CRISPR-Cas genome editing system in the diagnosis and therapy of infection caused by herpes simplex virus type 1 (Orthoherpesviridae: Alphaherpesviridae: Simplexvirus: Simplexvirus humanalpha1)

Cover Image

Cite item

Abstract

Herpes simplex virus type 1 (HSV-1), newly named as Simplexvirus humanalpha1 is one of the most common pathogens in the human population, which can cause severe disease, often with fatal outcomes. Diagnostic methods currently in use are specific and sensitive, but time-consuming, require expensive laboratory equipment and highly qualified personnel. Existing therapeutic agents have a number of significant drawbacks. To successfully treat and prevent the spread of the infection, new rapid, easy-to-use, and highly sensitive diagnostic tools and effective therapeutic agents are required. One approach to achieve this goal is CRISPR-based technology.

This review analyzes information obtained from a literature search in the Scopus, Web of Science and MedLine databases on the topics «HSV-1, structure, distribution, life cycle», «new methods for molecular diagnosis of HSV-1-infection», «classification of CRISPR-Cas systems», «nucleic acid amplification methods», «CRISPR-Cas effector proteins», «application of CRISPR-Cas systems in molecular diagnostics of HSV-1-infection», «application of CRISPR-Cas systems in therapy of HSV-1-infection». New approaches of CRISPR using effector proteins Cas12 and Cas13 in the diagnosis of HSV-1 infections are reviewed. The article discusses the progress in the development of CRISPR-Cas-based therapies against HSV-1-infection in vitro and in vivo. CRISPR gene therapy in vivo has a great clinical potential, but its safety and efficacy require further investigation. An analysis of the available data suggests that CRISPR-based technologies offer promising prospects for expanding the arsenal of diagnostic tools and antiviral drugs in the context of current and future outbreaks of viral diseases.

About the authors

Natalia A. Demidova

Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation

Email: ailande@yandex.ru
ORCID iD: 0000-0003-1961-9789

Researcher of the Laboratory of Cell Engineering

Russian Federation, 123098, Moscow

Regina R. Klimova

Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation

Email: regi.K@mail.ru
ORCID iD: 0000-0002-4147-8444

PhD (Biology), Senior Researcher of the Laboratory of Cell Engineering

Russian Federation, 123098, Moscow

Alla A. Kushch

Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation

Email: vitallku@mail.ru
ORCID iD: 0000-0002-3396-5533

D.Sci. (Biology), Professor, Chief Researcher of the Laboratory of Cell Engineering

Russian Federation, 123098, Moscow

Dmitry S. Karpov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Author for correspondence.
Email: aleom@yandex.ru
ORCID iD: 0000-0001-5203-0787

PhD (Biology), Leading Researcher

Russian Federation, 119991, Moscow

References

  1. James C., Harfouche M., Welton N.J., Turner K.M., Abu-Raddad L.J., Gottlieb S.L., et al. Herpes simplex virus: global infection prevalence and incidence estimates, 2016. Bull. World Health Organ. 2020; 98(5): 315. https://doi.org/10.2471/BLT.19.237149
  2. Marcocci M.E., Napoletani G., Protto V., Kolesova O., Piacentini R., Li Puma D.D., et al. Herpes simplex virus-1 in the brain: the dark side of a sneaky infection. Trends Microbiol. 2020; 28(10): 808. https://doi.org/10.1016/j.tim.2020.03.003
  3. de Sousa R.M.P., Garcia L.S., Lemos F.S., de Campos V.S., Machado Ferreira E., de Almeida N.A.A., et al. CRISPR/Cas9 eye drop HSV-1 treatment reduces brain viral load: a novel application to prevent neuronal damage. Pathogens. 2024; 13(12): 1087. https://doi.org/10.3390/pathogens13121087
  4. Stahl J.P., Mailles A. Herpes simplex virus encephalitis update. Curr. Opin. Infect. Dis. 2019; 32(3): 239. https://doi.org/10.1097/QCO.0000000000000554
  5. Akkaya O. Prevalence of herpes simplex virus infections in the central nervous system. Clin. Lab. 2021; 67(7). https://doi.org/10.7754/Clin.Lab.2020.201111
  6. Rippee-Brooks M.D., Wu W., Dong J., Pappolla M., Fang X., Bao X. Viral infections, are they a trigger and risk factor of Alzheimer’s disease? Pathogens. 2024; 13(3): 240. https://doi.org/10.3390/pathogens13030240
  7. Vestin E., Bostrom G., Olsson J., Elgh F., Lind L., Kilander L., et al. Herpes simplex viral infection doubles the risk of dementia in a contemporary cohort of older adults: a prospective study. J. Alzheimers Dis. 2024; 97(4): 1841. https://doi.org/10.3233/JAD-230718
  8. Van Wagoner N., Qushair F., Johnston C. Genital herpes infection: progress and problems. Infect. Dis. Clin. North Am. 2023; 37(2): 351. https://doi.org/10.1016/j.idc.2023.02.011
  9. Wang H. Practical updates in clinical antiviral resistance testing. J. Clin. Microbiol. 2024; 62(8): e0072823. https://doi.org/10.1128/jcm.00728-23
  10. Sadowski L.A., Upadhyay R., Greeley Z.W., Margulies B.J. Current drugs to treat infections with herpes simplex viruses-1 and -2. Viruses. 2021; 13(7): 1228. https://doi.org/10.3390/v13071228
  11. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337(6096): 816. https://doi.org/10.1126/science.1225829
  12. van Diemen F.R., Kruse E.M., Hooykaas M.J., Bruggeling C.E., Schurch A.C., van Ham P.M., et al. CRISPR/Cas9-mediated genome editing of herpesviruses limits productive and latent infections. PLoS Pathog. 2016; 12(6): e1005701. https://doi.org/10.1371/journal.ppat.1005701
  13. Zhang I., Hsiao Z., Liu F. Development of genome editing approaches against herpes simplex virus infections. Viruses. 2021; 13(2): 338. https://doi.org/10.3390/v13020338
  14. Karpov D.S., Demidova N.A., Kulagin K.A., Shuvalova A.I., Kovalev M.A., Simonov R.A., et al. Complete and prolonged inhibition of herpes simplex virus type 1 infection in vitro by CRISPR/Cas9 and CRISPR/CasX systems. Int. J. Mol. Sci. 2022; 23(23): 14847. https://doi.org/10.3390/ijms232314847
  15. Dou B., Zhang Y., Gao H., Zhang S., Zheng J., Lu X., et al. CRISPR/Cas12a-based MUSCA-PEC strategy for HSV-1 assay. Anal. Chim. Acta. 2023; 1250: 340955. https://doi.org/10.1016/j.aca.2023.340955
  16. Du K., Zeng Q., Jiang M., Hu Z., Zhou M., Xia K. CRISPR/Cas12a-based biosensing: advances in mechanisms and applications for nucleic acid detection. Biosensors (Basel). 2025; 15(6): 360. https://doi.org/10.3390/bios15060360
  17. Packard J.E., Dembowski J.A. HSV-1 DNA replication-coordinated regulation by viral and cellular factors. Viruses. 2021; 13(10): 2015. https://doi.org/10.3390/v13102015
  18. Jambunathan N., Clark C.M., Musarrat F., Chouljenko V.N., Rudd J., Kousoulas K.G. Two sides to every story: herpes simplex type-1 viral glycoproteins gB, gD, gH/gL, gK, and cellular receptors function as key players in membrane fusion. Viruses. 2021; 13(9): 1849. https://doi.org/10.3390/v13091849
  19. Rivas T., Goodrich J.A., Kugel J.F. The herpes simplex virus 1 protein ICP4 acts as both an activator and a repressor of host genome transcription during infection. Mol. Cell. Biol. 2021; 41(10): e0017121. https://doi.org/10.1128/MCB.00171-21
  20. Ding X., Neumann D.M., Zhu L. Host factors associated with either VP16 or VP16-induced complex differentially affect HSV-1 lytic infection. Rev. Med. Virol. 2022; 32(6): e2394. https://doi.org/10.1002/rmv.2394
  21. Sosnovtseva A.O., Demidova N.A., Klimova R.R., Kovalev M.A., Kushch A.A., Starodubova E.S., et al. Control of HSV-1 infection: directions for the development of CRISPR/Cas-Based therapeutics and diagnostics. Int. J. Mol. Sci. 2024; 25(22): 12346. https://doi.org/10.3390/ijms252212346
  22. Jiang S., Li H., Zhang L., Mu W., Zhang Y., Chen T., et al. Generic Diagramming Platform (GDP): a comprehensive database of high-quality biomedical graphics. Nucleic Acids Res. 2025; 53(D1): D1670–6. https://doi.org/10.1093/nar/gkae973
  23. Fox H.L., Dembowski J.A., DeLuca N.A. A herpesviral immediate early protein promotes transcription elongation of viral transcripts. mBio. 2017; 8(3): e00745-17. https://doi.org/10.1128/mBio.00745-17
  24. Renner D.W., Szpara M.L. Impacts of genome-wide analyses on our understanding of human herpesvirus diversity and evolution. J. Virol. 2018; 92(1): e00908-17. https://doi.org/10.1128/JVI.00908-17
  25. Grady L.M., Szczepaniak R., Murelli R.P., Masaoka T., Le Grice S.F.J., Wright D.L., et al. The exonuclease activity of herpes simplex virus 1 UL12 is required for production of viral DNA that can be packaged to produce infectious virus. J. Virol. 2017; 91(23): e01380-17. https://doi.org/10.1128/JVI.01380-17
  26. Waisner H., Lasnier S., Suma S.M., Kalamvoki M. Effects on exocytosis by two HSV-1 mutants unable to block autophagy. J. Virol. 2023; 97(10): e0075723. https://doi.org/10.1128/jvi.00757-23
  27. Suzich J.B., Cliffe A.R. Strength in diversity: Understanding the pathways to herpes simplex virus reactivation. Virology. 2018; 522: 81. https://doi.org/10.1016/j.virol.2018.07.011
  28. Nicoll M.P., Hann W., Shivkumar M., Harman L.E., Connor V., Coleman H.M., et al. The HSV-1 latency-associated transcript functions to repress latent phase lytic gene expression and suppress virus reactivation from latently infected neurons. PLoS Pathog. 2016; 12(4): e1005539. https://doi.org/10.1371/journal.ppat.1005539
  29. Sawtell N.M., Thompson R.L. De novo herpes simplex virus VP16 expression gates a dynamic programmatic transition and sets the latent/lytic balance during acute infection in trigeminal ganglia. PLoS Pathog. 2016; 12(9): e1005877. https://doi.org/10.1371/journal.ppat.1005877
  30. Cuddy S.R., Schinlever A.R., Dochnal S., Seegren P.V., Suzich J., Kundu P., et al. Neuronal hyperexcitability is a DLK-dependent trigger of herpes simplex virus reactivation that can be induced by IL-1. Elife. 2020; 9: e58037. https://doi.org/10.7554/eLife.58037
  31. Kostyusheva A., Brezgin S., Babin Y., Vasilyeva I., Glebe D., Kostyushev D., et al. CRISPR-Cas systems for diagnosing infectious diseases. Methods. 2022; 203: 431–46. https://doi.org/10.1016/j.ymeth.2021.04.007
  32. Freije C.A., Sabeti P.C. Detect and destroy: CRISPR-based technologies for the response against viruses. Cell Host Microbe. 2021; 29(5): 689–703. https://doi.org/10.1016/j.chom.2021.04.003
  33. Bairqdar A., Karitskaya P.E., Stepanov G.A. Expanding horizons of CRISPR/Cas technology: clinical advancements, therapeutic applications, and challenges in gene therapy. Int. J. Mol. Sci. 2024; 25(24): 13321. https://doi.org/10.3390/ijms252413321
  34. Boonbanjong P., Treerattrakoon K., Waiwinya W., Pitikultham P., Japrung D. Isothermal amplification technology for disease diagnosis. Biosensors (Basel). 2022; 12(9): 677. https://doi.org/10.3390/bios12090677
  35. Liu D.N., Wu H.P., Zhou G.H. Research progress of visual detection in rapid on-site detection of pathogen nucleic acid. Yi Chuan. 2023; 45(4): 306–23. https://doi.org/10.16288/j.yczz.22-323
  36. Mao X., Xu M., Luo S., Yang Y., Zhong J., Zhou J., et al. Advancements in the synergy of isothermal amplification and CRISPR-cas technologies for pathogen detection. Front. Bioeng. Biotechnol. 2023; 11: 1273988. https://doi.org/10.3389/fbioe.2023.1273988
  37. Volkov A., Dolgova A., Dedkov V. CRISPR/Cas-based diagnostic platforms. Infektsiya i immunitet. 2022; 12(1): 9–20. https://doi.org/10.15789/2220-7619-CCB-1843 https://elibrary.ru/fdhjgz (in Russian)
  38. Geojith G., Dhanasekaran S., Chandran S.P., Kenneth J. Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting. J. Microbiol. Methods. 2011; 84(1): 71–3. https://doi.org/10.1016/j.mimet.2010.10.015
  39. Uttam I., Sudarsan S., Ray R., Chinnappan R., Yaqinuddin A., Al-Kattan K., et al. A hypothetical approach to concentrate microorganisms from human urine samples using paper-based adsorbents for point-of-care molecular assays. Life (Basel). 2023; 14(1): 38. https://doi.org/10.3390/life14010038
  40. Lobato I.M., O’Sullivan C.K. Recombinase polymerase amplification: Basics, applications and recent advances. Trends Analyt. Chem. 2018; 98: 19–35. https://doi.org/10.1016/j.trac.2017.10.015
  41. Wang H., La Russa M., Qi L.S. CRISPR/Cas9 in genome editing and beyond. Annu. Rev. Biochem. 2016; 85: 227. https://doi.org/10.1146/annurev-biochem-060815-014607
  42. Chen Y., Zhao R., Hu X., Wang X. The current status and future prospects of CRISPR-based detection of monkeypox virus: A review. Anal. Chim. Acta. 2025; 1336: 343295. https://doi.org/10.1016/j.aca.2024.343295
  43. Gootenberg J.S., Abudayyeh O.O., Lee J.W., Essletzbichler P., Dy A.J., Joung J., et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017; 356(6336): 438. https://doi.org/10.1126/science.aam9321
  44. Myhrvold C., Freije C.A., Gootenberg J.S., Abudayyeh O.O., Metsky H.C., Durbin A.F., et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 2018; 360(6387): 444–8. https://doi.org/10.1126/science.aas8836
  45. Srivastava S., Upadhyay D.J., Srivastava A. Next-generation molecular diagnostics development by CRISPR/Cas tool: rapid detection and surveillance of viral disease outbreaks. Front. Mol. Biosci. 2020; 7: 582499. https://doi.org/10.3389/fmolb.2020.582499
  46. Shi P., Wu X. Programmable RNA targeting with CRISPR-Cas13. RNA Biol. 2024; 21(1): 1–9. https://doi.org/10.1080/15476286.2024.2351657
  47. Calvert A.E., Biggerstaff B.J., Tanner N.A., Lauterbach M., Lanciotti R.S. Rapid colorimetric detection of Zika virus from serum and urine specimens by reverse transcription loop-mediated isothermal amplification (RT-LAMP). PLoS One. 2017; 12(9): e0185340. https://doi.org/10.1371/journal.pone.0185340
  48. Hang X.M., Liu P.F., Tian S., Wang H.Y., Zhao K.R., Wang L. Rapid and sensitive detection of Ebola RNA in an unamplified sample based on CRISPR-Cas13a and DNA roller machine. Biosens. Bioelectron. 2022; 211: 114393. https://doi.org/10.1016/j.bios.2022.114393
  49. Niu M., Dong Z., Yu L., Dong X., An J., Han Y., et al. Anti-RNA virus crRNA targets efficient screening platform based on bioinformatics and CRISPR detection. Mol. Ther. Nucleic Acids. 2025; 36(3): 102619. https://doi.org/10.1016/j.omtn.2025.102619
  50. Saju A.F., Mukundan A., Divyashree M., Chandrashekhar R., Mahadev Rao A. RNA diagnostics and therapeutics: a comprehensive review. RNA Biol. 2025; 22(1): 1–11. https://doi.org/10.1080/15476286.2024.2449277
  51. Cherkaoui D., Huang D., Miller B.S., Turbe V., McKendry R.A. Harnessing recombinase polymerase amplification for rapid multi-gene detection of SARS-CoV-2 in resource-limited settings. Biosens. Bioelectron. 2021; 189: 113328. https://doi.org/10.1016/j.bios.2021.113328
  52. Ramadan N.K., Gaber N., Ali N.M., Amer O.S.O., Soliman H. SHERLOCK, a novel CRISPR-Cas13a-based assay for detection of infectious bursal disease virus. J. Virol. Methods. 2025; 337: 115185. https://doi.org/10.1016/j.jviromet.2025.115185
  53. Chen J.S., Ma E., Harrington L.B., Da Costa M., Tian X., Palefsky J.M., et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018; 360(6387): 436. https://doi.org/10.1126/science.aar6245
  54. Li L., Li S., Wu N., Wu J., Wang G., Zhao G., et al. HOLMESv2: A CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth. Biol. 2019; 8(10): 2228–37. https://doi.org/10.1021/acssynbio.9b00209
  55. Zhuang S., Hu T., Zhou H., He S., Li J., Zhang Y., et al. CRISPR-HOLMES-based NAD(+) detection. Front. Bioeng. Biotechnol. 2024; 12: 1355640. https://doi.org/10.3389/fbioe.2024.1355640
  56. Yang D., Shi Y., Tang Y., Yin H., Guo Y., Wen S., et al. Effect of HPV infection on the occurrence and development of laryngeal cancer: a review. J. Cancer. 2019; 10(19): 4455–62. https://doi.org/10.7150/jca.34016
  57. Yin L., Zhao Z., Wang C., Zhou C., Wu X., Gao B., et al. Development and evaluation of a CRISPR/Cas12a-based diagnostic test for rapid detection and genotyping of HR-HPV in clinical specimens. Microbiol. Spectr. 2025; 13(1): e0225324. https://doi.org/10.1128/spectrum.02253-24
  58. Wu X., Chan C., Springs S.L., Lee Y.H., Lu T.K., Yu H. A warm-start digital CRISPR/Cas-based method for the quantitative detection of nucleic acids. Anal. Chim. Acta. 2022; 1196: 339494. https://doi.org/10.1016/j.aca.2022.339494
  59. Yin X., Luo H., Zhou H., Zhang Z., Lan Y., Feng Z., et al. A rapid isothermal CRISPR-Cas13a diagnostic test for genital herpes simplex virus infection. iScience. 2024; 27(1): 108581. https://doi.org/10.1016/j.isci.2023.108581
  60. Huang M., Chen Y., Zheng L., Yao Y.F. Highly sensitive and naked-eye detection of herpes simplex virus type 1 using LAMP-CRISPR/Cas12 diagnostic technology and gold nanoparticles. Heliyon. 2023; 9(11): e22146. https://doi.org/10.1016/j.heliyon.2023.e22146
  61. FDA Approves first gene therapies to treat patients with sickle cell disease. Available at: https://fda.gov/news-events/press-announcements/fda-approves-first-gene-therapies-treat-patients-sickle-cell-disease
  62. Bellizzi A., Cakir S., Donadoni M., Sariyer R., Liao S., Liu H., et al. Suppression of HSV-1 infection and viral reactivation by CRISPR-Cas9 gene editing in 2D and 3D culture models. Mol. Ther. Nucleic Acids. 2024; 35(3): 102282. https://doi.org/10.1016/j.omtn.2024.102282
  63. Katson M., Gorenshtein A., Pepys J., Mina Y., Shelly S. Mortality and prognosis in herpes simplex Virus-1 encephalitis long-term follow up study. J. Neurol. Sci. 2025; 468: 123330. https://doi.org/10.1016/j.jns.2024.123330
  64. Ying M., Wang H., Liu T., Han Z., Lin K., Shi Q., et al. CLEAR strategy inhibited HSV proliferation using viral vectors delivered CRISPR-Cas9. Pathogens. 2023; 12(6): 814. https://doi.org/10.3390/pathogens12060814
  65. McCormick I., James C., Welton N.J., Mayaud P., Turner K.M.E., Gottlieb S.L., et al. Incidence of herpes simplex virus keratitis and other ocular disease: global review and estimates. Ophthalmic Epidemiol. 2022; 29(4): 353–62. https://doi.org/10.1080/09286586.2021.1962919
  66. Yin D., Ling S., Wang D., Dai Y., Jiang H., Zhou X., et al. Targeting herpes simplex virus with CRISPR-Cas9 cures herpetic stromal keratitis in mice. Nat. Biotechnol. 2021; 39(5): 567–77. https://doi.org/10.1038/s41587-020-00781-8
  67. Amrani N., Luk K., Singh P., Shipley M., Isik M., Donadoni M., et al. CRISPR-Cas9-mediated genome editing delivered by a single AAV9 vector inhibits HSV-1 reactivation in a latent rabbit keratitis model. Mol. Ther. Methods Clin. Dev. 2024; 32(3): 101303. https://doi.org/10.1016/j.omtm.2024.101303
  68. Dutton A.J., Turnbaugh E.M., Patel C.D., Garland C.R., Taylor S.A., Alers-Velazquez R., et al. Asymptomatic neonatal herpes simplex virus infection in mice leads to persistent CNS infection and long-term cognitive impairment. PLoS Pathog. 2025; 21(2): e1012935. https://doi.org/10.1371/journal.ppat.1012935
  69. Wei A., Yin D., Zhai Z., Ling S., Le H., Tian L., et al. In vivo CRISPR gene editing in patients with herpetic stromal keratitis. Mol. Ther. 2023; 31(11): 3163–75. https://doi.org/10.1016/j.ymthe.2023.08.021
  70. ClinicalTrials.gov. A Study of the Safety, Tolerability and Prelinminary Efficacy of BD111 in Herpes Simplex Virus Type I Stromal Keratitis; 2025. Available at: https://clinicaltrials.gov/study/NCT06474416

Supplementary files

Supplementary Files
Action
1. JATS XML

Copyright (c) 2025 Demidova N.A., Klimova R.R., Kushch A.A., Karpov D.S.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Согласие на обработку персональных данных

 

Используя сайт https://journals.rcsi.science, я (далее – «Пользователь» или «Субъект персональных данных») даю согласие на обработку персональных данных на этом сайте (текст Согласия) и на обработку персональных данных с помощью сервиса «Яндекс.Метрика» (текст Согласия).