Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Thu, 13 Dec 2018 11:27:07 J. gen. Virol. (1987), 68, 749-764. Printedin Great Britain Key words: H S V-1/ cleavage patterns /genome structure 749 Genomic Comparison of Herpes Simplex Virus Type 1 Isolates from Japan, Sweden and Kenya By HIROSHI SAKAOKA, l* HITOSHI SAITO, 1 KIYOSHI SEKINE, 1 TSUGUMITSU AOMORI, 1 LENA GRILLNER, 2 GORAN WADELL 3 AND KEI FUJINAGA ~ IDepartment of Oral Bacteriology, School of Dentistry, Hokkaido University, N-13 W-7, Kita-Ku, Sapporo 060, Japan, '-Department of Clinical Microbiology, Karolinska Hospital, 104 01 Stockholm, 3Department of Virology, University of Umeh, S-90185 Umeh, Sweden and 4Department of Molecular Biology, Cancer Research Institute, Sapporo Medical College, Sapporo 060, Japan (Accepted 20 November 1986) SUMMARY One-hundred and seventy-two epidemiologically unrelated herpes simplex virus type 1 (HSV-I) strains isolated in Japan (104 strains) and Sweden (68 strains) were compared by analysis of their genome structures using four restriction endonucleases, BamHI, KpnI, SalI and HindlII. In addition, 32 Kenyan HSV-1 isolates previously compared to Japanese isolates were included for further comparison with the Swedish isolates. Remarkable and statistically significant differences were found between the HSV-1 isolates from the three countries. One-hundred and thirty cleavage sites were examined, and it was shown that isolates from two of the three countries were statistically distinguishable at 27 of these loci. Pairwise comparison between isolates from Japan and Sweden, Kenya and Sweden, and Japan and Kenya revealed variation in 18, 16 and 23 sites, respectively. By considering gains and losses of 19 sites, the total of 204 strains could be classified into 92 distinct cleavage patterns. Isolates from the three countries could be distinguished from each other by the pattern, except for one Swedish and two Kenyan isolates which shared a pattern. Twenty-one fragments that were present or absent only in individual isolates from one or other of the three countries could be detected. These results show that HSV-1 strains from geographically separate countries or anthropologically different races have distinct distributions of endonuclease recognition sites. INTRODUCTION Restriction endonuclease (RE) analyses of herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) have provided information on the wide extent of intratypic genetic variation among herpesvirus strains (Hayward et al., 1975; Skare et al., 1975; Buchman et al., 1978, 1980; Lonsdale et al., 1979; Maitland et al., 1982; Chancy et al., 1983a, b; Umene et al., 1984). They have also been used to analyse the transmission and reactivation of the viruses (Linneman et al., 1978; Buchman et al., 1979; Roizman & Buchman, 1979; Halperin et al., 1980; Hammer et al., 1980; Adams et al., 1981 ; Whitley et al., 1982; Hammerberg et al., 1983; Roizman & Tognon, 1983; Sakaoka et al., 1984, 1986b). These results show that cleavage site analysis of HSV DNA provides a powerful tool for epidemiological surveys. Previously, we established a practical method for strain differentiation by using unlabelled DNA from HSV-infected cells (Ueno et al., 1982). Using this method, we demonstrated that the genomes of HSV-1 isolates from three separate areas of Japan differed significantly (Sakaoka et al., 1985). We have also detected a clear-cut genetic difference between HSV-1 isolates from Japan and Kenya, which are geographically and anthropologically distant from each other (Sakaoka et al., 1986a). In the present study, we analysed 104 HSV-1 isolates from Japan and 68 0000-7139 O 1987 SGM