Efficacy of Nirmatrelvir/ritonavir in reducing the risk of severe outcome in patients with SARS-CoV-2 infection: a real-life full-matched case-control study (SAVALO Study)

Abstract

Background

Ritonavir-boosted nirmatrelvir (N/r) is an antiviral which targets the main viral protease, administered to prevent the progression of SARS-CoV-2 infection in patients at high risk for severe COVID-19. We present a real-life case-control study evaluating the efficacy of N/r therapy in SARS-CoV-2 omicron variants positive outpatients in Campania region, Italy, with the aim of assessing the occurrence of three outcomes (hospital admission, admission in ICU and death) in cases and controls.

Methods

We enrolled SARS-CoV-2 positive subjects that came to our attention in Early antiviral treatment ambulatory of Infectious Diseases ward of University Federico II of Naples, Italy from January 1st, 2022, to December 31st, 2022, during the first five days from symptoms occurrence. Patients were enrolled as cases or controls if they were treated with N/r or not treated at all, respectively.

Results

1607 patients were included (cases: 423, controls: 1184). Cases showed a lower mortality compared with controls while no differences were observed for other outcomes. Vaccinated patients showed a lower mortality compared with non-vaccinated ones (0.5% vs. 7.8%, p < 0.001). After full-matching propensity score, N/r reduced hospitalization rate only in unvaccinated patients. In contrast N/r significantly reduced mortality regardless of vaccination status.

Conclusions

Treatment with N/r has proven effective in reducing mortality among outpatients with SARS-CoV-2 infection during several omicron variant surges. The beneficial effect of N/r treatment in reducing progression is more pronounced in unvaccinated patients.

Background

Coronavirus disease 2019 (COVID-19) is caused by the β-coronavirus SARS-CoV-2, which first emerged in Wuhan, China, in late 2019. It rapidly spread worldwide, resulting in over 774 million cases and 7 million deaths to date [1, 2]. Early oral antiviral treatment is a crucial strategy in managing mild to moderate COVID-19, as it prevents the deterioration of patients, particularly those at high risk of developing severe disease [3]. Nirmatrelvir is an orally administered antiviral agent that targets the SARS-CoV-2 3-chymotrypsin–like cysteine protease enzyme (Mpro), a key component of SARS-CoV-2 viral replication. In the EPIC-HR trial, treatment with ritonavir-boosted nirmatrelvir within 5 days of symptom onset resulted in 87.8% reduction in the risk of progression to severe disease compared to placebo. This was observed among non-hospitalized, unvaccinated adults at high risk of serious illness during the pre-Delta and Delta (B.1.617.2) pandemic waves [4].

However, the Omicron lineage variants and subvariants of SARS-CoV-2 have progressively displaced previous variants due to their higher transmission rates and ability to evade the immune system. Despite this, N/r has maintained in-vitro activity, largely due to the low mutation rate of the Mpro gene [5]. Nevertheless, gathering real-world data on its effectiveness against the emergent Omicron variants, which have predominated since early 2022 [6], is now a research priority. It is also important to note that the population sample enrolled in the phase 3 trial was unvaccinated, contrasting with the current population, which is predominantly vaccinated or possesses hybrid immunity. This difference could potentially impact on the treatment’s effectiveness in real-world settings.

The aim of the present study is to assess the occurrence of hospital admission, ICU admission, and death in cases and controls, including patients with previous SARS-CoV-2 immunity, and to evaluate the effectiveness of N/r against the emergent Omicron variants.

Methods

Study design and population

This study was conducted as a retrospective case-control study. The eligibility criteria for participants were as follows: they had to be outpatients who tested positive for SARS-CoV-2 from January 2022 to December 2022, and they had to be aged 18 years or older. Subjects who were undergoing other therapies for COVID-19 (such as molnupiravir, remdesivir, sotrovimab, tixagevimab/cilgavimab or other anti-SARS-CoV-2 monoclonal antibodies), even in combination with N/r, were excluded from the study.

Cases in this study were defined as participants who sought care at the outpatient service of the Infectious Diseases Unit of the University Federico II of Naples, Italy, and received N/r within 5 days of symptoms onset at a dosage of 300 mg of nirmatrelvir plus 100 mg of ritonavir twice daily for 5 days. All treated patients had risk factors for disease progression as outlined by the Italian Drug Agency. These risk factors include being over 65 years of age, having a solid or haematological cancer, immunodeficiency, chronic liver or kidney disease, cardiovascular disease, uncontrolled diabetes mellitus, haemoglobinopathies, neurological disorders, chronic bronchopneumopathy, or severe obesity (BMI ≥ 30) [7]. Immunodeficiency was defined by the presence of medical conditions or treatment according to the criteria provided by CDC [8], as listed below:

• Active treatment for solid tumors and hematologic malignancies.

• Receipt of solid-organ transplant or an islet transplant and taking immunosuppressive therapy.

• Moderate or severe primary immunodeficiency.

• Advanced or untreated HIV infection (people with HIV and CD4 cell counts less than 200/mm3, history of an AIDS-defining illness without immune reconstitution, or clinical manifestations of symptomatic HIV).

• Active treatment with high-dose corticosteroids (i.e., 20 or more mg of prednisone or equivalent per day when administered for 2 or more weeks), alkylating agents, antimetabolites, transplant-related immunosuppressive drugs, cancer chemotherapeutic agents classified as severely immunosuppressive, tumor necrosis factor (TNF) blockers, and other biologic agents that are immunosuppressive or immunomodulatory.

Control participants were selected from a regional database that included all patients who tested positive for SARS-CoV-2 during the study period and did not receive any antiviral treatment. These control participants were identified and confirmed through telephone interviews designed by the authors and conducted by healthcare professionals (see Supplementary Document 1 for the full text of the interview).

Data collection and definitions

We collected information on patients’ demographic characteristics (age, sex), comorbid conditions (such as diabetes mellitus, hypertension, heart disease, lung disease, immunodeficiency, renal disease, neurological disease), vaccination status, and the predominant variant in our area during each segment of the study period. Patients were classified as vaccinated if they had received at least two doses of a COVID-19 vaccine. Adherence to treatment and the incidence of adverse drug reactions were self-reported during a telephonic interview performed between 3 and 5 days from the date of planned treatment initiation (cases only).

For each patient, we calculated the Monoclonal Antibody Screening Score (MASS), originally developed to quickly identify and stratify patients who should be prioritized for monoclonal antibody administration according to their risk of hospitalization [9]. Additionally, we created a simplified Comorbidity Score. This score was assigned as follows: 2 points were given if the patient had at least 3 comorbidities, 1 point was given if the patient had 1 or 2 comorbidities, and 0 points were given if the patient had no comorbidity.

Propensity score matching

We performed a propensity score (PS)–matched analysis to minimize selection bias and ensure an even distribution of confounding variables between the two groups under investigation: those treated with N/r and those untreated (receiving no treatment against COVID-19 at all) [10].

In conducting and reporting our PS methods, we adhered to the recommendations provided by Eikenboom et al., which aim to improve the quality of research on the effectiveness of antimicrobial therapy [11].

We estimated a PS model. Each subject was assigned a probability of receiving N/r based on their baseline characteristics, which included: age, sex, vaccination status, comorbid conditions (such as diabetes mellitus, hypertension, heart disease, lung disease, immunodeficiency, renal disease, neurological disease), MASS and Comorbidity score, and the predominant variant. Probabilities were estimated through probit regression. The balance of PS matching was evaluated using the absolute standardized mean difference (SMD) of covariates (both continuous and categorical) between groups. We considered an SMD value less than 0.1 to represent acceptable balance. Various matching algorithms, including greedy (with different ratios and calipers), optimal, and full, were assessed [12]. The best balance, while retaining the entire sample size, was achieved with full matching. This method assigned all units in the sample to one subclass each, either containing one treated unit and one or more control units, or one control unit and one or more treated units. The chosen number of subclasses and the assignment of units to subclasses minimized the sum of the absolute within-subclass distances in the matched sample [13].

Outcomes

The primary outcomes of the study were:

• The proportions of hospital admission, intensive care unit (ICU) admission, and 28-day all-cause mortality among both the treated individuals and the propensity-matched untreated individuals.

• A composite outcome, defined as the occurrence of at least one of the following: hospital admission, ICU admission and all-cause death.

The follow-up duration was 28 days from symptom onset or the first positive test for SARS-CoV-2.

Statistical analysis

In this study, categorical variables are presented as numbers and percentages, while continuous variables are presented as median values and interquartile ranges (IQRs). The Mann-Whitney U test was used to determine differences in baseline characteristics between groups for continuous variables, and Pearson’s χ2 test was used for categorical variables.

After matching, the effect of N/r on the outcomes under investigation was estimated. The chosen estimand was the average treatment effect on the treated (ATT), representing the average effect of treatment for those who receive it. This approach addressed the archetypical question: should medical providers withhold treatment from those currently receiving it [14]?

Marginal effects, comparing the expected potential outcomes under treatment and control, were estimated and expressed as odds ratios (ORs) with their 95% confidence intervals (CIs). Estimation was performed through g-computation with a cluster-robust standard to account for pair membership, considering binary outcomes with covariates using logistic regression [15]. Including covariates in the outcome model after matching serves several functions: it can increase precision in the effect estimate, reduce the bias due to residual imbalance, and make the effect estimate “doubly robust”. This means the estimate remains consistent if either the matching sufficiently reduces covariate imbalance or if the outcome model is correct [16].

Analyses were performed using R, version 4.1.0 (R Core Team), with the following packages: MatchIt, cobalt, marginal effects.

Secondary analysis

We conducted a moderation analysis to determine if the treatment effect varied across different levels of another variable, specifically vaccination status. The aim was to achieve balance within each subgroup of the moderating variable. This was accomplished by performing matching across the full dataset [17].

Results

The study included a total of 1,607 patients who met the inclusion/exclusion criteria, comprising 423 cases (26.3%) and 1184 controls (73.7%). The baseline characteristics of these cases and controls are detailed in Table 1.

Table 1 Baseline features of pre-matched sample (N = 1607)

IQR: interquartile range; COPD: chronic obstructive pulmonary disease; CKD: chronic kidney disease

Treatment with N/r among cases was initiated within three days of a positive SARS-CoV-2 swab, and the median delay between symptoms onset and first positive SARS-CoV-2 swab was 1 day (IQR: 0–1). All cases self-reported full adherence to treatment. No cases discontinued treatment due to ADRs, which were all mild to moderate in severity: 175 patients (41.4%) reported dysgeusia, 8 (1.9%) reported nausea, and 5 patients (1.2%) reported diarrhoea and headache, respectively. In total, 27 patients (1.7%) required hospitalization, and 2 (0.1%) were admitted to the ICU. Remarkably, none of the 423 patients treated with N/r died, while 15 (1.3%) of the controls died (p < 0.05). However, there were no significant differences in the rates of hospital admission, ICU admission, and in the composite outcome between the treated and untreated groups (Table 2).

Table 2 Outcome rates among cases and controls

Following the full-matching PS analysis (see Supplementary Fig. 1 and Supplementary Fig. 2 for covariate balance and distribution of PS between groups) it was confirmed that treatment with N/r significantly and drastically reduced the risk of death among patients with SARS-CoV-2 infection (Table 3). Furthermore, N/r significantly reduced the risk of the composite outcome. However, no effect of N/r on hospital admission alone was observed.

Table 3 Effect of N/r on different outcomes after full-matched propensity score

When comparing outcomes based on vaccination status, it was found that patients who had received the SARS-CoV-2 vaccine had a significant lower rate of death (p < 0.001). They also had a significantly lower rate of the composite outcome (p = 0.001).

In the subgroup analysis conducted among both cases and control who received the SARS-CoV-2 vaccine, the effect of N/r on reducing the risk of death was confirmed in both vaccinated and unvaccinated subjects after full-matched propensity score analysis (Table 4). However, N/r was found to be effective in reducing the risk of hospital admission (p < 0.001) and the risk of the composite outcome (p < 0.001) only in non-vaccinated individuals.

Table 4 Effect of N/r on different outcomes after full-matched propensity score, according to vaccination status

Discussion

In this retrospective matched cohort study, we evaluated the real-world effectiveness of N/r in reducing hospital admissions and mortality among patients with SARS-CoV-2 infection, particularly in unvaccinated individuals. We compared the outcomes of untreated individuals infected with SARS-CoV-2 during the same period, using a full-matching propensity score to ensure a fair and balanced comparison between the treated and untreated groups.

The majority of patients in this study contracted the infection during the surge of the Omicron variant. Specifically, Omicron BA.2 and BA.5 were the most prevalent variants, affecting an estimated 86.3% of cases and 72.6% of controls, respectively. Additionally, most of both cases and controls in our study (> 90%) had received at least two doses of the SARS-CoV-2 vaccine. Given this high rate of vaccination and the prevalence of the Omicron subvariants, it is unsurprising that the rates of hospitalization, ICU admission and mortality were remarkably low, aligning with worldwide epidemiological data [18,19,20]. However, a significant finding was that all the 15 recorded deaths in this study occurred among the control group. This is a crucial result, particularly considering that the cases were considerably more vulnerable than the controls. Patients treated with N/r were indeed older than the controls and more frequently had obesity and immunodeficiency, resulting in higher comorbidity and MASS scores, as shown in Table 1. This outcome was confirmed after full matching PS analysis. We cannot retrieve data on the reason for hospitalization of controls, but it is likely that a part of them did not receive treatment for SARS-CoV-2 as they were hospitalized for reasons unrelated to COVID-19, or due to the severity of their clinical condition from other morbidities. This may have influenced the 28-days all-cause mortality among controls. The comparison analysis conducted after matching cases and controls also demonstrated a significant reduction in the composite outcome (at least one of hospital admission, ICU admission, or death). Despite utilizing the propensity score, we did not observe any difference in ICU admission rates between cases and controls due to the low incidence of this outcome. Our results are consistent with those of other cohorts. For instance, Aggarwal et al. conducted a large propensity-matched, retrospective, observational cohort study of non-hospitalised patients infected with SARS-CoV-2 using records from a health system in Colorado, USA, between March and August 2022. This period corresponded to the widespread presence of the BA.4 and BA.5 variants. In this cohort N/r treatment was associated with a reduced 28-day all-cause hospitalisation compared with no antiviral treatment (adjusted odds ratio (OR) 0.45 [95% CI 0.33–0.62]; p < 0.0001) and reduced 28-day all-cause mortality (adjusted OR 0.15 [95% CI 0.03–0.50]; p = 0.001) [5]. Another study conducted using health data records between November 2022 and March 2023, during which the predominant SARS-CoV-2 variants were BQ.1, BQ.1.1 and XBB.1.5, showed a similar efficacy of N/r treatment in preventing hospitalisation [21]. In addition to the data from Aggarwal et al., our results also demonstrated a reduction in the risk of severe outcome (namely, the risk of the composite outcome: hospital admission, ICU admission, or all-cause death) among patients with SARS-CoV-2 treated with N/r.

Indeed, the value of real-world studies on N/r extends to evaluating its effectiveness among patients with prior immunity to SARS-CoV-2, whether acquired through vaccination or through natural infection. While the pivotal EPIC-HR trial only included unvaccinated patients, the landscape has significantly changed since then. Vaccination against COVID-19 has become widespread, with most of the general population having received at least two doses of the vaccine. Consequently, some studies assessing the efficacy of N/r have considered the impact of vaccination status on the outcomes in their multivariate analysis.

A real-world retrospective study published in September 2022 found that N/r demonstrated higher efficacy, particularly among unvaccinated patients older than 65 years [22]. Similar results were observed by Dryden-Peterson et al. in a cohort study conducted during the Omicron epidemic in a context of high vaccination prevalence. They reported an increased protective activity of N/r, with an 81% risk reduction among incompletely vaccinated individuals and patients who had received their most recent vaccine dose more than 20 weeks prior [20]. In a population-based cohort study conducted in Quebec, Canada, a 96% reduction in the hospitalisation rate was reported among incompletely vaccinated outpatients [23]. However, in this cohort, no benefit was observed among the vaccinated population, excluding severely immunocompromised patients and high-risk patients aged 70 years or older who had received their last vaccine dose more than 6 months prior. Despite this, further real-world studies have reported that N/r maintains its efficacy in preventing disease progression in subgroup analyses of patients who had received at least two doses of the COVID-19 vaccine [24, 25].

In our cohort, the majority of patients (1,504, 93.6%) had received at least two doses of the SARS-CoV-2 vaccine. However, our analysis conducted after full-matching PS revealed that the effects of N/r were more pronounced on non-vaccinated patients. This was evidenced by a significant impact on hospital admission, death, and the composite outcome (see Table 4). However, it is important to emphasize that even among vaccinated patients, treatment with N/r significantly reduced mortality, underscoring the potential benefits of N/r treatment across different patient populations, regardless of their vaccination status.

The use of full-matching PS is a major strength of our study. Full matching can be viewed as a form of propensity score weighting that is less sensitive to the form of the propensity score model, allowing for the estimation of a weighted treatment effect ideally free of confounding by the measured covariates [26]. One significant advantage of this matching algorithm is that all individuals are retained, often resulting in more balance than 1:1 matching [27]. This was the case in our study, where there was a marked baseline disproportion between the two groups in a key variable, namely the immunodeficiency status: 49.4% among treated and 5.3% among untreated, respectively. In contrast, the most commonly employed, nearest neighbour matching would have resulted in poor balance and also discarded a large number of observations, leading to a reduced power [28].

The central finding of our study is the positive impact of N/r on survival in a population where the majority (> 90%) of patients were vaccinated. This contrasts with the recent findings form EPIC-SR study [29]. This new randomized trial initially planned to exclude individuals with significant comorbidities, including immunosuppression, but later amended its protocol to include such participants if they had received a full course of vaccination. Notably, the EPIC-HR trial, which demonstrated a significant reduction in COVID-19–related hospitalization or death associated with N/r use compared to placebo, did not include vaccinated individuals [4]. In the EPIC-SR study, where 56.9% of participants were vaccinated, no differences were detected between the N/r arm and placebo arm regarding time to sustained alleviation (the primary outcome). However, in a planned subgroup analysis involving high-risk patients (all vaccinated with comorbidities) the relative reduction of N/r versus placebo in terms of hospitalization and death was 57% (3/317, 8/314), though this was not statistically significant [29]. In contrast, our results showed a significant reduction in mortality among patients treated with N/r (Table 3). Furthermore, while we observed no efficacy of N/r in reducing the risk of hospitalization in the entire sample, we found that non-vaccinated patients treated with N/r showed a significant reduction in hospitalization risk compared with untreated subjects (Table 4). Even if a weak signal of benefit linked with N/r regarding major outcomes was detected in frail vaccinated subjects, for which the latest trial was not powered [29], a greater benefit can be inferred in unvaccinated high-risk patients. In our cohort, 10.7% of unvaccinated individuals had immunodeficiency (See Supplementary Table 1). As is the case with many medical interventions, there is likely to be a gradient of benefit for the antiviral treatment, with the greatest benefit observed in subjects at highest risk for progression [30].

We recognize that our study has several limitations. Firstly, it is subject to all the biases inherent to its retrospective study design. While data for the cases were collected prospectively, data for the controls, who represent a significant percentage of all the included patients (73.7%), were retrieved retrospectively. Specifically, it is plausible that a proportion of the controls, identified through telephone interviews directly or via their relatives, may not have accurately reported baseline features (e.g., vaccination status) or outcomes. For instance, hospital admissions beyond the predefined follow-up window might have been reported as occurring earlier due to recall bias. Despite efforts to track relatives of deceased patients, it is possible that a significant percentage of controls (or their relatives) who had an unfavourable outcome declined to be interviewed. However, given the large number of controls included in the study, this bias may have been mitigated. Moreover, the lack of data regarding vaccination status (e.g. number of vaccine doses received, and date of last dose received) precluded us from analysing the effect of booster vaccine on the outcome of enrolled patients. Similarly, we were unable to retrieve data on previous SARS-CoV-2 infections, as these infections may have been underreported, either due to being asymptomatic or because patients with suggestive symptoms did not undergo diagnostic testing for SARS-CoV-2. To address this limitation, we assessed the presence of anti-SARS-CoV-2 spike protein antibodies when such data was available. However, the vast majority of patients had never undergone serological testing. Additionally, a positive serology for SARS-CoV-2 spike protein could not differentiate between past infection and vaccine-acquired immunity, rendering these data not useful for our analysis. Concerning the endpoints, we aimed to retrieve objective outcomes, discarding more subjective endpoints such as symptom resolution, which would have been difficult to reliably verify in the control group. It should also be noted that the collection of clinical data through telephone interviews, in the absence of reliable clinical files and interaction with healthcare professionals, compromises the trustworthiness and accuracy of such data. For this reason, the Charlson score was unsuitable for our analysis, and we had to identify a surrogate score to stratify each patient’s risk. Additionally, in our study, we were unable to trace back the time span since the last vaccine administration among the vaccinated population. Another limitation is the lack of detection of SARS-CoV-2 rebound, typically described as a recurrence of symptoms or a new positive viral test after testing negative, although definitions vary widely. Both interventional and observational studies have shown that subjects undergoing treatment with N/r may experience viral rebound [31]. In fact, there is no consistent association between N/r and COVID-19 rebound, as it can occur after any other antiviral treatment and even in untreated subjects, likely due to a combination of factors such as immunosuppression, delayed viral clearance, and variable host-mounted immune response [32].

Conclusions

N/r has been confirmed to effectively reduce the risk of death and severe outcomes in a population of patients primarily infected with the SARS-CoV-2 Omicron BA.2 and BA.5 variants. This population notably includes a significant proportion of immunosuppressed individuals. The efficacy of N/r is especially pronounced in non-vaccinated patients, where it has also been shown to decrease the risk of hospitalization. Interestingly, N/r has been found to significantly reduce mortality even in vaccinated patients. Given these findings, treatment with N/r should be considered in all patients with early SARS-CoV-2 infection and risk factors for progression to severe COVID-19. However, high-quality randomized controlled trials should be conducted to further strengthen this recommendation.