Herpes simplex virus type 1 restriction fragment polymorphism determined using southern hybridization

SUMMARYOne-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.

Section: Introductionmentioning

confidence: 99%

Genomic Comparison of Herpes Simplex Virus Type 1 Isolates from Japan, Sweden and Kenya

Sakaoka

Saitô

Sekine

et al. 1987

“…The analysis of herpes simplex virus (HSV) strains by restriction endonuclease (RE) cleavage sites has been used not only to distinguish between HSV types 1 and 2 but also for strain differentiation within an HSV type (Roizman, 1979(Roizman, , 1980Lonsdale et al, 1979Lonsdale et al, , 1980Maitland et al, 1982;Ueno et al, 1982;Umene et al, 1984;Sakaoka et al, 1987 a, b;Umene & Yoshida, 1989;Umene & Sakaoka, 1991). The existence of intratypic polymorphism in HSV genomes led to the establishment of a new field in terms of molecular epidemiology (Roizman & Buchman, 1979;Buchman et al, 1980;Roizman & Tognon, 1983;Sakaoka et al, 1984Sakaoka et al, , 1985.…”

Section: Introductionmentioning

confidence: 99%

Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus

Sakaoka¹,

Kurita²,

Iida

et al. 1994

Self Cite

159

110

Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients (] r ] > 0.42; P < 0.01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolutionarily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (~), was estimated for HSV-1 genomes within (~x or ~y) and between (~xY) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0-0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (~xY) was highest between isolates from the three Asian countries and Kenya (0.0075 to 0.0081) and lowest among those from the three Asian countries (0.0032 to 0.0040). The mutation rate (k) for HSV-1 was estimated to be 3-5 x 10 S/site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.

“…Genomic differences between intratypic strains of herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) have been identified by restriction endonuclease (RE) cleavage analysis (Hayward et al, 1975;Buchman et al, 1978;Lonsdale et al, 1979;Roizman, 1979Roizman, , 1980Maitland et al, 1982;Chancy et al, 1983 a, b;Umene et al, 1984). In addition, this technique has been applied to trace the transmission of these viruses in clinical situations (Buchman et al, 1980;Roizman & Tognon, 1983;Sakaoka et a1.,1984Sakaoka et a1., , 1986b.…”

Section: Introductionmentioning

confidence: 99%

Genome Variations in Herpes Simplex Virus Type 2 Strains Isolated in Japan and Sweden

Sakaoka

Kawana

Grillner

et al. 1987

SUMMARYOne-hundred and twenty-three epidemiologically unrelated strains of herpes simplex virus type 2 (HSV-2) isolated in Japan and Sweden (68 Japanese and 55 Swedish isolates) were compared by analysis of their genomes using five restriction endonucleases: BamHI, KpnI, EcoRI, HindIII and BglII. Seven of the 93 restriction sites examined showed statistically significant variation between isolates from the two countries. However, HSV-2 isolates were less variable than the HSV-1 isolates previously analysed from the same countries. Using 12 restriction sites as markers, the HSV-2 isolates were classified into 41 cleavage patterns; 17 were specific for Japanese isolates and 15 were specific for Swedish isolates. Correlation coefficients between some sets of 12 markers were significant, but significant correlations between Japanese and Swedish isolates were distinct for each country. Both Japanese and Swedish isolates were assigned to three major patterns with no significant difference in incidence. In contrast, in two other major patterns, differences in incidence between the isolates were statistically significant. These results suggest that HSV-2 populations in geographically separated countries have distinct cleavage site distributions.