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

Abstract

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.

Global phylogeography and evolution of chelonid fibropapilloma-associated herpesvirus

“…The FP panzootic has emerged over the last few decades, with the disease spreading rapidly and reaching high prevalence in many localities (Herbst, 1994;Herbst et al, 2008), consistently associated with recent environmental changes (Aguirre & Lutz, 2004;Herbst, 1994;Herbst & Klein, 1995;Van Houtan et al, 2010). It is possible that virus transmission and replication rates have been enhanced during this pandemic with an inherent increase in evolutionary rates.The estimated TMRCA of the CFPHV variants ranged from 192.90 to 429.71 years, which is much more recent than previous estimates placing the emergence of modern CFPHV variants on a scale of several thousand to several million years ago (Herbst et al, 2004), predicted under assumptions of co-divergence with the host species (McGeoch et al, 2000;Sakaoka et al, 1994) or indicating a vicariance event between the eastern Pacific and western Atlantic (Herbst et al, 2004). Nevertheless, our estimates still place the TMRCA previous to the emergence of the current FP panzootic, agreeing with the conclusion by Herbst et al (2004) that the CFPHV variants acquired the shared mutation(s) responsible for FP oncogenesis prior to their divergence and that this panzootic is not due to the emergence and global spread of a single virulent CFPHV strain, but instead is due to recent environmental changes that favour disease expression.…”

“…; Sakaoka et al, 1994) to test the prior likelihoods. The MCMC analysis using the faster rate had a higher prior likelihood and subsequent higher marginal posterior mean: 29662 (95 % HPD529678 to 29647) compared with 29920 (95 % HPD529935 to 29903) when the MCMC was run under the slower rate, demonstrating a better fit of our substitution rate to the dataset.…”

High rate of viral evolution associated with the emergence of carnivore parvovirus

“…Estimates of long-term rates of nucleotide substitution, primarily based on cases where virus and host are thought to have undergone cospeciation, show that this assumption is true for large double-stranded DNA (dsDNA) viruses such as the herpesviruses and possibly for small dsDNA viruses such as human papillomavirus and JC polyomavirus (13)(14)(15)(16). However, few such rate estimates are available for ssDNA viruses.…”

Polysaccharides from Red Algae: Genesis of a Renaissance

“…This panorama may account for a "symbiotic evolution" of cell and virus, although viruses have much shorter generation times than cells. Studies of genomic polymorphism of HSV-1 suggest that the evolution of this virus would be very slow and host-dependent [73].…”