{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T01:07:49Z","timestamp":1789088869906,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.pntd.0011404","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,7,17]],"date-time":"2023-07-17T00:00:00Z","timestamp":1689552000000}}],"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T00:00:00Z","timestamp":1688515200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2018-05851"],"award-info":[{"award-number":["2018-05851"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2021-01145"],"award-info":[{"award-number":["2021-01145"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["CDA00047\/2017-C"],"award-info":[{"award-number":["CDA00047\/2017-C"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>Alphaviruses are mosquito-borne, positive-sense single-stranded RNA viruses. Amongst the alphaviruses, chikungunya virus is notable as a large source of human illness, especially in tropical and subtropical regions. When they invade a cell, alphaviruses generate dedicated organelles for viral genome replication, so-called spherules. Spherules form as outward-facing buds at the plasma membrane, and it has recently been shown that the thin membrane neck that connects this membrane bud with the cytoplasm is guarded by a two-megadalton protein complex that contains all the enzymatic functions necessary for RNA replication. The lumen of the spherules contains a single copy of the negative-strand template RNA, present in a duplex with newly synthesized positive-sense RNA. Less is known about the organization of this double-stranded RNA as compared to the protein components of the spherule. Here, we analyzed cryo-electron tomograms of chikungunya virus spherules in terms of the organization of the double-stranded RNA replication intermediate. We find that the double-stranded RNA has a shortened apparent persistence length as compared to unconstrained double-stranded RNA. Around half of the genome is present in either of five conformations identified by subtomogram classification, each representing a relatively straight segment of ~25\u201332 nm. Finally, the RNA occupies the spherule lumen at a homogeneous density, but has a preferred orientation to be perpendicular to a vector pointing from the membrane neck towards the spherule center. Taken together, this analysis lays another piece of the puzzle of the highly coordinated alphavirus genome replication.<\/jats:p>","DOI":"10.1371\/journal.pntd.0011404","type":"journal-article","created":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T13:28:56Z","timestamp":1688563736000},"page":"e0011404","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["The organization of double-stranded RNA in the chikungunya virus replication organelle"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0174-723X","authenticated-orcid":true,"given":"Timoth\u00e9e","family":"Laurent","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2342-6488","authenticated-orcid":true,"given":"Lars-Anders","family":"Carlson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,7,5]]},"reference":[{"issue":"1","key":"pntd.0011404.ref001","doi-asserted-by":"crossref","first-page":"e0006919","DOI":"10.1371\/journal.pntd.0006919","article-title":"Chikungunya as a paradigm for emerging viral diseases: Evaluating disease impact and hurdles to vaccine development","volume":"13","author":"G Rezza","year":"2019","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0011404.ref002","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.jiph.2016.09.008","article-title":"Zika virus: Endemic and epidemic ranges of Aedes mosquito transmission.","volume":"10","author":"DF Attaway","year":"2017","journal-title":"J Infect Public Health"},{"issue":"10","key":"pntd.0011404.ref003","doi-asserted-by":"crossref","first-page":"e1008876","DOI":"10.1371\/journal.ppat.1008876","article-title":"A molecular understanding of alphavirus entry.","volume":"16","author":"AC Holmes","year":"2020","journal-title":"PLoS Pathog"},{"issue":"2","key":"pntd.0011404.ref004","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.chom.2011.06.009","article-title":"Natural resistance-associated macrophage protein is a cellular receptor for sindbis virus in both insect and mammalian hosts","volume":"10","author":"PP Rose","year":"2011","journal-title":"Cell Host Microbe"},{"issue":"5","key":"pntd.0011404.ref005","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/S1473-3099(07)70107-X","article-title":"Chikungunya, an epidemic arbovirosis","volume":"7","author":"G Pialoux","year":"2007","journal-title":"Lancet Infect Dis"},{"key":"pntd.0011404.ref006","doi-asserted-by":"crossref","first-page":"e08347","DOI":"10.7554\/eLife.08347","article-title":"The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus","volume":"4","author":"MU Kraemer","year":"2015","journal-title":"Elife"},{"issue":"10","key":"pntd.0011404.ref007","doi-asserted-by":"crossref","first-page":"e270","DOI":"10.1371\/journal.pbio.0060270","article-title":"Seeking membranes: positive-strand RNA virus replication complexes","volume":"6","author":"MR Denison","year":"2008","journal-title":"PLoS Biol"},{"issue":"5","key":"pntd.0011404.ref008","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nrmicro1890","article-title":"Modification of intracellular membrane structures for virus replication","volume":"6","author":"S Miller","year":"2008","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"pntd.0011404.ref009","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.3390\/v2051055","article-title":"Role of cellular lipids in positive-sense RNA virus replication complex assembly and function","volume":"2","author":"KA Stapleford","year":"2010","journal-title":"Viruses"},{"key":"pntd.0011404.ref010","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/bs.aivir.2021.07.003","article-title":"Alphavirus RNA replication in vertebrate cells","volume":"111","author":"T Ahola","year":"2021","journal-title":"Adv Virus Res"},{"issue":"8","key":"pntd.0011404.ref011","doi-asserted-by":"crossref","first-page":"3873","DOI":"10.1128\/JVI.75.8.3873-3884.2001","article-title":"Biogenesis of the Semliki Forest virus RNA replication complex","volume":"75","author":"P Kujala","year":"2001","journal-title":"J Virol"},{"key":"pntd.0011404.ref012","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1146\/annurev-immunol-042718-041356","article-title":"Double-Stranded RNA Sensors and Modulators in Innate Immunity","volume":"37","author":"S. 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