Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03) Krishnan Nair Balakrishnan, Ashwaq Ahmed Abdullah, Jamilu Abubakar Bala, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-44829/v2 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 27 Oct, 2020 Read the published version in Virology Journal → Version 2 posted 4 You are reading this latest preprint version Show more versions Abstract Background : Cytomegalovirus (CMV) is an opportunistic pathogen that causes severe complications in congenitally infected newborns and non-immunocompetent individuals. Developing an effective vaccine is a major public health priority and current drugs are fronting resistance and side effects on recipients. In the present study, with the aim of exploring new strategies to counteract CMV replication, several anti-CMV siRNAs targeting IE2 and DNA polymerase gene regions were characterized and used as in combinations for antiviral therapy. Methods : The rat embryo fibroblast (REF) cells were transfected with multi siRNA before infecting with CMV strain ALL-03. Viral growth inhibition was measured by tissue culture infectious dose (TCID50), cytopathic effect (CPE) and droplet digital PCR (ddPCR) while IE2 and DNA polymerase gene knockdown was determined by real-time PCR. Ganciclovir was deployed as a control to benchmark the efficacy of antiviral activities of respective individual siRNAs. Results: There was no significant cytotoxicity encountered for all the combinations of siRNAs on REF cells analyzed by MTT colorimetric assay (P>0.05). Cytopathic effects (CPE) in cells infected by RCMV ALL-03 had developed significantly less and at much slower rate compared to control group. The expression of targeted genes was downregulated successfully resulted in significant reduction (P<0.05) of viral mRNA and DNA copies (dpb+dpc: 79%, 68%; dpb+ie2b: 68%, 60%; dpb+dpc+ie2b: 48%, 42%). Flow cytometry analysis showed a greater percentage of viable and early apoptosis of combined siRNAs-treated cells compared to control group. Notably, the siRNAs targeting gene regions were sequenced and mutations were not encountered, thereby avoiding the formation of mutant with potential resistant viruses. Conclusions : In conclusion. The study demonstrated a tremendous promise of innovative approach with the deployment of combined siRNAs targeting at several genes simultaneously with the aim to control CMV replication in host cells. Pathology Applied & Industrial Microbiology Cytomegalovirus combinations small interfering RNA replication gene expression Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Full Text Supplementary Files Supplementaryfile.docx Cite Share Download PDF Status: Published Journal Publication published 27 Oct, 2020 Read the published version in Virology Journal → Version 2 posted Editorial decision: Accept 15 Oct, 2020 Editor assigned by journal 06 Oct, 2020 Submission checks completed at journal 05 Oct, 2020 Editor invited by journal 05 Oct, 2020 You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-44829","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research","associatedPublications":[],"authors":[{"id":3366707,"identity":"831394d3-3106-4af0-864a-461ae1299dcf","order_by":0,"name":"Krishnan Nair Balakrishnan","email":"","orcid":"","institution":"Universiti Putra Malaysia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Krishnan","middleName":"Nair","lastName":"Balakrishnan","suffix":""},{"id":3366708,"identity":"2a6eb4c4-7090-4b0c-82e8-17bad8505522","order_by":1,"name":"Ashwaq Ahmed Abdullah","email":"","orcid":"","institution":"Taiz University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ashwaq","middleName":"Ahmed","lastName":"Abdullah","suffix":""},{"id":3366709,"identity":"92fcb094-11ab-4b17-8c30-3610d5e00ce0","order_by":2,"name":"Jamilu Abubakar Bala","email":"","orcid":"","institution":"Bayero University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jamilu","middleName":"Abubakar","lastName":"Bala","suffix":""},{"id":3366710,"identity":"895e414e-d53c-4d22-a7aa-c5ad680da8a1","order_by":3,"name":"Faez Firdaus Abdullah Jesse","email":"","orcid":"","institution":"Universiti Putra Malaysia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Faez","middleName":"Firdaus Abdullah","lastName":"Jesse","suffix":""},{"id":3366711,"identity":"0b328edb-86fd-4715-851b-932c789f9f24","order_by":4,"name":"Che Azurahanim Che Abdullah","email":"","orcid":"","institution":"Universiti Putra Malaysia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Che","middleName":"Azurahanim Che","lastName":"Abdullah","suffix":""},{"id":3366712,"identity":"1ea73aa5-8fd8-4c68-9cc1-6878465126ff","order_by":5,"name":"Mustapha Mohamed Noordin","email":"","orcid":"","institution":"Universiti Putra Malaysia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Mustapha","middleName":"Mohamed","lastName":"Noordin","suffix":""},{"id":3366713,"identity":"f7a75f45-4da2-4285-becc-2c5b48bd4541","order_by":6,"name":"Mohd Lila Mohd Azmi","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAArklEQVRIiWNgGAWjYJCCAx8gtAHxWg7OIFkLMw9JWvj7Tycetm27E83A3rxNgjHnMGEtEgfObjic2/Yst4HnWJkE4zYitDAc7AVpOZzbIJFjRpwW+cO8Gw5bgrTIvyFSi8ExoBZGsC08RGoxPMO74WDPuWe5bTxpxRaJ29IJa5E7f3bzhx9ld3L72Q9vvPFxmzVhLVBwgIENRCUwNJOgBQrqiNYyCkbBKBgFIwcAALxCP2VTiiSCAAAAAElFTkSuQmCC","orcid":"","institution":"Universiti Putra Malaysia","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Mohd","middleName":"Lila Mohd","lastName":"Azmi","suffix":""}],"badges":[],"createdAt":"2020-07-17 10:49:46","currentVersionCode":2,"declarations":"","doi":"10.21203/rs.3.rs-44829/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-44829/v2","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12985-020-01436-5","type":"published","date":"2020-10-27T15:03:01+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":3073885,"identity":"5060d9f2-1434-49d9-826d-b8f18b294227","added_by":"auto","created_at":"2020-10-20 01:27:01","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":24609,"visible":true,"origin":"","legend":"Results of a TCID50 assay to illustrate the effect of combinations siRNA on the yield of RCMV ALL-03 progeny virus in REF cells. The REF cells were transfected with combinations siRNAs at 300pmol concentration, negative control siRNA and positive control GCV. At day 10 and 18 p.i, the plates were removed from incubator to calculate the TCID50 and the data represent the mean ± SD of 2 independent experiments. ","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/65cde917008fedadbd58bed8.png"},{"id":3073887,"identity":"486dbd89-defe-4ff5-a158-3bef6d1b2fda","added_by":"auto","created_at":"2020-10-20 01:27:02","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":44131,"visible":true,"origin":"","legend":"Results of RCMV ALL-03 absolute viral load quantification by droplet digital PCR. (A) The RCMV ALL-03 viral load (DNA copies/µl) in all the treatment groups (P\u003c0.0001). (B) The percentage of RCMV ALL-03 DNA copies reduction compared to untreated control group.","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/eb4428dda9ca4c40f950ef85.png"},{"id":3073888,"identity":"014146c1-a71b-44b9-923c-fe0c01d221fd","added_by":"auto","created_at":"2020-10-20 01:27:02","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1651772,"visible":true,"origin":"","legend":"REF cells were transfected with dpb+dpc (A) and dpb+ie2b (B) combination siRNAs followed by RCMV ALL-03 infection. The virus induces specific CPE characterized by rounding of the cells, shrinkage, ballooning and destruction and detachment of cell layers. The cells were visualized at day 14 using an inverted microscope at 10x magnification. \n\n","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/905bd2fa7129e5ff92259dc3.png"},{"id":3073889,"identity":"fab14f71-eff1-41b9-a34c-3c12d1b0f451","added_by":"auto","created_at":"2020-10-20 01:27:02","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1552673,"visible":true,"origin":"","legend":"REF cells were transfected with dpc+ie2b (A) and dpb+dpc+ie2b (B) combination siRNAs followed by RCMV ALL-03 infection. The virus induces specific CPE characterized by rounding of the cells, shrinkage, ballooning and destruction and detachment of cell layers. The cells were visualized at day 14 using an inverted microscope at 10x magnification. \n\n","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/ffca75722440cc125fbd2b23.png"},{"id":3073890,"identity":"6aeed845-18fb-436c-bd85-e5699a353ac4","added_by":"auto","created_at":"2020-10-20 01:27:02","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":2453025,"visible":true,"origin":"","legend":" REF cells were transfected with GCV (A) and negative control siRNA (B) treated followed by RCMV ALL-03 infection. The virus induces specific CPE characterized by rounding of the cells, shrinkage, ballooning and destruction and detachment of cell layers. The cells were visualized at day 14 using an inverted microscope at 10x magnification. \n\n","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/9d316158fd4f228dd6e5f4c4.png"},{"id":3073891,"identity":"26e991d4-7e07-4b06-aa33-d4d6cc452f1f","added_by":"auto","created_at":"2020-10-20 01:27:03","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":2604639,"visible":true,"origin":"","legend":"REF cells were transfected with untreated (A) and uninfected (B) followed by RCMV ALL-03 infection. The virus induces specific CPE characterized by rounding of the cells, shrinkage, ballooning and destruction and detachment of cell layers. The cells were visualized at day 14 using an inverted microscope at 10x magnification. \n\n","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/5f90f8445e62ca8c590f2a29.png"},{"id":3073892,"identity":"77fee0d1-61e9-4887-954c-9dd057938771","added_by":"auto","created_at":"2020-10-20 01:27:03","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":56640,"visible":true,"origin":"","legend":"(A) Quantification of mRNA expression levels of different treatment groups. (B) The percentage of knockdown efficiency among siRNA treated and non-treated groups. The data shown are representative of three independent experiments at p\u003c0.05.","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/494da13a55507189d56f3af0.png"},{"id":3073893,"identity":"b12bda89-6c1b-4bf5-99e3-d49f7936f6ba","added_by":"auto","created_at":"2020-10-20 01:27:03","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":591161,"visible":true,"origin":"","legend":"Alignment of DNA sequences from combiantion siRNAs treated group with stock virus for mutation identification. The siRNAs treated RCMV ALL-03 DNA was extracted and subjected for Sanger sequencing. The obtained results were aligned using online clustal omega software. The synthesized siRNA sequences was highlighted in blue. A: dpb+dpc, B: dpb+ie2b, C: dpc+ie2b, D: dpb+dpc+ie2b \n\n","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/d8270d071be62bd3d48e8f48.png"},{"id":13604463,"identity":"429d4271-d42d-42f8-9fc3-de950da1b57c","added_by":"auto","created_at":"2021-09-17 05:59:57","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1490502,"visible":true,"origin":"","legend":"","description":"","filename":"Revisedmanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2_covered.pdf"},{"id":13544687,"identity":"7ce58083-3a24-4c3e-b4e9-36a98c629a56","added_by":"auto","created_at":"2021-09-17 02:03:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1177067,"visible":true,"origin":"","legend":"","description":"","filename":"Revisedmanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2_covered.pdf"},{"id":3073898,"identity":"77c5a371-e1c2-4176-9ff7-d39413287b89","added_by":"auto","created_at":"2020-10-20 01:29:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1579549,"visible":true,"origin":"","legend":"","description":"","filename":"Revisedmanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2_stamped.pdf"},{"id":3073897,"identity":"a1726d66-939b-4437-8065-6f953b53b14d","added_by":"auto","created_at":"2020-10-20 01:29:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1579549,"visible":true,"origin":"","legend":"","description":"","filename":"Revisedmanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2_stamped.pdf"},{"id":3073896,"identity":"0d4bdbff-bfef-4720-a0e9-74e2db9c7ca7","added_by":"auto","created_at":"2020-10-20 01:29:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1579549,"visible":true,"origin":"","legend":"","description":"","filename":"Revisedmanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2_stamped.pdf"},{"id":3073886,"identity":"a470def1-7622-4ca0-93ec-eaf7b3aa65ac","added_by":"auto","created_at":"2020-10-20 01:27:02","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":7733394,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementaryfile.docx","url":"https://assets-eu.researchsquare.com/files/rs-44829/v2/fe86424e9b79d38c1c9e5ad9.docx"}],"financialInterests":"","formattedTitle":"Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03)","fulltext":[{"header":"Full Text","content":"\u003cp\u003eThis preprint is available for \u003ca href='/article/rs-44829/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e.\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"
[email protected]","identity":"virology-journal","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"virj","sideBox":"Learn more about [Virology Journal](http://virologyj.biomedcentral.com/)","snPcode":"12985","submissionUrl":"https://submission.nature.com/new-submission/12985/3","title":"Virology Journal","twitterHandle":"@VirologyJ","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Cytomegalovirus, combinations, small interfering RNA, replication, gene expression","lastPublishedDoi":"10.21203/rs.3.rs-44829/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-44829/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e: Cytomegalovirus (CMV) is an opportunistic pathogen that causes severe complications in congenitally infected newborns and non-immunocompetent individuals. Developing an effective vaccine is a major public health priority and current drugs are fronting resistance and side effects on recipients. In the present study, with the aim of exploring new strategies to counteract CMV replication, several anti-CMV siRNAs targeting IE2 and DNA polymerase gene regions were characterized and used as in combinations for antiviral therapy. \u003c/p\u003e\u003cp\u003e\u003cstrong\u003eMethods\u003c/strong\u003e: The rat embryo fibroblast (REF) cells were transfected with multi siRNA before infecting with CMV strain ALL-03. Viral growth inhibition was measured by tissue culture infectious dose (TCID50), cytopathic effect (CPE) and droplet digital PCR (ddPCR) while IE2 and DNA polymerase gene knockdown was determined by real-time PCR. Ganciclovir was deployed as a control to benchmark the efficacy of antiviral activities of respective individual siRNAs.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults:\u003c/strong\u003e There was no significant cytotoxicity encountered for all the combinations of siRNAs on REF cells analyzed by MTT colorimetric assay (P\u0026gt;0.05). Cytopathic effects (CPE) in cells infected by RCMV ALL-03 had developed significantly less and at much slower rate compared to control group. The expression of targeted genes was downregulated successfully resulted in significant reduction (P\u0026lt;0.05) of viral mRNA and DNA copies (dpb+dpc: 79%, 68%; dpb+ie2b: 68%, 60%; dpb+dpc+ie2b: 48%, 42%). Flow cytometry analysis showed a greater percentage of viable and early apoptosis of combined siRNAs-treated cells compared to control group. Notably, the siRNAs targeting gene regions were sequenced and mutations were not encountered, thereby avoiding the formation of mutant with potential resistant viruses. \u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e: In conclusion. The study demonstrated a tremendous promise of\u0026nbsp;innovative approach with the deployment of combined siRNAs targeting at several genes simultaneously with the aim to control CMV replication in host cells.\u003c/p\u003e","manuscriptTitle":"Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03)","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2020-10-20 01:26:59","doi":"10.21203/rs.3.rs-44829/v2","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Accept","date":"2020-10-15T12:00:00+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2020-10-06T12:00:00+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2020-10-05T12:00:00+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2020-10-05T12:00:00+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"
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