{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T15:31:00Z","timestamp":1793633460203,"version":"4.5.1"},"reference-count":94,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre Poland","doi-asserted-by":"publisher","award":["2020\/39\/B\/NZ1\/03054"],"award-info":[{"award-number":["2020\/39\/B\/NZ1\/03054"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004281","name":"National Science Centre Poland","doi-asserted-by":"publisher","award":["2022\/45\/B\/ST4\/03586"],"award-info":[{"award-number":["2022\/45\/B\/ST4\/03586"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004281","name":"National Science Centre Poland","doi-asserted-by":"publisher","award":["2021\/41\/B\/NZ1\/03819"],"award-info":[{"award-number":["2021\/41\/B\/NZ1\/03819"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular Therapy Nucleic Acids"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1016\/j.omtn.2026.103098","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T23:53:56Z","timestamp":1789516436000},"page":"103098","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Bridging the antiviral gap: A BAC-based non-infectious SARS-CoV-2 replicon reveals potent antisense gapmers"],"prefix":"10.1016","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9862-4406","authenticated-orcid":false,"given":"Agnieszka","family":"Ruszkowska","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0504-6086","authenticated-orcid":false,"given":"Agnieszka","family":"Baliga-Gil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1261-3878","authenticated-orcid":false,"given":"Julita","family":"Piasecka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Ciechanowska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7644-0016","authenticated-orcid":false,"given":"Ryszard","family":"Kierzek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5563-003X","authenticated-orcid":false,"given":"Elzbieta","family":"Kierzek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.omtn.2026.103098_bib1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2","volume":"19","author":"V'Kovski","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.omtn.2026.103098_bib2","doi-asserted-by":"crossref","first-page":"3017","DOI":"10.1002\/jmv.27738","article-title":"Reverse genetics systems for SARS-CoV-2","volume":"94","author":"Wang","year":"2022","journal-title":"J. Med. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib3","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01342-25","article-title":"Increased pathogenicity and transmission of SARS-CoV-2 Omicron XBB.1.9 subvariants, including HK.3 and EG.5.1, relative to BA.2","volume":"99","author":"Jin","year":"2025","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib5","doi-asserted-by":"crossref","first-page":"10900","DOI":"10.1128\/JVI.00385-06","article-title":"Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis","volume":"80","author":"Almaz\u00e1n","year":"2006","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib6","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00687-21","article-title":"Construction of a Noninfectious SARS-CoV-2 Replicon for Antiviral-Drug Testing and Gene Function Studies","volume":"95","author":"Nguyen","year":"2021","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib7","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02168-20","article-title":"Rescue of SARS-CoV-2 from a Single Bacterial Artificial Chromosome","volume":"11","author":"Ye","year":"2020","journal-title":"mBio"},{"key":"10.1016\/j.omtn.2026.103098_bib8","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2025866118","article-title":"Generation of SARS-CoV-2 reporter replicon for high-throughput antiviral screening and testing","volume":"118","author":"He","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.antiviral.2020.104974","article-title":"A bacterial artificial chromosome (BAC)-vectored noninfectious replicon of SARS-CoV-2","volume":"185","author":"Zhang","year":"2021","journal-title":"Antivir. Res."},{"key":"10.1016\/j.omtn.2026.103098_bib10","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3001091","article-title":"A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research","volume":"19","author":"Rihn","year":"2021","journal-title":"PLoS Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib11","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.virusres.2014.05.026","article-title":"Coronavirus reverse genetic systems: infectious clones and replicons","volume":"189","author":"Almaz\u00e1n","year":"2014","journal-title":"Virus Res."},{"key":"10.1016\/j.omtn.2026.103098_bib12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0032857","article-title":"Reverse genetics of SARS-related coronavirus using vaccinia virus-based recombination","volume":"7","author":"van den Worm","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.omtn.2026.103098_bib13","doi-asserted-by":"crossref","first-page":"12995","DOI":"10.1073\/pnas.1735582100","article-title":"Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus","volume":"100","author":"Yount","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib14","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1016\/j.chom.2020.04.004","article-title":"An Infectious cDNA Clone of SARS-CoV-2","volume":"27","author":"Xie","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.omtn.2026.103098_bib15","doi-asserted-by":"crossref","DOI":"10.1099\/jgv.0.001583","article-title":"SARS-CoV-2 replicon for high-throughput antiviral screening","volume":"102","author":"Zhang","year":"2021","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib16","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009439","article-title":"A novel cell culture system modeling the SARS-CoV-2 life cycle","volume":"17","author":"Ju","year":"2021","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.omtn.2026.103098_bib17","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/s41586-020-2294-9","article-title":"Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform","volume":"582","author":"Thi Nhu Thao","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.omtn.2026.103098_bib18","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1126\/science.abj8430","article-title":"Replication and single-cycle delivery of SARS-CoV-2 replicons","volume":"374","author":"Ricardo-Lax","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.omtn.2026.103098_bib19","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1007\/s12250-021-00369-9","article-title":"Construction of Non-infectious SARS-CoV-2 Replicons and Their Application in Drug Evaluation","volume":"36","author":"Wang","year":"2021","journal-title":"Virol. Sin."},{"key":"10.1016\/j.omtn.2026.103098_bib20","doi-asserted-by":"crossref","first-page":"3431","DOI":"10.1038\/s41467-021-23779-5","article-title":"A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses","volume":"12","author":"Amarilla","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.omtn.2026.103098_bib21","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109014","article-title":"Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction","volume":"35","author":"Torii","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.omtn.2026.103098_bib22","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02754-20","article-title":"Engineering a Reliable and Convenient SARS-CoV-2 Replicon System for Analysis of Viral RNA Synthesis and Screening of Antiviral Inhibitors","volume":"12","author":"Luo","year":"2021","journal-title":"mBio"},{"key":"10.1016\/j.omtn.2026.103098_bib23","doi-asserted-by":"crossref","DOI":"10.1016\/j.antiviral.2022.105268","article-title":"Establishment of a stable SARS-CoV-2 replicon system for application in high-throughput screening","volume":"199","author":"Tanaka","year":"2022","journal-title":"Antiviral Res."},{"key":"10.1016\/j.omtn.2026.103098_bib24","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1007\/s12250-021-00385-9","article-title":"A Convenient and Biosafe Replicon with Accessory Genes of SARS-CoV-2 and Its Potential Application in Antiviral Drug Discovery","volume":"36","author":"Jin","year":"2021","journal-title":"Virol. Sin."},{"key":"10.1016\/j.omtn.2026.103098_bib25","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.bbrc.2008.06.129","article-title":"Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function","volume":"374","author":"Wang","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.omtn.2026.103098_bib26","doi-asserted-by":"crossref","DOI":"10.1016\/j.mib.2024.102483","article-title":"Alpha- and betacoronavirus cis-acting RNA elements","volume":"79","author":"Madhugiri","year":"2024","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.omtn.2026.103098_bib27","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1093\/nar\/gkac1184","article-title":"Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function","volume":"51","author":"Pekarek","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib28","doi-asserted-by":"crossref","DOI":"10.1099\/jgv.0.002070","article-title":"Linking the function of cis-acting RNA elements to coronavirus replication using interactomes","volume":"106","author":"Yao","year":"2025","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib29","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1038\/s41467-022-28603-2","article-title":"Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells","volume":"13","author":"Lan","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.omtn.2026.103098_bib30","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1021\/jacsau.3c00641","article-title":"NMR Studies of Genomic RNA in 3' Untranslated Region Unveil Pseudoknot Structure that Initiates Viral RNA Replication in SARS-CoV-2","volume":"4","author":"Ohyama","year":"2024","journal-title":"JACS Au"},{"key":"10.1016\/j.omtn.2026.103098_bib31","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.3390\/ijms24021232","article-title":"Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors","volume":"24","author":"Szczesniak","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.omtn.2026.103098_bib32","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf503","article-title":"The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure","volume":"53","author":"Haddox","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib33","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.98102.3","article-title":"Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency","volume":"13","author":"Hensel","year":"2025","journal-title":"eLife"},{"key":"10.1016\/j.omtn.2026.103098_bib34","doi-asserted-by":"crossref","DOI":"10.1128\/mmbr.00057-21","article-title":"Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication","volume":"86","author":"Bassett","year":"2022","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.omtn.2026.103098_bib35","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.3390\/v13061115","article-title":"The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation","volume":"13","author":"Bai","year":"2021","journal-title":"Viruses"},{"key":"10.1016\/j.omtn.2026.103098_bib36","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2024.1450114","article-title":"M protein ectodomain-specific immunity restrains SARS-CoV-2 variants replication","volume":"15","author":"Tang","year":"2024","journal-title":"Front. Immunol."},{"key":"10.1016\/j.omtn.2026.103098_bib37","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1016\/j.jmb.2009.09.040","article-title":"Coronavirus N protein N-terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes","volume":"394","author":"Grossoehme","year":"2009","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib38","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1128\/JVI.02011-09","article-title":"Coronavirus nucleocapsid protein facilitates template switching and is required for efficient transcription","volume":"84","author":"Z\u00fa\u00f1iga","year":"2010","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib39","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.virol.2006.07.046","article-title":"Coronavirus nucleocapsid protein is an RNA chaperone","volume":"357","author":"Z\u00fa\u00f1iga","year":"2007","journal-title":"Virology"},{"key":"10.1016\/j.omtn.2026.103098_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2025.169312","article-title":"Chaperone Activity of SARS-CoV-2 Nucleocapsid Protein: RNA Annealing and Destabilization Mechanisms","volume":"437","author":"Zargarian","year":"2025","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib41","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbc.2024.107834","article-title":"Structural basis for the participation of the SARS-CoV-2 nucleocapsid protein in the template switch mechanism and genomic RNA reorganization","volume":"300","author":"Bezerra","year":"2024","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.omtn.2026.103098_bib42","doi-asserted-by":"crossref","first-page":"992","DOI":"10.2144\/97236bm04","article-title":"Complete nucleotide sequence of two generations of a bacterial artificial chromosome cloning vector","volume":"23","author":"Wang","year":"1997","journal-title":"Biotechniques"},{"key":"10.1016\/j.omtn.2026.103098_bib43","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1128\/JVI.01467-06","article-title":"A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo","volume":"81","author":"DeDiego","year":"2007","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib44","doi-asserted-by":"crossref","first-page":"25856","DOI":"10.1016\/S0021-9258(18)47325-5","article-title":"In vitro and in vivo comparison of hammerhead, hairpin, and hepatitis delta virus self-processing ribozyme cassettes","volume":"269","author":"Chowrira","year":"1994","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.omtn.2026.103098_bib45","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107940","article-title":"Remdesivir Inhibits SARS-CoV-2 in Human Lung Cells and Chimeric SARS-CoV Expressing the SARS-CoV-2 RNA Polymerase in Mice","volume":"32","author":"Pruijssers","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.omtn.2026.103098_bib46","doi-asserted-by":"crossref","DOI":"10.1016\/j.antiviral.2024.105946","article-title":"Targeting sgRNA N secondary structure as a way of inhibiting SARS-CoV-2 replication","volume":"228","author":"Baliga-Gil","year":"2024","journal-title":"Antiviral Res."},{"key":"10.1016\/j.omtn.2026.103098_bib47","doi-asserted-by":"crossref","first-page":"322","DOI":"10.3390\/v14020322","article-title":"Secondary Structure of Subgenomic RNA M of SARS-CoV-2","volume":"14","author":"Soszynska-Jozwiak","year":"2022","journal-title":"Viruses"},{"key":"10.1016\/j.omtn.2026.103098_bib48","doi-asserted-by":"crossref","first-page":"12436","DOI":"10.1093\/nar\/gkaa1053","article-title":"Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements","volume":"48","author":"Manfredonia","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib49","doi-asserted-by":"crossref","DOI":"10.3390\/v12121473","article-title":"The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region","volume":"12","author":"Zhao","year":"2020","journal-title":"Viruses"},{"key":"10.1016\/j.omtn.2026.103098_bib50","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.cbpa.2016.06.014","article-title":"Pseudouridine: the fifth RNA nucleotide with renewed interests","volume":"33","author":"Li","year":"2016","journal-title":"Curr. Opin. Chem. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib51","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1089\/nat.2022.0067","article-title":"Systematic Analysis of Chemical Modifications of Phosphorothioate Antisense Oligonucleotides that Modulate Their Innate Immune Response","volume":"33","author":"Pollak","year":"2023","journal-title":"Nucleic Acid Ther."},{"key":"10.1016\/j.omtn.2026.103098_bib52","doi-asserted-by":"crossref","first-page":"6082","DOI":"10.1093\/nar\/gkab451","article-title":"Sequence-dependent inhibition of cGAS and TLR9 DNA sensing by 2'-O-methyl gapmer oligonucleotides","volume":"49","author":"Valentin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib53","doi-asserted-by":"crossref","first-page":"8107","DOI":"10.1093\/nar\/gkac618","article-title":"Insights into innate immune activation via PS-ASO-protein-TLR9 interactions","volume":"50","author":"Pollak","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib54","doi-asserted-by":"crossref","DOI":"10.1016\/j.omtn.2023.102078","article-title":"Cooperative activation of human TLR9 and consequences for the clinical development of antisense and CpG oligodeoxynucleotides","volume":"34","author":"Hartmann","year":"2023","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"10.1016\/j.omtn.2026.103098_bib55","doi-asserted-by":"crossref","DOI":"10.1016\/j.omtn.2025.102612","article-title":"Antisense oligonucleotides targeting the SARS-CoV-2 nucleocapsid gene decrease viral titers in hamsters","volume":"36","author":"Fitzpatrick","year":"2025","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"10.1016\/j.omtn.2026.103098_bib56","doi-asserted-by":"crossref","first-page":"3670","DOI":"10.1128\/JVI.80.7.3670-3674.2006","article-title":"Recovery of a neurovirulent human coronavirus OC43 from an infectious cDNA clone","volume":"80","author":"St-Jean","year":"2006","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib57","doi-asserted-by":"crossref","first-page":"5516","DOI":"10.1073\/pnas.97.10.5516","article-title":"Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome","volume":"97","author":"Almaz\u00e1n","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib58","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01208-19","article-title":"Establishment of a Virulent Full-Length cDNA Clone for Type I Feline Coronavirus Strain C3663","volume":"93","author":"Terada","year":"2019","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib59","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00650-13","article-title":"Engineering a replication-competent, propagation-defective Middle East respiratory syndrome coronavirus as a vaccine candidate","volume":"4","author":"Almaz\u00e1n","year":"2013","journal-title":"mBio"},{"key":"10.1016\/j.omtn.2026.103098_bib60","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1007\/s12250-020-00341-z","article-title":"Development of A MERS-CoV Replicon Cell Line for Antiviral Screening","volume":"36","author":"Chen","year":"2021","journal-title":"Virol. Sin."},{"key":"10.1016\/j.omtn.2026.103098_bib61","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.virol.2019.08.006","article-title":"Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone","volume":"536","author":"Yang","year":"2019","journal-title":"Virology"},{"key":"10.1016\/j.omtn.2026.103098_bib62","doi-asserted-by":"crossref","first-page":"5193","DOI":"10.1016\/j.csbj.2022.08.044","article-title":"A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis","volume":"20","author":"Feng","year":"2022","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.omtn.2026.103098_bib63","doi-asserted-by":"crossref","first-page":"8794","DOI":"10.1073\/pnas.89.18.8794","article-title":"Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector","volume":"89","author":"Shizuya","year":"1992","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0022-2836(86)90459-6","article-title":"Structure and function of the F plasmid genes essential for partitioning","volume":"192","author":"Mori","year":"1986","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib65","doi-asserted-by":"crossref","DOI":"10.1101\/pdb.top097998","article-title":"Working with Bacterial Artificial Chromosomes (BACs) and Other High-Capacity Vectors","volume":"2020","author":"Heintz","year":"2020","journal-title":"Cold Spring Harb. Protoc."},{"key":"10.1016\/j.omtn.2026.103098_bib66","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1038\/s41598-021-82055-0","article-title":"A PCR amplicon-based SARS-CoV-2 replicon for antiviral evaluation","volume":"11","author":"Kotaki","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.omtn.2026.103098_bib67","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1016\/j.virs.2023.10.001","article-title":"Reverse genetics systems for SARS-CoV-2: Development and applications","volume":"38","author":"Cai","year":"2023","journal-title":"Virol. Sin."},{"key":"10.1016\/j.omtn.2026.103098_bib68","doi-asserted-by":"crossref","first-page":"708","DOI":"10.3390\/v16050708","article-title":"Development of a Cell Culture Model for Inducible SARS-CoV-2 Replication","volume":"16","author":"Wang","year":"2024","journal-title":"Viruses"},{"key":"10.1016\/j.omtn.2026.103098_bib69","doi-asserted-by":"crossref","DOI":"10.3390\/v17050597","article-title":"A Novel Toolkit of SARS-CoV-2 Sub-Genomic Replicons for Efficient Antiviral Screening","volume":"17","author":"Erdmann","year":"2025","journal-title":"Viruses"},{"key":"10.1016\/j.omtn.2026.103098_bib70","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1038\/s41467-025-59533-4","article-title":"SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform","volume":"16","author":"Kuroda","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.omtn.2026.103098_bib71","article-title":"Deletion of the Envelope gene attenuates SARS-CoV-2 infection by altered Spike localization and increased cell-to-cell transmission","author":"Fischer","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.omtn.2026.103098_bib72","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1128\/JVI.01690-07","article-title":"Genetic interactions between an essential 3' cis-acting RNA pseudoknot, replicase gene products, and the extreme 3' end of the mouse coronavirus genome","volume":"82","author":"Z\u00fcst","year":"2008","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib73","doi-asserted-by":"crossref","first-page":"8349","DOI":"10.1128\/JVI.73.10.8349-8355.1999","article-title":"A phylogenetically conserved hairpin-type 3' untranslated region pseudoknot functions in coronavirus RNA replication","volume":"73","author":"Williams","year":"1999","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib74","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1128\/JVI.78.2.669-682.2004","article-title":"Characterization of the RNA components of a putative molecular switch in the 3' untranslated region of the murine coronavirus genome","volume":"78","author":"Goebel","year":"2004","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib75","doi-asserted-by":"crossref","first-page":"7236","DOI":"10.1128\/jvi.70.10.7236-7240.1996","article-title":"The 3' untranslated region of coronavirus RNA is required for subgenomic mRNA transcription from a defective interfering RNA","volume":"70","author":"Lin","year":"1996","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib76","article-title":"Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes","volume":"6","author":"Jones","year":"2022","journal-title":"J. Struct. Biol. X"},{"key":"10.1016\/j.omtn.2026.103098_bib77","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/pro.3978","article-title":"The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions","volume":"30","author":"Oughtred","year":"2021","journal-title":"Protein Sci."},{"key":"10.1016\/j.omtn.2026.103098_bib78","doi-asserted-by":"crossref","DOI":"10.31083\/FBL27294","article-title":"Reviewing the Developing Significance of the Serine Protease PRSS23","volume":"30","author":"Schulten","year":"2025","journal-title":"Front. Biosci."},{"key":"10.1016\/j.omtn.2026.103098_bib79","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2320493121","article-title":"Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses","volume":"121","author":"Kretsch","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib80","doi-asserted-by":"crossref","first-page":"3419","DOI":"10.1093\/nar\/gkae144","article-title":"Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes","volume":"52","author":"de Moura","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib81","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/s42003-022-03647-8","article-title":"Identification of a guanine-specific pocket in the protein N of SARS-CoV-2","volume":"5","author":"Rafael Ciges-Tomas","year":"2022","journal-title":"Commun. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib82","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.02190-20","article-title":"The global and local distribution of RNA structure throughout the SARS-CoV-2 genome","volume":"95","author":"Tavares","year":"2021","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib83","doi-asserted-by":"crossref","first-page":"3385","DOI":"10.1038\/s41467-023-39091-3","article-title":"A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon","volume":"14","author":"Khan","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.omtn.2026.103098_bib84","doi-asserted-by":"crossref","first-page":"4503","DOI":"10.1038\/s41467-022-32216-0","article-title":"An intranasal ASO therapeutic targeting SARS-CoV-2","volume":"13","author":"Zhu","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.omtn.2026.103098_bib85","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2117198119","article-title":"Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral translation and Nsp1 evasion","volume":"119","author":"Vora","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib86","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00663-21","article-title":"Targeting the Conserved Stem Loop 2 Motif in the SARS-CoV-2 Genome","volume":"95","author":"Lulla","year":"2021","journal-title":"J. Virol."},{"key":"10.1016\/j.omtn.2026.103098_bib87","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/s41594-021-00653-y","article-title":"Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome","volume":"28","author":"Zhang","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib88","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2023051118","article-title":"Restriction of SARS-CoV-2 replication by targeting programmed -1 ribosomal frameshifting","volume":"118","author":"Sun","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.omtn.2026.103098_bib89","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2024.e33914","article-title":"Peptide nucleic acids (PNAs) control function of SARS-CoV-2 frameshifting stimulatory element trough PNA-RNA-PNA triplex formation","volume":"10","author":"Rahman","year":"2024","journal-title":"Heliyon"},{"key":"10.1016\/j.omtn.2026.103098_bib90","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.7150\/ijbs.59151","article-title":"Developing effective siRNAs to reduce the expression of key viral genes of COVID-19","volume":"17","author":"Wu","year":"2021","journal-title":"Int. J. Biol. Sci."},{"key":"10.1016\/j.omtn.2026.103098_bib91","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiolchem.2022.107687","article-title":"Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains","volume":"98","author":"Madanagopal","year":"2022","journal-title":"Comput. Biol. Chem."},{"key":"10.1016\/j.omtn.2026.103098_bib92","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/978-1-59745-196-3_6","article-title":"The Polymerase Incomplete Primer Extension (PIPE) method applied to high-throughput cloning and site-directed mutagenesis","volume":"498","author":"Klock","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.omtn.2026.103098_bib93","doi-asserted-by":"crossref","first-page":"14719","DOI":"10.1021\/bi9809425","article-title":"Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs","volume":"37","author":"Xia","year":"1998","journal-title":"Biochemistry"},{"key":"10.1016\/j.omtn.2026.103098_bib94","doi-asserted-by":"crossref","first-page":"4472","DOI":"10.1093\/nar\/gkg633","article-title":"The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines","volume":"31","author":"Kierzek","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.omtn.2026.103098_bib95","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1038\/s41467-022-28817-4","article-title":"Secondary structure prediction for RNA sequences including N(6)-methyladenosine","volume":"13","author":"Kierzek","year":"2022","journal-title":"Nat. Commun."}],"container-title":["Molecular Therapy Nucleic Acids"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2162253126002696?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2162253126002696?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T15:12:22Z","timestamp":1793632342000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2162253126002696"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,12]]},"references-count":94,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["S2162253126002696"],"URL":"https:\/\/doi.org\/10.1016\/j.omtn.2026.103098","relation":{},"ISSN":["2162-2531"],"issn-type":[{"value":"2162-2531","type":"print"}],"subject":[],"published":{"date-parts":[[2026,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Bridging the antiviral gap: A BAC-based non-infectious SARS-CoV-2 replicon reveals potent antisense gapmers","name":"articletitle","label":"Article Title"},{"value":"Molecular Therapy Nucleic Acids","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.omtn.2026.103098","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc. on behalf of The American Society of Gene and Cell Therapy.","name":"copyright","label":"Copyright"}],"article-number":"103098"}}