Sequence analysis of isolated strains of herpes zoster virus among patients with shingles
,
Abstract
Background and Objectives: Herpes zoster, or shingles, is caused by the varicella-zoster virus (VZV), which initially presents as chickenpox in children. VZV is a global health concern, especially in winter and spring, affecting 10-20% of adults over 50 and posing a 30% risk for the general population. This study used PCR to detect VZV, confirming results with duplicated DNA samples and identifying 234 bp fragments by targeting the gpB gene.
Materials and Methods: This study examined 50 herpes zoster cases from October 2020 to April 2021, involving 30 males and 20 females aged 10 to 90, diagnosed by dermatologists. Data were collected via a questionnaire. PCR detected VZV by amplifying the gpB and MCP genes from skin lesion samples. Six positive 234-bp PCR products were sequenced at Macrogen Inc. in Seoul, South Korea.
Results: Six DNA samples with 234 bp amplicons were sequenced, showing 99-100% similarity to human alpha herpesvirus sequences in the gpB gene. NCBI BLAST matched these sequences to a reference (GenBank acc. MT370830.1), assigning accession numbers LC642111, LC642112, and LC642113. Eight nucleic acid substitutions caused amino acid changes in the gpB protein: isoleucine to threonine, serine to isoleucine, and threonine to Proline. These variants were deposited in NCBI GenBank as gpB3 samples.
Conclusion: The study found high sequence similarity to known VZV sequences, identifying six nucleic acid variations and eight SNPs. Notable amino acid changes in the gpB protein were deposited in NCBI GenBank as the gpB3 sample.
1. Weidner-Glunde M, Kruminis-Kaszkiel E, Savanagouder M. Herpesviral latency-common themes. Pathogens 2020; 9: 125.
2. Własiuk A, Giannopoulos K. Herpes zoster infections: epidemiology, diagnostics, and prophylaxis in light of a growing clinical problem. Hematol Clin Pract 2023; 14: 69-79.
3. Johnson RW, Bouhassira D, Kassianos G, Leplège A, Schmader KE, Weinke T. The impact of herpes zoster and post-herpetic neuralgia on quality-of-life. BMC Med 2010; 8: 37.
4. Lukas K, Edte A, Bertrand I. The impact of herpes zoster and post-herpetic neuralgia on quality of life: patient-reported outcomes in six European countries. Z Gesundh Wiss 2012; 20: 441-451.
5. Nagel MA, Gilden D. Update on varicella zoster virus vasculopathy. Curr Infect Dis Rep 2014; 16: 407.
6. Koshy E, Mengting L, Kumar H, Jianbo W. Epidemiology, treatment and prevention of herpes zoster: A comprehensive review. Indian J Dermatol Venereol Leprol 2018; 84: 251-262.
7. Patil A, Goldust M, Wollina U. Herpes zoster: A review of clinical manifestations and management. Viruses 2022; 14: 192.
8. Gubareva LV, Mishin VP, Patel MC, Chesnokov A, Nguyen HT, De La Cruz J, et al. Assessing baloxavir susceptibility of influenza viruses circulating in the United States during the 2016/17 and 2017/18 seasons. Euro Surveill 2019; 24: 1800666.
9. Arvin A, Campadelli-Fiume G, Mocarski E, Moore PS, Roizman B, Whitley R, et al. Human herpesviruses: Biology, therapy, and immunoprophylaxis. cambridge: cambridge university press; 2007.
10. Carmichael JC, Yokota H, Craven RC, Schmitt A, Wills JW. The HSV-1 mechanisms of cell-to-cell spread and fusion are critically dependent on host PTP1B. PLoS Pathog 2018; 14(5): e1007054.
11. Nikolic D, Kohn D, Yen-Lieberman B, Procop GW. Detection of herpes simplex virus and Varicella-Zoster virus by traditional and multiplex molecular methods. Am J Clin Pathol 2019; 151: 122-126.
12. Kennedy PGE, Gershon AA. Clinical features of Varicella-Zoster virus infection. Viruses 2018; 10: 609.
13. Gershon AA, Gershon MD. Pathogenesis and current approaches to control of varicella-zoster virus infections. Clin Microbiol Rev 2013; 26: 728-743.
14. Campsall PA, Au NH, Prendiville JS, Speert DP, Tan R, Thomas EE. Detection and genotyping of varicella-zoster virus by TaqMan allelic discrimination real-time PCR. J Clin Microbiol 2004; 42: 1409-1413.
15. Loparev VN, Rubtcova EN, Bostik V, Tzaneva V, Sauerbrei A, Robo A, et al. Distribution of varicella-zoster virus (VZV) wild-type genotypes in northern and southern Europe: evidence for high conservation of circulating genotypes. Virology 2009; 383: 216-225.
16. Aubaid AH, Abed A, Alrodhan MA. A surveillance of varicella zoster virus among school age children in Al-Diwaniyah governorate. Indian J Public Health Res Dev 2020; 11: 1662.
17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35: 1547-1549.
18. Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004; 21: 255-265.
19. Birlea M, Cohrs RJ, Bos N, Mehta SK, Pierson DL, Gilden D. Search for varicella zoster virus DNA in saliva of healthy individuals aged 20-59 years. J Med Virol 2014; 86: 360-362.
20. Nei M, Kumar S (2000). Molecular evolution and phylogenetics. New York, NY: Oxford University Press.
21. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870-1874.
22. Yawn BP, Itzler RI, Wollan PC, Pellissier JM, Sy LS, Saddier P. Health care utilization and cost burden of herpes zoster in a community population. Mayo Clin Proc 2009; 84: 787-794.
23. Gnann JW, Whitley RJ. Clinical practice. Herpes zoster. N Engl J Med 2002; 347: 340-346.
24. Patil A, Goldust M, Wollina U. Herpes zoster: A Review of clinical manifestations and management. Viruses 2022; 14: 192.
25. Nikolic D, Kohn D, Yen-Lieberman B, Procop GW. Detection of herpes simplex virus and Varicella-Zoster virus by traditional and multiplex molecular methods. Am J Clin Pathol 2019; 151: 122-126.
26. Jevšnik M, Lusa L, Uršič T, Glinšek Biškup U, Petrovec M. Detection of herpes simplex and varicella-zoster virus from skin lesions: comparison of RT-PCR and isothermal amplification for rapid identification. Diagn Microbiol Infect Dis 2020; 97: 115015.
27. Pan D, Wang W, Cheng T. Current methods for the detection of antibodies of Varicella-Zoster virus: A review. Microorganisms 2023; 11: 519.
28. Harpaz R, Leung JW. The epidemiology of herpes zoster in the United States during the era of varicella and herpes zoster vaccines: changing patterns among older adults. Clin Infect Dis 2019; 69: 341-344.
29. Cohen JI. clinical practice: herpes zoster. N Engl J Med 2013; 369: 255-263.
30. Gershon AA, Breuer J, Cohen JI, Cohrs RJ, Gershon MD, Gilden D, et al. Varicella zoster virus infection. Nat Rev Dis Primers 2015; 1: 15016.
31. Eisenberg RJ, Atanasiu D, Cairns TM, Gallagher JR, Krummenacher C, Cohen GH. Herpes virus fusion and entry: a story with many characters. Viruses 2012; 4: 800-832.
32. Connolly SA, Jardetzky TS, Longnecker R. The structural basis of herpesvirus entry. Nat Rev Microbiol 2021; 19: 110-121.
33. Aberle SW, Aberle JH, Steininger C, Puchhammer-Stöckl E. Quantitative real time PCR detection of Varicella-zoster virus DNA in cerebrospinal fluid in patients with neurological disease. Med Microbiol Immunol 2005; 194: 7-12.
34. Bai X, Rogers BB, Harkins PC, Sommerauer J, Squires R, Rotondo K, et al. Predictive value of quantitative PCR-Based viral burden analysis for eight human herpesviruses in pediatric solid organ transplant patients. J Mol Diagn 2000; 2: 191-201.
35. Loparev VN, Rubtcova EN, Bostik V, Govil D, Birch CJ, Druce JD, et al. Identification of five major and two minor genotypes of varicella-zoster virus strains: a practical two-amplicon approach used to genotype clinical isolates in Australia and New Zealand. J Virol 2007; 81: 12758-12765.
36. Kennedy PG. Varicella-zoster virus latency in human ganglia. Rev Med Viro 2002; 12: 327-334.
37. Norberg P, Depledge DP, Kundu S, Atkinson C, Brown J, Haque T, et al. Recombination of globally circulating varicella-zoster virus. J Virol 2015; 89: 7133-7146.
38. Sadaoka T, Depledge DP, Rajbhandari L, Breuer J, Venkatesan A, Cohen JI. A variant allele in varicella-zoster virus glycoprotein B selected during production of the varicella vaccine contributes to its attenuation. mBio 2022; 13(4): e0186422.
39. Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006; 7: 61-80.
40. Kim JI, Jung GS, Kim YY, Ji GY, Kim HS, Wang WD, et al. Sequencing and characterization of Varicella-zoster virus vaccine strain SuduVax. Virol J 2011; 8: 547.
41. Lezhnyova V, Davidyuk Y, Mullakhmetova A, Markelova M, Zakharov A, Khaiboullina S, et al. Analysis of herpesvirus infection and genome single nucleotide polymorphism risk factors in multiple sclerosis, Volga federal district, Russia. Front Immunol 2022; 13: 1010605.
42. López-Muñoz AD, Rastrojo A, Martín R, Alcamí A. Herpes simplex virus 2 (HSV-2) evolves faster in cell culture than HSV-1 by generating greater genetic diversity. PLoS Pathog 2021; 17(8): e1009541.
43. Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev 2012; 76: 159-216.
44. Nicola AV, Straus SE. Cellular and viral requirements for rapid endocytic entry of herpes simplex virus. J Virol 2004; 78: 7508-7517.
45. Isaacson MK, Ploegh HL. Ubiquitination, ubiquitin-like modifiers, and deubiquitination in viral infection. Cell Host Microbe 2009; 5: 559-570.
46. Wang Z, Moult J. SNPs, protein structure, and disease. Hum Mutat 2001; 17: 263-270.
47. Sievers F, Higgins DG. Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol 2014; 1079: 105-116.
48. Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006; 17: 61-80.
49. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res 2013; 41: D36-D42.
50. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res 2017; 45: D37-D42.
2. Własiuk A, Giannopoulos K. Herpes zoster infections: epidemiology, diagnostics, and prophylaxis in light of a growing clinical problem. Hematol Clin Pract 2023; 14: 69-79.
3. Johnson RW, Bouhassira D, Kassianos G, Leplège A, Schmader KE, Weinke T. The impact of herpes zoster and post-herpetic neuralgia on quality-of-life. BMC Med 2010; 8: 37.
4. Lukas K, Edte A, Bertrand I. The impact of herpes zoster and post-herpetic neuralgia on quality of life: patient-reported outcomes in six European countries. Z Gesundh Wiss 2012; 20: 441-451.
5. Nagel MA, Gilden D. Update on varicella zoster virus vasculopathy. Curr Infect Dis Rep 2014; 16: 407.
6. Koshy E, Mengting L, Kumar H, Jianbo W. Epidemiology, treatment and prevention of herpes zoster: A comprehensive review. Indian J Dermatol Venereol Leprol 2018; 84: 251-262.
7. Patil A, Goldust M, Wollina U. Herpes zoster: A review of clinical manifestations and management. Viruses 2022; 14: 192.
8. Gubareva LV, Mishin VP, Patel MC, Chesnokov A, Nguyen HT, De La Cruz J, et al. Assessing baloxavir susceptibility of influenza viruses circulating in the United States during the 2016/17 and 2017/18 seasons. Euro Surveill 2019; 24: 1800666.
9. Arvin A, Campadelli-Fiume G, Mocarski E, Moore PS, Roizman B, Whitley R, et al. Human herpesviruses: Biology, therapy, and immunoprophylaxis. cambridge: cambridge university press; 2007.
10. Carmichael JC, Yokota H, Craven RC, Schmitt A, Wills JW. The HSV-1 mechanisms of cell-to-cell spread and fusion are critically dependent on host PTP1B. PLoS Pathog 2018; 14(5): e1007054.
11. Nikolic D, Kohn D, Yen-Lieberman B, Procop GW. Detection of herpes simplex virus and Varicella-Zoster virus by traditional and multiplex molecular methods. Am J Clin Pathol 2019; 151: 122-126.
12. Kennedy PGE, Gershon AA. Clinical features of Varicella-Zoster virus infection. Viruses 2018; 10: 609.
13. Gershon AA, Gershon MD. Pathogenesis and current approaches to control of varicella-zoster virus infections. Clin Microbiol Rev 2013; 26: 728-743.
14. Campsall PA, Au NH, Prendiville JS, Speert DP, Tan R, Thomas EE. Detection and genotyping of varicella-zoster virus by TaqMan allelic discrimination real-time PCR. J Clin Microbiol 2004; 42: 1409-1413.
15. Loparev VN, Rubtcova EN, Bostik V, Tzaneva V, Sauerbrei A, Robo A, et al. Distribution of varicella-zoster virus (VZV) wild-type genotypes in northern and southern Europe: evidence for high conservation of circulating genotypes. Virology 2009; 383: 216-225.
16. Aubaid AH, Abed A, Alrodhan MA. A surveillance of varicella zoster virus among school age children in Al-Diwaniyah governorate. Indian J Public Health Res Dev 2020; 11: 1662.
17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35: 1547-1549.
18. Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004; 21: 255-265.
19. Birlea M, Cohrs RJ, Bos N, Mehta SK, Pierson DL, Gilden D. Search for varicella zoster virus DNA in saliva of healthy individuals aged 20-59 years. J Med Virol 2014; 86: 360-362.
20. Nei M, Kumar S (2000). Molecular evolution and phylogenetics. New York, NY: Oxford University Press.
21. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870-1874.
22. Yawn BP, Itzler RI, Wollan PC, Pellissier JM, Sy LS, Saddier P. Health care utilization and cost burden of herpes zoster in a community population. Mayo Clin Proc 2009; 84: 787-794.
23. Gnann JW, Whitley RJ. Clinical practice. Herpes zoster. N Engl J Med 2002; 347: 340-346.
24. Patil A, Goldust M, Wollina U. Herpes zoster: A Review of clinical manifestations and management. Viruses 2022; 14: 192.
25. Nikolic D, Kohn D, Yen-Lieberman B, Procop GW. Detection of herpes simplex virus and Varicella-Zoster virus by traditional and multiplex molecular methods. Am J Clin Pathol 2019; 151: 122-126.
26. Jevšnik M, Lusa L, Uršič T, Glinšek Biškup U, Petrovec M. Detection of herpes simplex and varicella-zoster virus from skin lesions: comparison of RT-PCR and isothermal amplification for rapid identification. Diagn Microbiol Infect Dis 2020; 97: 115015.
27. Pan D, Wang W, Cheng T. Current methods for the detection of antibodies of Varicella-Zoster virus: A review. Microorganisms 2023; 11: 519.
28. Harpaz R, Leung JW. The epidemiology of herpes zoster in the United States during the era of varicella and herpes zoster vaccines: changing patterns among older adults. Clin Infect Dis 2019; 69: 341-344.
29. Cohen JI. clinical practice: herpes zoster. N Engl J Med 2013; 369: 255-263.
30. Gershon AA, Breuer J, Cohen JI, Cohrs RJ, Gershon MD, Gilden D, et al. Varicella zoster virus infection. Nat Rev Dis Primers 2015; 1: 15016.
31. Eisenberg RJ, Atanasiu D, Cairns TM, Gallagher JR, Krummenacher C, Cohen GH. Herpes virus fusion and entry: a story with many characters. Viruses 2012; 4: 800-832.
32. Connolly SA, Jardetzky TS, Longnecker R. The structural basis of herpesvirus entry. Nat Rev Microbiol 2021; 19: 110-121.
33. Aberle SW, Aberle JH, Steininger C, Puchhammer-Stöckl E. Quantitative real time PCR detection of Varicella-zoster virus DNA in cerebrospinal fluid in patients with neurological disease. Med Microbiol Immunol 2005; 194: 7-12.
34. Bai X, Rogers BB, Harkins PC, Sommerauer J, Squires R, Rotondo K, et al. Predictive value of quantitative PCR-Based viral burden analysis for eight human herpesviruses in pediatric solid organ transplant patients. J Mol Diagn 2000; 2: 191-201.
35. Loparev VN, Rubtcova EN, Bostik V, Govil D, Birch CJ, Druce JD, et al. Identification of five major and two minor genotypes of varicella-zoster virus strains: a practical two-amplicon approach used to genotype clinical isolates in Australia and New Zealand. J Virol 2007; 81: 12758-12765.
36. Kennedy PG. Varicella-zoster virus latency in human ganglia. Rev Med Viro 2002; 12: 327-334.
37. Norberg P, Depledge DP, Kundu S, Atkinson C, Brown J, Haque T, et al. Recombination of globally circulating varicella-zoster virus. J Virol 2015; 89: 7133-7146.
38. Sadaoka T, Depledge DP, Rajbhandari L, Breuer J, Venkatesan A, Cohen JI. A variant allele in varicella-zoster virus glycoprotein B selected during production of the varicella vaccine contributes to its attenuation. mBio 2022; 13(4): e0186422.
39. Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006; 7: 61-80.
40. Kim JI, Jung GS, Kim YY, Ji GY, Kim HS, Wang WD, et al. Sequencing and characterization of Varicella-zoster virus vaccine strain SuduVax. Virol J 2011; 8: 547.
41. Lezhnyova V, Davidyuk Y, Mullakhmetova A, Markelova M, Zakharov A, Khaiboullina S, et al. Analysis of herpesvirus infection and genome single nucleotide polymorphism risk factors in multiple sclerosis, Volga federal district, Russia. Front Immunol 2022; 13: 1010605.
42. López-Muñoz AD, Rastrojo A, Martín R, Alcamí A. Herpes simplex virus 2 (HSV-2) evolves faster in cell culture than HSV-1 by generating greater genetic diversity. PLoS Pathog 2021; 17(8): e1009541.
43. Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev 2012; 76: 159-216.
44. Nicola AV, Straus SE. Cellular and viral requirements for rapid endocytic entry of herpes simplex virus. J Virol 2004; 78: 7508-7517.
45. Isaacson MK, Ploegh HL. Ubiquitination, ubiquitin-like modifiers, and deubiquitination in viral infection. Cell Host Microbe 2009; 5: 559-570.
46. Wang Z, Moult J. SNPs, protein structure, and disease. Hum Mutat 2001; 17: 263-270.
47. Sievers F, Higgins DG. Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol 2014; 1079: 105-116.
48. Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006; 17: 61-80.
49. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res 2013; 41: D36-D42.
50. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res 2017; 45: D37-D42.
| Files | ||
| Issue | Vol 16 No 4 (2024) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v16i4.16312 | |
| Keywords | ||
| Herpes zoster virus; Human herpesvirus 3 (HHV-3); Varicella zoster virus; Shingles; Major capsid protein (HSV-1 capsid protein ICP5); Herpesvirus 3 (alpha) | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Mohammed Shallal MJ, Nasser H, Abdul Hassen Naif A. Sequence analysis of isolated strains of herpes zoster virus among patients with shingles. Iran J Microbiol. 2024;16(4):524-535.
