Abstract
A number of tandemly reiterated sequences are present on the herpes simplex virus type 1 (HSV-1) DNA molecule of 152 kbp. While regions containing tandem reiterations were usually unstable, reiteration VII, which is present within the protein coding regions of gene US10 and US11, was stable; hence, reiteration VII could be used as a genetic marker. In the present study, the nucleotide sequences (159–213 bp) of a region encompassing reiteration VII of 62 HSV-1 isolates were compared with that of strain 17 as the standard strain, and the genetic variability of base substitutions, deletions, and multiplications was revealed. Base substitution was observed in nine residues on the region flanking reiteration VII and sixty-two HSV-1 isolates were classified into twelve groups based on these base substitutions. Deletions, which were present in all sixty-two isolates, were classified into six groups. Multiplications, which were present in 19 isolates having the same deletion (named del-2), were classified into four groups. The sixty-two isolates were classified into twenty patterns based on variations in the region encompassing reiteration VII, and the region encompassing reiteration VII was considered to be useful for studies on the molecular epidemiology and evolution of HSV-1. The lengths of these deletions and multiplications were multiples of 3; thus, a frame-shift mutation was not induced, and a mechanism to maintain the functions of US10 and US11 was suggested. A series of multiplications, which consisted of the duplication, triplication, and tetraplication of the same sequence, were found. Since all isolates with a multiplication had del-2, multiplications were assumed to be generated after the generation of del-2, and an isolate with del-2 was considered to have the ability to generate a multiplication. Recombination between a pair of direct repeats in and around reiteration VII was accountable for the generation of deletions and multiplications, indicating the recombinogenic property of the region encompassing reiteration VII. A correlation was revealed between a set of 20 DNA polymorphisms widely present on the HSV-1 genome and the base substitutions and deletions of the region encompassing reiteration VII, using discriminant analyses.
Highlights
Herpes simplex virus (HSV), which is a widespread infectious agent in human populations and latently infects neural cells in the spinal ganglia, is classified into two serotypes, herpes simplex virus type 1 (HSV-1) and Herpes simplex virus type 2 (HSV-2) (Nahmias et al 2006)
Determination of nucleotide sequences of the region encompassing reiteration VII of HSV-1 isolates To study the variability in the nucleotide sequences of the region encompassing reiteration VII, the DNA regions encompassing reiteration VII of fifty-eight HSV-1 isolates were amplified by polymerase chain reaction (PCR), and the nucleotide sequences of amplified DNAs were determined
The nucleotide sequences of the region encompassing reiteration VII of four HSV-1 isolates (Y68 (Umene et al 2007), Y70 (Umene et al 2007), C81 (Umene et al 2009), and C85 (Umene et al 2009)) were reported in previous studies
Summary
Herpes simplex virus (HSV), which is a widespread infectious agent in human populations and latently infects neural cells in the spinal ganglia, is classified into two serotypes, HSV-1 and HSV-2 (Nahmias et al 2006). HSV-1 is the predominant cause of oral infection and is often acquired during childhood. The HSV-1 genome is a linear double-stranded DNA of 152 kbp, consisting of two covalently linked components, L and S (McGeoch et al 1988; Roizman 1979). Each component consists of unique sequences flanked by inverted repeat sequences. The HSV-1 genome contains a number of different short, tandemly repeated DNA sequences (McGeoch et al 1988; Rixon et al 1984). Their copy numbers often vary, and variations in copy numbers can cause size heterogeneities in DNA regions containing reiterations (Maertzdorf et al 1999; Umene 1998; Umene and Yoshida 1989)
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