1887

Abstract

A previous phylogenetic analysis based on 32 full-length sequences of herpes simplex virus type 1 (HSV-1) suggested three major phylogenetic groups (phylogroups) with distinct geographic distribution: (1) western strains from Europe and North America, (2) isolates from Asia and one American strain and (3) isolates from Africa only. Here, we sequenced the genomes of additional 10 clinical HSV-1 isolates from Germany, and subsequently compared these sequences to 40 published HSV-1 genomes. The present data demonstrate that HSV-1 is the most diverse human alphaherpesvirus (mean pairwise p-distance of 0.756 %) and confirm the tripartite tree. However, as the German isolates cluster with strains of both phylogroups I and II, it is demonstrated that the latter is also present in Europe and thus is a Eurasian phylogroup. Tree-order scans indicate that HSV-1 evolution is massively influenced by recombination including all investigated strains regardless of the areal distribution of the phylogroups. Numerous recombination events in the evolution of HSV-1 may also influence genotyping as the present HSV-1 genotyping schemes do not yield results consistent with phylogroup classification. Genotyping of HSV-1 is currently based on analyses of intragenic sequence polymorphisms of US2, glycoprotein G (gG, US4) and gI (US7). Each of the 10 German HSV-1 isolates displayed a different US2/gG/gI-genotype combination, but clustered either in phylogroup I or II. In conclusion, the phylogroup concept provides a HSV-1 typing scheme that largely reflects human migration history, whereas the analysis of single-nucleotide polymorphisms fails to render significant biological properties, but allows description of individual genetic traits.

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2016-10-13
2021-10-28
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References

  1. Bowden R., Sakaoka H., Donnelly P., Ward R. 2004; High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection. Infect Genet Evol 4:115–123 [View Article][PubMed]
    [Google Scholar]
  2. Breuer J., Grose C., Norberg P., Tipples G., Schmid D. S. 2010; A proposal for a common nomenclature for viral clades that form the species varicella-zoster virus: summary of VZV Nomenclature Meeting 2008, Barts and the London School of Medicine and Dentistry, 24-25 July 2008. J Gen Virol 91:821–828 [View Article][PubMed]
    [Google Scholar]
  3. Buchman T. G., Roizman B., Adams G., Stover B. H. 1978; Restriction endonuclease fingerprinting of herpes simplex virus DNA: a novel epidemiological tool applied to a nosocomial outbreak. J Infect Dis 138:488–498 [View Article][PubMed]
    [Google Scholar]
  4. Buchman T. G., Roizman B., Nahmias A. J. 1979; Demonstration of exogenous genital reinfection with herpes simplex virus type 2 by restriction endonuclease fingerprinting of viral DNA. J Infect Dis 140:295–304 [View Article][PubMed]
    [Google Scholar]
  5. Chaney S. M., Warren K. G., Kettyls J., Zbitnue A., Subak-Sharpe J. H. 1983; A comparative analysis of restriction enzyme digests of the DNA of herpes simplex virus isolated from genital and facial lesions. J Gen Virol 64:357–371 [View Article][PubMed]
    [Google Scholar]
  6. Dolan A., Jamieson F. E., Cunningham C., Barnett B. C., McGeoch D. J. 1998; The genome sequence of herpes simplex virus type 2. J Virol 72:2010–2021[PubMed]
    [Google Scholar]
  7. Duan R., van Dun J. M., Remeijer L., Siemerink M., Mulder P. G., Norberg P., Osterhaus A. D., Verjans G. M. 2008; Prevalence of herpes simplex virus type 1 glycoprotein G (gG) and gI genotypes in patients with herpetic keratitis. Br J Ophthalmol 92:1195–1200 [View Article][PubMed]
    [Google Scholar]
  8. Glück B., Möbius S., Pfaff F., Zell R., Sauerbrei A. 2015; Novel method for genotyping clinical herpes simplex virus type 1 isolates. Arch Virol 160:2807–2811 [View Article][PubMed]
    [Google Scholar]
  9. Grose C. 2012; Pangaea and the out-of-Africa model of varicella-zoster virus evolution and phylogeography. J Virol 86:9558–9565 [View Article][PubMed]
    [Google Scholar]
  10. Grose C. 2014; Korean war and the origin of herpes simplex virus 1 strain KOS. J Virol 88:3911 [View Article][PubMed]
    [Google Scholar]
  11. Görzer I., Guelly C., Trajanoski S., Puchhammer-Stöckl E. 2010; Deep sequencing reveals highly complex dynamics of human cytomegalovirus genotypes in transplant patients over time. J Virol 84:7195–7203 [View Article][PubMed]
    [Google Scholar]
  12. Halperin S. A., Hendley J. O., Nosal C., Roizman B. 1980; DNA fingerprinting in investigation of apparent nosocomial acquisition of neonatal herpes simplex. J Pediatr 97:91–93 [View Article][PubMed]
    [Google Scholar]
  13. Hammer S. M., Buchman T. G., D'Angelo L. J., Karchmer A. W., Roizman B., Hirsch M. S. 1980; Temporal cluster of herpes simplex encephalitis: investigation by restriction endonuclease cleavage of viral DNA. J Infect Dis 141:436–440 [View Article][PubMed]
    [Google Scholar]
  14. Harishankar A., Jambulingam M., Gowrishankar R., Venkatachalam A., Vetrivel U., Ravichandran S., Yesupadam S. M., Madhavan H. N. 2012; Phylogenetic comparison of exonic US4, US7 and UL44 regions of clinical herpes simplex virus type 1 isolates showed lack of association between their anatomic sites of infection and genotypic/sub genotypic classification. Virol J 9:65 [View Article][PubMed]
    [Google Scholar]
  15. Huson D. H., Bryant D. 2006; Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267 [View Article][PubMed]
    [Google Scholar]
  16. Katoh K., Standley D. M. 2013; mafft multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780 [View Article][PubMed]
    [Google Scholar]
  17. Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S. et al. 2012; Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649 [View Article][PubMed]
    [Google Scholar]
  18. Kent W. J. 2002; BLAT – the blast-like alignment tool. Genome Res 12:656–664 [View Article] Article published online before March 2002 [PubMed]
    [Google Scholar]
  19. Kolb A. W., Adams M., Cabot E. L., Craven M., Brandt C. R. 2011; Multiplex sequencing of seven ocular herpes simplex virus type-1 genomes: phylogeny, sequence variability, and SNP distribution. Invest Ophthalmol Vis Sci 52:9061–9073 [View Article][PubMed]
    [Google Scholar]
  20. Kolb A. W., Ané C., Brandt C. R. 2013; Using HSV-1 genome phylogenetics to track past human migrations. PLoS One 8:e76267 [View Article][PubMed]
    [Google Scholar]
  21. Kurtz S., Phillippy A., Delcher A. L., Smoot M., Shumway M., Antonescu C., Salzberg S. L. 2004; Versatile and open software for comparing large genomes. Genome Biol 5:R12 [View Article][PubMed]
    [Google Scholar]
  22. Lakeman A. D., Nahmias A. J., Whitley R. J. 1986; Analysis of DNA from recurrent genital herpes simplex virus isolates by restriction endonuclease digestion. Sex Transm Dis 13:61–66 [View Article][PubMed]
    [Google Scholar]
  23. Landry M. L., Berkovits N., Summers W. P., Booss J., Hsiung G. D., Summers W. C. 1983; Herpes simplex encephalitis: analysis of a cluster of cases by restriction endonuclease mapping of virus isolates. Neurology 33:831–835 [View Article][PubMed]
    [Google Scholar]
  24. Linnemann C. C., Buchman T. G., Light I. J., Ballard J. L. 1978; Transmission of herpes-simplex virus type 1 in a nursery for the newborn. Identification of viral isolates by D.N.A. ‘fingerprinting’. Lancet 1:964–966[PubMed] [CrossRef]
    [Google Scholar]
  25. McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. 1988; The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol 69:1531–1574 [View Article]
    [Google Scholar]
  26. Mertz G. J., Coombs R. W., Ashley R., Jourden J., Remington M., Winter C., Fahnlander A., Guinan M., Ducey H. et al. 1988; Transmission of genital herpes in couples with one symptomatic and one asymptomatic partner: a prospective study. J Infect Dis 157:1169–1177 [View Article][PubMed]
    [Google Scholar]
  27. Minh B. Q., Nguyen M. A., von Haeseler A. 2013; Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188–1195 [View Article][PubMed]
    [Google Scholar]
  28. Muir W. B., Nichols R., Breuer J. 2002; Phylogenetic analysis of varicella-zoster virus: evidence of intercontinental spread of genotypes and recombination. J Virol 76:1971–1979 [View Article][PubMed]
    [Google Scholar]
  29. Newman R. M., Lamers S. L., Weiner B., Ray S. C., Colgrove R. C., Diaz F., Jing L., Wang K., Saif S. et al. 2015; Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. J Virol 89:8219–8232 [View Article][PubMed]
    [Google Scholar]
  30. Nguyen L. T., Schmidt H. A., von Haeseler A., Minh B. Q. 2015; IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274 [View Article][PubMed]
    [Google Scholar]
  31. Norberg P. 2010; Divergence and genotyping of human alpha-herpesviruses: an overview. Infect Genet Evol 10:14–25 [View Article][PubMed]
    [Google Scholar]
  32. Norberg P., Bergström T., Rekabdar E., Lindh M., Liljeqvist J. A. 2004; Phylogenetic analysis of clinical herpes simplex virus type 1 isolates identified three genetic groups and recombinant viruses. J Virol 78:10755–10764 [View Article][PubMed]
    [Google Scholar]
  33. Norberg P., Bergström T., Liljeqvist J. A. 2006; Genotyping of clinical herpes simplex virus type 1 isolates by use of restriction enzymes. J Clin Microbiol 44:4511–4514 [View Article][PubMed]
    [Google Scholar]
  34. Olp L. N., Jeanniard A., Marimo C., West J. T., Wood C. 2015; Whole-genome sequencing of Kaposi's sarcoma-associated herpesvirus from Zambian Kaposi's sarcoma biopsy specimens reveals unique viral diversity. J Virol 89:12299–12308 [View Article][PubMed]
    [Google Scholar]
  35. Palser A. L., Grayson N. E., White R. E., Corton C., Correia S., Ba Abdullah M. M., Watson S. J., Cotten M., Arrand J. R. et al. 2015; Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection. J Virol 89:5222–5237 [View Article][PubMed]
    [Google Scholar]
  36. Parsons L. R., Tafuri Y. R., Shreve J. T., Bowen C. D., Shipley M. M., Enquist L. W., Szpara M. L. 2015; Rapid genome assembly and comparison decode intrastrain variation in human alphaherpesviruses. MBio 6:e02213e02214 [View Article][PubMed]
    [Google Scholar]
  37. Roizman B., Sears A. E. 1996; Herpes simplex viruses and their replication. In Fields Virology , pp. 2231–2295 Edited by Fields B. N., Knipe D. M., Howley P. M. Philadelphia, PA: Lippincott-Raven Publishers;
    [Google Scholar]
  38. Sakaoka H., Aomori T., Ozaki I., Ishida S., Fujinaga K. 1984; Restriction endonuclease cleavage analysis of herpes simplex virus isolates obtained from three pairs of siblings. Infect Immun 43:771–774[PubMed]
    [Google Scholar]
  39. Sakaoka H., Saheki Y., Uzuki K., Nakakita T., Saito H., Sekine K., Fujinaga K. 1986; Two outbreaks of herpes simplex virus type 1 nosocomial infection among newborns. J Clin Microbiol 24:36–40[PubMed]
    [Google Scholar]
  40. Sakaoka H., Saito H., Sekine K., Aomori T., Grillner L., Wadell G., Fujinaga K. 1987; Genomic comparison of herpes simplex virus type 1 isolates from Japan, Sweden and Kenya. J Gen Virol 68:749–764 [View Article][PubMed]
    [Google Scholar]
  41. Sauerbrei A., Pfaff F., Zell R., Wutzler P. 2012; Prevalence of herpes simplex virus type 1 glycoprotein G (gG) and gI genotypes in patients with different herpetic diseases during the last four decades. J Med Virol 84:651–656 [View Article][PubMed]
    [Google Scholar]
  42. Schmidt-Chanasit J., Bialonski A., Heinemann P., Ulrich R. G., Günther S., Rabenau H. F., Doerr H. W. 2009; A 10-year molecular survey of herpes simplex virus type 1 in Germany demonstrates a stable and high prevalence of genotypes A and B. J Clin Virol 44:235–237 [View Article][PubMed]
    [Google Scholar]
  43. Sijmons S., Thys K., Mbong Ngwese M., Van Damme E., Dvorak J., Van Loock M., Li G., Tachezy R., Busson L. et al. 2015; High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination. J Virol 89:7673–7695 [View Article]
    [Google Scholar]
  44. Simmonds P. 2012; SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes 5:50 [View Article][PubMed]
    [Google Scholar]
  45. Szpara M. L., Gatherer D., Ochoa A., Greenbaum B., Dolan A., Bowden R. J., Enquist L. W., Legendre M., Davison A. J. 2014; Evolution and diversity in human herpes simplex virus genomes. J Virol 88:1209–1227 [View Article][PubMed]
    [Google Scholar]
  46. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  47. Umene K., Yoshida M., Sakaoka H. 1996; Comparison of the association with eczema herpeticum in the two predominant genotypes of herpes simplex virus type 1. J Med Virol 49:329–332 [View Article][PubMed]
    [Google Scholar]
  48. Wertheim J. O., Smith M. D., Smith D. M., Scheffler K., Kosakovsky Pond S. L. 2014; Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol 31:2356–2364 [View Article][PubMed]
    [Google Scholar]
  49. Zell R., Taudien S., Pfaff F., Wutzler P., Platzer M., Sauerbrei A. 2012; Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination. J Virol 86:1608–1622 [View Article][PubMed]
    [Google Scholar]
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