{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:45:36Z","timestamp":1785422736110,"version":"3.56.0"},"reference-count":50,"publisher":"National Academy of Sciences","issue":"24","license":[{"start":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T00:00:00Z","timestamp":1780963200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"Institut Pasteur Centenary Prize","award":["Alumni 2013"],"award-info":[{"award-number":["Alumni 2013"]}]},{"DOI":"10.13039\/100015118","name":"Institute of France | Acad\u00e9mie des Sciences, Institut de France","doi-asserted-by":"publisher","award":["Simone & Cino de Duca"],"award-info":[{"award-number":["Simone & Cino de Duca"]}],"id":[{"id":"10.13039\/100015118","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fondation CNRS","award":["XPLORE"],"award-info":[{"award-number":["XPLORE"]}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2026,6,16]]},"abstract":"<jats:p>\n                    Nucleotide analogues (NAs) have been successfully used for the treatment of various RNA virus infections by selectively targeting the viral RNA-dependent RNA polymerase (RdRp) for incorporation into the viral genome. However two major families of human-infecting RNA viruses,\n                    <jats:italic toggle=\"yes\">Coronaviridae<\/jats:italic>\n                    (CoV) and\n                    <jats:italic toggle=\"yes\">Arenaviridae,<\/jats:italic>\n                    encode exonuclease domains that may recognize and remove incorporated NAs, thus providing natural resistance against some of these drugs. Both polymerization and excision reactions are mechanistically centered on the nucleotide \u03b1-phosphate, enabling the potential for sequential inhibition of both RNA synthesis and repair. Here, we provide structural evidence of inversion of configuration at the phosphorus center during polymerization, demonstrating that the SARS-CoV-2 RdRp proceeds through an S\n                    <jats:sub>N<\/jats:sub>\n                    2 mechanism. A 2.39 \u00c5 resolution cryo-EM structure of a ternary replication complex bound to RNA and an \u03b1-thio\u2013modified NTP shows that incorporation of the preferred\n                    <jats:italic toggle=\"yes\">S<\/jats:italic>\n                    <jats:sub>P<\/jats:sub>\n                    isomer at the 3\u2032 end of the RNA yields a phosphorothioate linkage in the\n                    <jats:italic toggle=\"yes\">R<\/jats:italic>\n                    <jats:sub>P<\/jats:sub>\n                    configuration. This\n                    <jats:italic toggle=\"yes\">R<\/jats:italic>\n                    <jats:sub>P<\/jats:sub>\n                    -phosphorothioate RNA product shows reduced cleavage by both the SARS-CoV-2 and three arenavirus RNA exonucleases, revealing a stereochemical preference opposite to that of structurally related DNA exonucleases. This observation contradicts the prevailing assumption that sulfur substitution at the metal-coordinating oxygen universally blocks catalysis. Instead, RNA exonuclease stereoselectivity appears to be shaped not only by metal\u2013sulfur interactions but also by the geometry of nucleophile activation. These findings provide mechanistic insights into phosphoryl transfer in viral polymerases and exonucleases and highlight opportunities to counteract intrinsic nuclease-mediated resistance against antiviral nucleotide analogues.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2605725123","type":"journal-article","created":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T17:36:04Z","timestamp":1781026564000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":0,"title":["Consecutive catalytic steps of viral RNA polymerase and exonuclease suggest a way to overcome intrinsic nucleotide analogue resistance"],"prefix":"10.1073","volume":"123","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4290-8247","authenticated-orcid":false,"given":"Ashleigh","family":"Shannon","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04jm8zw14","id-type":"ROR","asserted-by":"publisher"}],"name":"Aix-Marseille University, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromol\u00e9cules Biologiques UMR7257","place":["Marseille, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6420-7949","authenticated-orcid":false,"given":"V\u00e9ronique","family":"Fattorini","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04jm8zw14","id-type":"ROR","asserted-by":"publisher"}],"name":"Aix-Marseille University, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromol\u00e9cules Biologiques UMR7257","place":["Marseille, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Candice","family":"Sartre","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04jm8zw14","id-type":"ROR","asserted-by":"publisher"}],"name":"Aix-Marseille University, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromol\u00e9cules Biologiques UMR7257","place":["Marseille, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aur\u00e9lie","family":"Chazot","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04jm8zw14","id-type":"ROR","asserted-by":"publisher"}],"name":"Aix-Marseille University, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromol\u00e9cules Biologiques UMR7257","place":["Marseille, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adel","family":"Moussa","sequence":"additional","affiliation":[{"name":"Atea Pharmaceuticals, Inc.","place":["Boston"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Pierre","family":"Sommadossi","sequence":"additional","affiliation":[{"name":"Atea Pharmaceuticals, Inc.","place":["Boston"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingxiao","family":"Zhu","sequence":"additional","affiliation":[{"name":"Biortus Discovery Co. Ltd.","place":["Wuxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manfu","family":"Wang","sequence":"additional","affiliation":[{"name":"Biortus Discovery Co. Ltd.","place":["Wuxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Shi","sequence":"additional","affiliation":[{"name":"Biortus Discovery Co. 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