Analysis of genomic polymorphism among herpes simplex virus type 2 isolates from four areas of Japan and three other countries

Abstract

Genomic polymorphism of 307 epidemiologically unrelated strains of herpes simplex virus type 2 (HSV-2) from four areas of Japan and three other countries (Korea, Sweden and the U.S.A.) was analysed by using 16 variable markers selected from 97 restriction endonuclease (RE) sites with five REs. In addition to the 16 markers, 26 rare variable RE sites were found in 307 isolates. Five and four of 16 markers (RE sites) were found to differ in the frequency of isolates with the markers between isolates from Japan and Sweden and between those from Japan and the U.S.A., respectively, suggesting that they are genomically different from each other. In this manner, 307 HSV-2 isolates from four countries could be classified into 68 different genotypes (no. of isolates/no. of genotypes = 4.5). Some isolates from one country or more than two countries at times were classified into the same genotypes, which were referred to as predominant genotypes. The most predominant genotypes for isolates from Japan, Sweden and the U.S.A. were genotypes 30, 26 (32) and 3, respectively, indicating that they are different by the country. In genotypes 1 and 6, the frequency of isolates was found to be significantly different between Japan and Sweden and between Japan and the U.S.A., respectively. Nine out of 16 markers differed in the most genomically distant isolates, each of which was obtained in Sweden and Japan. In addition, high correlation coefficients (r) in the Japanese isolates were detected in different pairs of markers from those in the Swedish isolates, suggesting that isolates from these two countries are evolutionarily distant.

Sensitive and Rapid Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA by Loop-Mediated Isothermal Amplification

“…Thus, the LAMP target and primer regions of HSV-1 are regarded as having adequately low degrees of variation. Compared to HSV-1, HSV-2 and VZV have little nucleotide diversity among strains (2,17,19). Our sequencing study indicated that the targeted regions of HSV-2 and VZV have no nucleotide sequence variation and are also adequate for the LAMP assay.…”

Natural recombination in alphaherpesviruses: Insights into viral evolution through full genome sequencing and sequence analysis

“…Early studies of alphaherpesvirus recombination used strain virulence as a marker to detect recombinants (Wildy, 1955). Analysis of partial genome sequences were then used extensively to study recombination in several alphaherpesviruses, using tools such as PCR followed by restriction endonuclease cleavage fragment analysis of PCR products (PCR plus restriction fragment length polymorphism [PCR-RFLP]), gene deletion mutants, PCR hydrolysis probe assays and bioinformatic comparisons of partial genome sequences to detect recombination (Bowden et al, 2004;Christensen and Lomniczi, 1993;Dangler et al, 1993;Dohner et al, 1988;Glazenburg et al, 1994;Henderson et al, 1990;Javier et al, 1986;Kintner et al, 1995;Muylkens et al, 2009;Norberg et al, 2004;Sakaoka et al, 1995;Sakaoka et al, 1994;Schynts et al, 2003;Umene and Sakaoka, 1997). More recently, lower costs, improved technologies and greater access to next generation sequencing (NGS) techniques (Capobianchi et al, 2013;Pareek et al, 2011), statistical analysis (Bruen et al, 2006;Posada, 2002) and software to detect and estimate the likelihood of recombination (Huson and Bryant, 2006;Kosakovsky Pond et al, 2006;Kuhner, 2006;Lole et al, 1999;Martin et al, 2010;Martin et al, 2011;Martin et al, 2015;Pond and Frost, 2005;Wilson and McVean, 2006) have helped us to better understand recombination, and thereby provide insights into the role of recombination in the natural evolution of alphaherpesviruses (Burrel et al, 2015;Hughes and Rivailler, 2007;Kolb et al, 2013;Kolb et al, 2015;…”

Discrimination of Herpes Simplex Virus Type 2 Strains by Nucleotide Sequence Variations

“…The study of the relationships between these diseases and virus strains, and the analysis of transmission between individuals, requires accurate and reproducible typing and phylogenic analyses of clinical strains (4, 9). To achieve this, molecular technologies, in particular restriction fragment length polymorphism (RFLP) analysis, have been widely employed (12,13,14). However, the RFLP assay is relatively troublesome, and comparison of results obtained in different laboratories is difficult.…”