Persistence of an infectious form of SARS-CoV-2 post protease inhibitor treatment of permissive cells in vitro

Nair et al., The Journal of Infectious Diseases, doi:10.1093/infdis/jiae385

Aug 2024

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In Vitro study showing the persistence of an infectious form of SARS-CoV-2 after treatment with 3CL^pro inhibitors nirmatrelvir and ensitrelvir, which may explain the rebound often seen with paxlovid.

3CL^pro is crucial for processing viral polyproteins into functional viral proteins necessary for the assembly of new virus particles. This study suggests that despite 3CL^pro inhibition, viral ribonucleoprotein complexes or replicating forms of the virus may still persist intracellularly. These persistent forms might not require immediate protease activity to survive in the short term and can potentially reinitiate replication once the drug is removed. This persistence could explain why the virus can cause a rebound after the cessation of paxlovid treatment.

4 preclinical studies support the efficacy of ensitrelvir for COVID-19:

2 In Vitro studies1,2

2 In Vivo animal studies2,3

In Vitro studies demonstrate efficacy in VeroE6/TMPRSS2A,2, HEK293T/ACE2-TMPRSS2B,2, and MucilAirC,2 cells. Animal studies demonstrate efficacy in BALB/c miceD,2,3 and Syrian hamstersE,2. Preclinical studies demonstrate efficacy for the ancestralF,2, deltaG,2, and omicronH,2 variants.

Important missing comments or errors? Let us know.

Study covers paxlovid and ensitrelvir.

1. Nair et al., Persistence of an infectious form of SARS-CoV-2 post protease inhibitor treatment of permissive cells in vitro, The Journal of Infectious Diseases, doi:10.1093/infdis/jiae385.oup.com, doi.org.

2. Kuroda et al., Efficacy comparison of 3CL protease inhibitors ensitrelvir and nirmatrelvir against SARS-CoV-2 in vitro and in vivo, Journal of Antimicrobial Chemotherapy, doi:10.1093/jac/dkad027.oup.com, doi.org.

3. Nobori et al., Prophylactic effect of ensitrelvir in mice infected with SARS-CoV-2, Antiviral Research, doi:10.1016/j.antiviral.2024.105852.sciencedirect.com, doi.org.

a. VeroE6/TMPRSS2 is a Vero E6 cell line engineered to express the human serine protease TMPRSS2, enabling SARS-CoV-2 S protein priming and entry.

b. HEK293T/ACE2-TMPRSS2 is a human embryonic kidney cell line engineered to express human ACE2 and TMPRSS2, making it highly susceptible to SARS-CoV-2 infection.

c. MucilAir cells are primary human nasal epithelial cells that mimic the structure and physiology of the human airway epithelium.

d. A mouse model commonly used in infectious disease and cancer research due to higher immune response and susceptibility to infection.

e. A small rodent model used in SARS-CoV-2 research that replicates key aspects of human infection including efficient replication in the upper and lower respiratory tract.

f. The original SARS-CoV-2 strain that emerged in Wuhan, China in late 2019. Also referred to as wild-type.

g. A variant of concern first identified in India in late 2020, delta (B.1.617.2) transmitted more efficiently than previous variants. It contains spike mutations including L452R which increases binding to the ACE2 receptor.

h. A highly transmissible variant of concern first detected in South Africa in late 2021. Omicron possesses many spike mutations which confer partial immune evasion, including deletions near the furin cleavage site.

Nair et al., 12 Aug 2024, USA, peer-reviewed, 5 authors. Contact: dh2994@cumc.columbia.edu, ys2581@cumc.columbia.edu.

In Vitro studies are an important part of preclinical research, however results may be very different in vivo.

This Paper Ensitrelvir All

Persistence of an infectious form of SARS-CoV-2 post protease inhibitor treatment of permissive cells in vitro

Manoj S Nair, Maria I Luck, Yaoxing Huang, Yosef Sabo, David D Ho

doi:10.1093/infdis/jiae3851

4 Lead contact Reports have described SARS-CoV-2 rebound in COVID-19 patients treated with nirmatrelvir, a 3CL protease inhibitor. The cause remains a mystery, although drug resistance, re-infection, and lack of adequate immune responses have been excluded. We now present virologic findings that provide a clue to the cause of viral rebound, which occurs in ~20% of the treated cases. Persistence of infectious SARS-CoV-2 was experimentally documented in vitro after treatment with nirmatrelvir or another 3CL protease inhibitor, but not with a polymerase inhibitor, remdesivir. This infectious form decayed slowly with a half-life of ~1 day, suggesting that its persistence could outlive the treatment course to re-ignite SARS-CoV-2 infection as the drug is eliminated. Notably, extending nirmatrelvir treatment beyond 8 days abolished viral rebound in vitro. Our findings point in a particular direction for future investigation of virus persistence and offer a specific treatment recommendation that should be tested clinically.

SUPPLEMENTARY DATA Supplementary materials are available at The Journal of Infectious Diseases online. NOTES AUTHOR NOTES: Potential conflict of interest: All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. Authors do not report any potential conflict of interest.

References

Anderson, Caubel, Rusnak, Investigators, Nirmatrelvir-Ritonavir and Viral Load Rebound in Covid-19, N Engl J Med

Boldogh, Albrecht, Porter, Persistent Viral Infections

Boucau, Uddin, Marino, Characterization of Virologic Rebound Following Nirmatrelvir-Ritonavir Treatment for Coronavirus Disease 2019 (COVID-19), Clin Infect Dis

Cao, Wang, Lu, Oral Simnotrelvir for Adult Patients with Mild -to-Moderate Covid-19, N Engl J Med

Carlin, Clark, Chaillon, Virologic and Immunologic Characterization of Coronavirus Disease 2019 Recrudescence After Nirmatrelvir/Ritonavir Treatment, Clin Infect Dis

Charness, Gupta, Stack, Rebound of SARS-CoV-2 Infection after Nirmatrelvir-Ritonavir Treatment, N Engl J Med

Choi, Choudhary, Regan, Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host, N Engl J Med

Deo, Choudhary, Moser, Symptom and Viral Rebound in Untreated SARS-CoV-2 Infection, Ann Intern Med

Ducharme, COVID-19 Antiviral Drugs Promise Speedier Recoveries

Edelstein, Boucau, Uddin, SARS-CoV-2 Virologic Rebound With Nirmatrelvir-Ritonavir Therapy : An Observational Study, Ann Intern Med

Epling, Rocco, Boswell, Clinical, Virologic, and Immunologic Evaluation of Symptomatic Coronavirus Disease 2019 Rebound Following Nirmatrelvir/Ritonavir Treatment, Clin Infect Dis

Fu, Ye, Feng, Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease, Nat Commun

Ghafari, Hall, Golubchik, Prevalence of persistent SARS-CoV-2 in a large community surveillance study, Nature

Hammond, Leister-Tebbe, Gardner, Oral Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19, N Engl J Med

Hay, Kissler, Fauver, Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study, Elife

Kochan, Wawro, Kasza, Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH, Biotechniques

Li, Choudhary, Regan, SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency, Sci Transl Med

Lieber, Kang, Sobolik, Efficacy of late-onset antiviral treatment in immunecompromised hosts with persistent SARS-CoV-2 infection, bioRxiv

Mukae, Yotsuyanagi, Ohmagari, Efficacy and safety of ensitrelvir in patients with mild-to-moderate COVID-19: the phase 2b part of a randomized, placebo-controlled, phase 2/3 study, Clin Infect Dis

Owen, Allerton, Anderson, An oral SARS-CoV-2 M(pro) inhibitor clinical candidate for the treatment of COVID-19, Science

Pandit, Radin, Chiang, The COVID-19 Rebound Study: A Prospective Cohort Study to Evaluate Viral and Symptom Rebound Differences in Participants Treated with Nirmatrelvir Plus Ritonavir Versus Untreated Controls, Clin Infect Dis

Puhach, Adea, Hulo, Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2, Nat Med

Ranganath, Horo, Challener, Rebound Phenomenon After Nirmatrelvir/Ritonavir Treatment of Coronavirus Disease 2019 (COVID-19) in High-Risk Persons, Clin Infect Dis

Rubin, From Positive to Negative to Positive Again-The Mystery of Why COVID-19 Rebounds in Some Patients Who Take Paxlovid, JAMA

Se, Biddle, Talbot, Symptoms, Viral Loads, and Rebound Among COVID-19 Outpatients Treated With Nirmatrelvir/Ritonavir Compared With Propensity Score-Matched Untreated Individuals, Clin Infect Dis

Unoh, Uehara, Nakahara, Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19, J Med Chem

Wong, Yip, Lai, Wong, Hui et al., Incidence of Viral Rebound After Treatment With Nirmatrelvir-Ritonavir and Molnupiravir, JAMA Netw Open

Xie, Muruato, Lokugamage, An Infectious cDNA Clone of SARS-CoV-2, Cell Host Microbe

Zuo, He, Liang, The persistence of SARS-CoV-2 in tissues and its association with long COVID symptoms: a cross-sectional cohort study in China, Lancet Infect Dis

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