SARS-CoV-2 virologic rebound with nirmatrelvir-ritonavir therapy
Brigham and Women’s Hospital, Boston, MA, USA
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
Massachusetts General Hospital, Boston, MA, USA
University of Pittsburgh Medical Center, Pittsburgh, PA, USA
Harvard Medical School, Boston, MA, USA
Broad Institute, Cambridge, MA, USA
†Corresponding author: Mark J. Siedner, MD MPH, Medical Practice Evaluation Center, Massachusetts General Hospital, 100 Cambridge Street, Suite 1600, Boston, MA 02114, msiedner@mgh.harvard.edu; +1-617-726-4686Abstract
Objective
To compare the frequency of replication-competent virologic rebound with and without nirmatrelvir-ritonavir treatment for acute COVID-19. Secondary aims were to estimate the validity of symptoms to detect rebound and the incidence of emergent nirmatrelvir-resistance mutations after rebound.
Design
Observational cohort study.
Setting
Multicenter healthcare system in Boston, Massachusetts.
Participants
We enrolled ambulatory adults with a positive COVID-19 test and/or a prescription for nirmatrelvir-ritonavir.
Exposures
Receipt of 5 days of nirmatrelvir-ritonavir treatment versus no COVID-19 therapy.
Main Outcome and Measures
The primary outcome was COVID-19 virologic rebound, defined as either (1) a positive SARS-CoV-2 viral culture following a prior negative culture or (2) two consecutive viral loads ≥4.0 log10 copies/milliliter after a prior reduction in viral load to <4.0 log10 copies/milliliter.
Results
Compared with untreated individuals (n=55), those taking nirmatrelvir-ritonavir (n=72) were older, received more COVID-19 vaccinations, and were more commonly immunosuppressed. Fifteen individuals (20.8%) taking nirmatrelvir-ritonavir experienced virologic rebound versus one (1.8%) of the untreated (absolute difference 19.0% [95%CI 9.0-29.0%], P=0.001). In multivariable models, only N-R was associated with VR (AOR 10.02, 95%CI 1.13-88.74). VR occurred more commonly among those with earlier nirmatrelvirritonavir initiation (29.0%, 16.7% and 0% when initiated days 0, 1, and ≥2 after diagnosis, respectively, P=0.089). Among participants on N-R, those experiencing rebound had prolonged shedding of replication-competent virus compared to those that did not rebound (median: 14 vs 3 days). Only 8/16 with virologic rebound reported worsening symptoms (50%, 95%CI 25%-75%); 2 were completely asymptomatic. We detected no post-rebound nirmatrelvir-resistance mutations in the NSP5 protease gene.
Conclusions and Relevance
Virologic rebound occurred in approximately one in five people taking nirmatrelvir-ritonavir and often occurred without worsening symptoms. Because it is associated with replication-competent viral shedding, close monitoring and potential isolation of those who rebound should be considered.
Article notes
Competing Interest Statement
AKB reports consulting for ICON Government and Public Health Solutions. JZL reports consulting for Abbvie and research funding from Merck. SPH reports research funding from GlaxoSmithKline and has served on an advisory board for Pfizer.
Funding Statement
This work was supported by the National Institutes of Health (U19 AI110818), the Massachusetts Consortium for Pathogen Readiness SARS-CoV-2 Variants Program and the MGH Department of Medicine. Drs. Sparks and Wallace are supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01 AR080659). Dr. Sparks is also supported by the Llura Gund Award for Rheumatoid Arthritis Research and Care. The funders had no role in study design; in the collection, analysis, and interpretation of data; in the writing of the manuscript; or in the decision to submit the manuscript for publication.
Introduction
Methods
The Post-vaccination Viral Characteristics Study (POSITIVES) is a prospective, observational cohort of individuals with acute COVID-19 with longitudinal sampling for viral load, viral culture, and symptom reporting (supplementary appendix).8,9 Participants are sampled from automated medical record reports in the Mass General Brigham healthcare system on individuals with positive testing or a prescription for COVID-19 therapeutics.
Participants self-collect anterior nasal swabs three times a week for two weeks and weekly thereafter until SARS-CoV-2 viral load testing is persistently undetectable. Specimens are analyzed for SARS-CoV-2 viral load, viral culture, and whole genome sequencing. Participants complete 10-item COVID-19 symptom surveys, graded as absent (0), mild (1), moderate (2), or severe (3), for a maximum total symptom score (TSS) of 30-points. Study physicians complete chart reviews to determine COVID-19 vaccination and treatment history, and immunosuppression status (STable1).
We sought to estimate the incidence of virologic rebound, which we defined in individuals with either 1) positive SARS-CoV-2 viral culture following a negative culture or 2) a viral load ≥1.0 log10 from a prior viral load and ≥4.0 log10 copies/mL for two consecutive timepoints after a prior reduction in viral load to <4.0 log10 copies/mL. We selected this outcome as a surrogate for putative transmission risk, based on data relating transmission to replication-competent virus with viral loads >4.0 log10 copies/mL.10,11 For a secondary outcome, we redefined VR as a viral load at days 10 and 14 ≥2.7 log10 and at least 0.5 log10 greater than the result at day 5, in order to compare our estimates to the EPIC-HR study, which considered fewer time points and did not incorporate culture methods.1
Our primary exposure of interest was exposure to N-R therapy. Therefore, we limited analysis to ambulatory participants enrolled after March 2022, when we began recruiting individuals initiating N-R. We also excluded participants without a nasal swab collected >11 days from their first positive COVID-19 test, because approximately 90% of rebound phenomena occur by this time,8 and individuals who received N-R for more or less than 5 days. We compared the frequency of VR by N-R use overall and stratified by potential confounders (i.e., immunosuppression, age, sex, and prior COVID-19 vaccinations) using two-sided Fisher’s exact tests, and after adjustment for confounders, in logistic regression models. We compared the frequency of VR by timing of N-R initiation, using a non-parametric test of trend. We compared our estimate of VR with the definition used in the EPIC-HR study.1 We used the Kaplan-Meier survival estimator to depict and compare days to initial and final viral culture negativity, stratified by N-R use and VR, using log-rank testing. We assessed the validity of symptom rebound, as defined by an increase in TSS by 3 or more points from a prior date, and the presence of any symptoms during the rebound period, to detect VR.6 Finally, we report the proportion of sequenced viruses before and after VR with mutations in the NSP5 gene encoding the main protease (Mpro) of SARS-CoV-2. Statistical analyses and figure production were conducted with Stata version 16.1 and GraphPad Prism version 9.5.
Ethical Considerations
All study participants provided verbal informed consent. Written consent was waived by the ethics committee, based on the involvement of participants with acute COVID-19 in a minimal risk study. The study procedures were approved by Institutional Review Board and the Institutional Biosafety Committee at Mass General Brigham.
Results
Compared with untreated individuals (n=55), those taking N-R (n=72) were older (57 vs 39 years, P<0.001), received more COVID-19 vaccinations (median 4 vs 3, P<0.001) and were more commonly immunosuppressed (32% vs 9%, P<0.001, SFig1/STable2). Fifteen individuals (20.8%) taking N-R experienced VR versus one (1.8%) untreated individual (Figures 1&2, absolute difference 19.0% [95%CI 9.0-29.0%], P=0.001). In sub-group analyses, VR was numerically more frequent in all demographic and clinical sub-groups (Figure 2). In multivariable logistic regression models including demographic and clinical characteristics, only N-R use remained associated with VR (STable 3). There was a trend towards higher rates of VR with earlier N-R initiation (29%, 16.7% and 0% when initiated days 0, 1, and ≥2 after diagnosis, P=0.089, Figure 2). When we restricted analyses to three timepoints, as done in the EPIC-HR study, only 3/124 (2.4%) had rebound detected, and 13/16 (81.2%) rebound events were not captured (Figure 1E-F). We detected no post-N-R drug resistance mutations in the NSP5 protease gene (SFig2).
N-R recipients achieved initial culture conversion sooner than those not treated (Figure 3/STable4, P<0.001). However, days to final culture conversion was similar (Figure 3, P=0.29) because those experiencing VR had significantly prolonged shedding (median 14 [IQR13-20] vs 3 days [IQR2-4], Figure 3/STable4/STable5). Only 8/16 with VR reported symptom rebound (50%, 95%CI 25-75%); 2 were totally asymptomatic. Only 8/27 with symptom rebound had VR (30%, 95% CI 14-50%, SFig3/STable6).
Discussion
VR with replication-competent viral shedding occurred in approximately 20% of those taking N-R and 2% of those not on therapy. N-R use remained associated with VR after adjustment for demographic and clinical characteristics, such as vaccination and immunosuppression status. Although N-R treated individuals took fewer days to achieve initial culture negativity, time to final culture negativity was similar, due to prolonged shedding of replication-competent virus among those experiencing VR (median 14 vs 3 days). These data support the presence of an N-R-associated virologic rebound phenomenon, which substantially increases the duration of shedding of replication-competent virus and has implications for post-N-R monitoring and isolation recommendations.
We found a higher incidence of VR with N-R use than prior studies. We believe this is due to use of frequent sampling and culture methods to detect VR. When we restricted our analysis to three PCR-based timepoints, as done in prior trials,1 we detected a 2.4% rate of VR, which approximates prior studies, but notably missed 80% of VR events.
VR appeared to be less common among those who delayed therapy by 1 or 2 days after their first positive test. This finding, in conjunction with the lack of drug resistance-associated mutations after VR events, promotes hypotheses that VR may occur due to incomplete viral eradication,12 and supports studies to evaluate longer durations of N-R therapy.13
Finally, symptoms should not be relied upon to detect or exclude VR. Two individuals with VR had a complete absence of symptoms during the VR period and less than half had symptom rebound. Conversely, the majority of those who did have symptom rebound did not experience VR.
Our study was limited by an observational design, with expected differences between those taking N-R and untreated individuals based on treatment guidelines for N-R14. Nonetheless, VR remained associated with N-R, even after adjustment for potential confounders. We used viral culture as a surrogate for transmission risk but did not measure contagiousness or transmission events directly.
These data support a relationship between N-R use and VR. Future work should elucidate the mechanistic pathways of VR, determine if delays in initiating N-R or longer courses of N-R may prevent VR among high-risk individuals, and evaluate larger samples to identify the risk factors for N-R-associated VR.
Supporting information
Data Availability
All data produced in the present study are available upon reasonable request to the authors
Acknowledgments
We would like to thank the study participants for their time and considerable efforts to provide specimens in the acute phase of illness as part of this project.