido et al., 1997(Hashido et al., , 1998 Kawana et al., 1982;Lafferty et al., 2000;Ribes et al., 2001;Stanberry et al., 1999;Vanderhooft & Kirby, 1992;White & Wardropper, 1997). HSV-1 genital infection is less likely to recur than that caused by HSV-2 (Kinghorn, 1993;Lafferty et al., 1987;Mertz et al., 1990;Sucato et al., 1998;Taylor et al., 1999).The genome of HSV-1 is a 152 kb linear duplex DNA molecule (McGeoch et al., 1988) (Fig. 1a). Epidemiologically unrelated HSV-1 strains can usually be differentiated by analysing variations in restriction endonuclease (RE) cleavage patterns (Buchman et al., 1978(Buchman et al., , 1980 Chaney et al., 1983; Lonsdale et al., 1980). Variations in RE cleavage patterns between HSV-1 strains are divided into two types (Umene et al., 1984;Umene & Yoshida, 1989, 1993 Umene, 1998a, b). One type of variation, termed 'restriction fragment length polymorphism' (RFLP), is due mostly to a gain or loss of an RE cleavage site and causes a ...

Evolution and Diversity in Human Herpes Simplex Virus Genomes

“…2, orange arrows) and have previously been shown to vary in length within a virus strain population, as well as among strains (64,(85)(86)(87)(88)(89). This makes determining their sizes a challenge, since a population of viral DNA used for sequencing may contain genomes with different lengths of a given SSR and high-throughput sequencing reads rarely span the full length of the larger SSRs.…”

“…In addition to the large inverted repeats, the HSV-1 genome contains a large number of SSRs, also known as variable number tandem repeats (VNTRs) or reiterations (82)(83)(84)(85)(86). We previously analyzed all classes of SSR in the HSV-1 reference strain 17, which in the trimmed format contains 87 minisatellites (Ն10-nucleotide repeating unit), 60 microsatellites (2-to 10-nucleotide repeating unit), and 499 homopolymers (Ն6 nucleotides long) (Fig.…”

Nuclear Egress and Envelopment of Herpes Simplex Virus Capsids Analyzed with Dual-Color Fluorescence HSV1(17 + )

“…In all clones, the 2.0-kb BamHI fragment spanning the transition between the US region and the adjoining inverted repeat was reduced by about 50 bp (not shown). Variations in a highly repetitive sequence in this noncoding region have been observed before for individual HSV1 isolates (90).…”

“…Another important question is whether these alterations are of functional relevance. The copy number and composition of the a-sequence varies between different HSV1 strains (6,27,74), isolates from the same individual during different episodes of recurrence (90), and within the population of a specific HSV1 strain (27,74,91). HSV1 BAC genomes with different a-sequences from E. coli can be used to study the biological fitness of such clones.…”

Sequence Variability in Clinical and Laboratory Isolates of Herpes Simplex Virus 1 Reveals New Mutations

“…Since HF10 was itself derived from the nonneuroinvasive and highly attenuated strain HF, the HF10 genome is informative for mutation-based variation but provides little insight into the sequence variation of virulent strains (45,70). Several studies of specific genes or genomic regions cloned in Escherichia coli have shed more light on interstrain variation in HSV-1, but these studies cannot address variation on a genome-wide scale encompassing every protein in the HSV genome (48,57,74,75). Highthroughput sequencing techniques have the potential to address the entire genome of a population without resorting to recombinant DNA techniques and have already enabled substantial inroads into novel pathogen discovery and the genetic characterization of other viruses and pathogens (13,34,54,79,81).…”