In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.

Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populat...

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Autores principales:	Agnieszka M Szemiel, Andres Merits, Richard J Orton, Oscar A MacLean, Rute Maria Pinto, Arthur Wickenhagen, Gauthier Lieber, Matthew L Turnbull, Sainan Wang, Wilhelm Furnon, Nicolas M Suarez, Daniel Mair, Ana da Silva Filipe, Brian J Willett, Sam J Wilson, Arvind H Patel, Emma C Thomson, Massimo Palmarini, Alain Kohl, Meredith E Stewart
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/7d89e76f634d4950a6f0243895093b37
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spelling	oai:doaj.org-article:7d89e76f634d4950a6f0243895093b372021-12-02T20:00:09ZIn vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.1553-73661553-737410.1371/journal.ppat.1009929https://doaj.org/article/7d89e76f634d4950a6f0243895093b372021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.ppat.1009929https://doaj.org/toc/1553-7366https://doaj.org/toc/1553-7374Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.Agnieszka M SzemielAndres MeritsRichard J OrtonOscar A MacLeanRute Maria PintoArthur WickenhagenGauthier LieberMatthew L TurnbullSainan WangWilhelm FurnonNicolas M SuarezDaniel MairAna da Silva FilipeBrian J WillettSam J WilsonArvind H PatelEmma C ThomsonMassimo PalmariniAlain KohlMeredith E StewartPublic Library of Science (PLoS)articleImmunologic diseases. AllergyRC581-607Biology (General)QH301-705.5ENPLoS Pathogens, Vol 17, Iss 9, p e1009929 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
spellingShingle	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5 Agnieszka M Szemiel Andres Merits Richard J Orton Oscar A MacLean Rute Maria Pinto Arthur Wickenhagen Gauthier Lieber Matthew L Turnbull Sainan Wang Wilhelm Furnon Nicolas M Suarez Daniel Mair Ana da Silva Filipe Brian J Willett Sam J Wilson Arvind H Patel Emma C Thomson Massimo Palmarini Alain Kohl Meredith E Stewart In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
description	Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.
format	article
author	Agnieszka M Szemiel Andres Merits Richard J Orton Oscar A MacLean Rute Maria Pinto Arthur Wickenhagen Gauthier Lieber Matthew L Turnbull Sainan Wang Wilhelm Furnon Nicolas M Suarez Daniel Mair Ana da Silva Filipe Brian J Willett Sam J Wilson Arvind H Patel Emma C Thomson Massimo Palmarini Alain Kohl Meredith E Stewart
author_facet	Agnieszka M Szemiel Andres Merits Richard J Orton Oscar A MacLean Rute Maria Pinto Arthur Wickenhagen Gauthier Lieber Matthew L Turnbull Sainan Wang Wilhelm Furnon Nicolas M Suarez Daniel Mair Ana da Silva Filipe Brian J Willett Sam J Wilson Arvind H Patel Emma C Thomson Massimo Palmarini Alain Kohl Meredith E Stewart
author_sort	Agnieszka M Szemiel
title	In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
title_short	In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
title_full	In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
title_fullStr	In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
title_full_unstemmed	In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
title_sort	in vitro selection of remdesivir resistance suggests evolutionary predictability of sars-cov-2.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/7d89e76f634d4950a6f0243895093b37
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In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.

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