{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T15:48:50Z","timestamp":1785944930248,"version":"3.56.0"},"reference-count":23,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2020,12,13]],"date-time":"2020-12-13T00:00:00Z","timestamp":1607817600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004012","name":"Jane ja Aatos Erkon S\u00e4\u00e4ti\u00f6","doi-asserted-by":"publisher","award":["170046"],"award-info":[{"award-number":["170046"]}],"id":[{"id":"10.13039\/501100004012","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["331627"],"award-info":[{"award-number":["331627"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Acyclovir is the drug of choice for the treatment of herpes simplex virus (HSV) infections. Acyclovir-resistant HSV strains may emerge, especially during long-term drug use, and subsequently cause difficult-to-treat exacerbations. Previously, we set up a novel treatment approach, based on enzymatically synthesized pools of siRNAs, or siRNA swarms. These swarms can cover kilobases-long target sequences, reducing the likelihood of resistance to treatment. Swarms targeting the UL29 essential gene of HSV-1 have demonstrated high efficacy against HSV-1 in vitro and in vivo. Here, we assessed the antiviral potential of a UL29 siRNA swarm against circulating strains of HSV-1, in comparison with acyclovir. All circulating strains were sensitive to both antivirals, with the half-maximal inhibitory concentrations (IC50) in the range of 350\u20131911 nM for acyclovir and 0.5\u20133 nM for the UL29 siRNA swarm. Additionally, we showed that an acyclovir-resistant HSV-1, devoid of thymidine kinase, is highly sensitive to UL29 siRNA treatment (IC50 1.0 nM; Imax 97%). Moreover, the detected minor variations in the RNAi target of the HSV strains had no effect on the potency or efficacy of UL29 siRNA swarm treatment. Our findings support the development of siRNA swarms for the treatment of HSV-1 infections, in order to circumvent any potential acyclovir resistance.<\/jats:p>","DOI":"10.3390\/v12121434","type":"journal-article","created":{"date-parts":[[2020,12,13]],"date-time":"2020-12-13T23:39:36Z","timestamp":1607902776000},"page":"1434","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Herpes Simplex Virus Type 1 Clinical Isolates Respond to UL29-Targeted siRNA Swarm Treatment Independent of Their Acyclovir Sensitivity"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7832-2021","authenticated-orcid":false,"given":"Kiira","family":"Kalke","sequence":"first","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenni","family":"Lehtinen","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jelena","family":"Gnjatovic","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0537-7651","authenticated-orcid":false,"given":"Liisa M.","family":"Lund","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie C.","family":"Nyman","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henrik","family":"Paavilainen","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9144-5296","authenticated-orcid":false,"given":"Julius","family":"Orpana","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuomas","family":"Lasanen","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fanny","family":"Frejborg","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alesia A.","family":"Levanova","sequence":"additional","affiliation":[{"name":"Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tytti","family":"Vuorinen","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"},{"name":"Clinical Microbiology, Turku University Hospital, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4775-3670","authenticated-orcid":false,"given":"Minna M.","family":"Poranen","sequence":"additional","affiliation":[{"name":"Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2867-7844","authenticated-orcid":false,"given":"Veijo","family":"Hukkanen","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine, University of Turku, 20520 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5716","DOI":"10.1073\/pnas.74.12.5716","article-title":"Selectivity of action of an antiherpetic agent, 9-(2-hydroxyethoxymethyl) guanine","volume":"74","author":"Elion","year":"1977","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/0002-9343(82)90055-9","article-title":"Mechanism of action and selectivity of acyclovir","volume":"73","author":"Elion","year":"1982","journal-title":"Am. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1086\/590668","article-title":"Acyclovir-resistant corneal HSV-1 isolates from patients with herpetic keratitis","volume":"198","author":"Duan","year":"2008","journal-title":"J. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1086\/606028","article-title":"Acyclovir susceptibility and genetic characteristics of sequential herpes simplex virus type 1 corneal isolates from patients with recurrent herpetic keratitis","volume":"200","author":"Duan","year":"2009","journal-title":"J. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1093\/infdis\/jit350","article-title":"Acyclovir prophylaxis predisposes to antiviral-resistant recurrent herpetic keratitis","volume":"208","author":"Osterhaus","year":"2013","journal-title":"J. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1093\/infdis\/jit437","article-title":"Common and new acyclovir resistant herpes simplex virus-1 mutants causing bilateral recurrent herpetic keratitis in an immunocompetent patient","volume":"209","author":"Pan","year":"2014","journal-title":"J. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4938","DOI":"10.1128\/AAC.00977-15","article-title":"Sequence analysis of herpes simplex virus 1 thymidine kinase and DNA polymerase genes from over 300 clinical isolates from 1973 to 2014 finds novel mutations that may be relevant for development of antiviral resistance","volume":"59","author":"Schmidt","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/0166-3542(95)00027-J","article-title":"Molecular mechanisms of antiviral resistance","volume":"26","author":"Kimberlin","year":"1995","journal-title":"Antiviral. Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e01824-18","DOI":"10.1128\/JVI.01824-18","article-title":"Comparison of herpes simplex virus 1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection","volume":"93","author":"Bowen","year":"2019","journal-title":"J. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.3389\/fmicb.2018.02151","article-title":"RNA Interference as a prospective tool for the control of human viral Infections","volume":"9","author":"Levanova","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2468","DOI":"10.1099\/vir.0.011338-0","article-title":"Inhibition of coxsackievirus B3 and related enteroviruses by antiviral short interfering RNA pools produced using phi6 RNA-dependent RNA polymerase","volume":"90","author":"Vuorinen","year":"2009","journal-title":"J. Gen. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nbt1051","article-title":"Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy","volume":"23","author":"Kim","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Romanovskaya, A., Paavilainen, H., Nygardas, M., Bamford, D.H., Hukkanen, V., and Poranen, M.M. (2012). Enzymatically produced pools of canonical and Dicer-substrate siRNA molecules display comparable gene silencing and antiviral activities against herpes simplex virus. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0051019"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e01916-18","DOI":"10.1128\/JVI.01916-18","article-title":"Efficient inhibition of avian and seasonal influenza A viruses by a virus-specific Dicer-substrate small interfering RNA swarm in human monocyte-derived macrophages and dendritic cells","volume":"93","author":"Jiang","year":"2019","journal-title":"J. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"104916","DOI":"10.1016\/j.antiviral.2020.104916","article-title":"Enzymatically synthesized 2\u2019-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity","volume":"182","author":"Levanova","year":"2020","journal-title":"Antiviral. Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"631","DOI":"10.3851\/IMP3153","article-title":"Topical treatment of herpes simplex virus infection with enzymatically created siRNA swarm","volume":"22","author":"Paavilainen","year":"2017","journal-title":"Antivir. Ther."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1177\/1753425914537921","article-title":"Innate responses to small interfering RNA pools inhibiting herpes simplex virus infection in astrocytoid and epithelial cells","volume":"21","author":"Paavilainen","year":"2015","journal-title":"Innate. Immun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1002\/jmv.24578","article-title":"Inhibition of clinical pathogenic herpes simplex virus 1 strains with enzymatically created siRNA pools","volume":"88","author":"Paavilainen","year":"2016","journal-title":"J. Med. Virol."},{"key":"ref_19","first-page":"1823","article-title":"Herpes Simplex Viruses","volume":"Volume 2","author":"Knipe","year":"2013","journal-title":"Fields Virology"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nature04263","article-title":"An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection","volume":"439","author":"Palliser","year":"2006","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/0092-8674(81)90346-9","article-title":"Regulation of a genes of herpes simplex virus: Expression of chimeric genes produced by fusion of thymidine kinase with a gene promoters","volume":"24","author":"Post","year":"1981","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1128\/jcm.26.10.2013-2017.1988","article-title":"Herpes simplex virus detection by macroscopic reading after overnight incubation and immunoperoxidase staining","volume":"26","author":"Ziegler","year":"1988","journal-title":"J. Clin. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.jcv.2014.08.015","article-title":"Simultaneous titration and phenotypic antiviral drug susceptibility testing for herpes simplex virus 1 and 2","volume":"61","author":"Tardif","year":"2014","journal-title":"J. Clin. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/12\/1434\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:44:36Z","timestamp":1760179476000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/12\/1434"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,13]]},"references-count":23,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["v12121434"],"URL":"https:\/\/doi.org\/10.3390\/v12121434","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,13]]}}}