Evidence map›Paper›PMID 40479048›Full record

ArticleScience advances2025

Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.

Grace Neilsen, Shuiyun Lan, Ryan L Slack, Zachary C Lorson, Andres Emanuelli Castaner, Rachel Lee, Kristin G Edwards, Huanchun Zhang, Jasper Lee, William A Cantara and 8 more

Abstract read
In one paragraph

Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Review
  6. Article
  7. Article
  8. Characterization of antiviral compounds using Bio-Layer Interferometry.bioRxiv : the preprint server for biology · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

Grace NeilsenCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0001-9344-1160
Shuiyun LanCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0009-0002-4101-9894
Ryan L SlackCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0002-5928-6205
Zachary C LorsonCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0009-0002-1404-9086
Andres Emanuelli CastanerCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Rachel LeeCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0002-5190-614X
Kristin G EdwardsCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Huanchun ZhangCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Jasper LeeCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0003-0472-827X
William A CantaraCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Maria E CilentoCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Hongwang ZhangCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Ramyani DeCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Franck AmblardCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Philip R TedburyCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0001-8151-4967
Karen A KirbyCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0003-2468-4796
Raymond F SchinaziCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0002-6688-3614
Stefan G SarafianosCenter for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.ORCID 0000-0002-5840-154X

Funding

X-ray Scattering Technology CoreP30GM133893 · NIGMS · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI Sean McSweeney · 2019 to 2026
$38.6M
Atlanta Clinical and Translational Science Institute (ACTSI) RenewalUL1TR000454 · NCATS · EMORY UNIVERSITY · PI STEPHENS, DAVID S · 2012 to 2016
$25.8M
Training Program in Biochemistry, Cell and Molecular BiologyT32GM008367 · NIGMS · EMORY UNIVERSITY · PI BOISE, LAWRENCE H., CORBETT, ANITA H. · 1990 to 2019
$5.6M
Discovery of SARS-CoV-2 antivirals using a replicon assayR01AI167356 · NIAID · EMORY UNIVERSITY · PI Stefan G Sarafianos, Zhengqiang Wang · 2022 to 2026
$3.5M
Broad-spectrum therapeutics against SARS-CoV-2 3CL proteaseR01AI161570 · NIAID · EMORY UNIVERSITY · PI FITZPATRICK, ELIZABETH ANN, KOVARI, LADISLAU CHRISTOPHER · 2021 to 2025
$3.3M
Emory Training Program in Translational Research to End the HIV EpidemicT32AI157855 · NIAID · EMORY UNIVERSITY · PI Ann M Chahroudi, Colleen F Kelley · 2021 to 2026
$2.8M
Training Program in Biochemistry, Cell and Molecular BiologyT32GM135060 · NIGMS · EMORY UNIVERSITY · PI Lawrence H. Boise, ANITA H. CORBETT · 2020 to 2026
$2.8M
Antimicrobial Resistance and Therapeutic Discovery Training ProgramT32AI106699 · NIAID · EMORY UNIVERSITY · PI Graeme L Conn, Joanna B Goldberg · 2014 to 2026
$2.7M
Multidisciplinary studies on overcoming SARS-CoV-2 main protease drug resistance and on fitness costsF31AI179181 · NIAID · EMORY UNIVERSITY · PI Grace Neilsen · 2025 to 2026
$99k
NCATS NIH HHS UL1 TR000454NIAID NIH HHS F31 AI179181NIAID NIH HHS R01 AI161570NIAID NIH HHS R01 AI167356NIAID NIH HHS T32 AI106699NIAID NIH HHS T32 AI157855NIGMS NIH HHS P30 GM133893NIGMS NIH HHS T32 GM008367NIGMS NIH HHS T32 GM135060
6 · The paper itself

Abstract

E166V in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp5 protease confers strong resistance to the antiviral component of Paxlovid, nirmatrelvir (NIR), in passaging and clinical samples. In SARS-CoV-2 replicons, E166V drastically decreased Washington (WA1) but not Omicron (BA.1) fitness (20- versus 2-fold), suggesting a lower barrier to resistance in the BA.1 strain and consistent with observed differences in respective nsp5 dimerization affinities. Crystal structures reveal a steric clash between the rigid, bulky NIR

Indexed as

Antiviral AgentsDrug Resistance, ViralSARS-CoV-2Viral Nonstructural ProteinsCoronavirus 3C ProteasesCOVID-19COVID-19 Drug TreatmentCrystallography, X-RayHumansLactamsLeucineNitrilesProlineSulfonic AcidsAntiviral AgentsCoronavirus 3C ProteasesGC376LactamsLeucinenirmatrelvirNitrilesProlineSulfonic AcidsViral Nonstructural Proteins

Identifiers

PMID40479048
PMCPMC12143351

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.