ABSTRACT
Background/Objectives: COVID-19 still represents a lifethreatening disease in individuals with a specific genetic background. We successfully applied a new Machine Learning method on WES data to extract a set of coding variants relevant for COVID- 19 severity. We aim to identify personalized add-on therapy. Method(s): A subset of identified variants, "actionable" by repurposed drugs, were functionally tested by in vitro and in vivo experiments. Result(s): Males with either rare loss of function variants in the TLR7 gene or L412F polymorphism in the TLR3 gene benefit from IFN-gamma, which is specifically defective in activated PBMCs, restoring innate immunity. Females heterozygous for rare variants in the ADAMTS13 gene and males with D603N homozygous polymorphism in the SELP gene benefit from Caplacizumab, which reduces vWF aggregation and thrombus formation. Males with either the low-frequency gain of function variant T201M in CYP19A1 gene or with poly-Q repeats >=23 in the AR gene benefit from Letrozole, an aromatase inhibitor, which restores normal testosterone levels, reducing inflammation and which rescues male golden hamsters from severe COVID-19. Conclusion(s): By adding these commonly used drugs to standard of care of selected patients, the rate of intubation is expected to decrease consistently, especially in patients with high penetrance rare genetic markers, mitigating the effect of the pandemic with a significant impact on the healthcare system.
ABSTRACT
Background: SARS-CoV-2 Omicron sublineages exhibit evolving escape to in vitro neutralization by monoclonal antibodies (mAbs), with an unclear impact on in vivo treatment response. Our aim is to assess the impact of SARS-Cov-2 variants on the decline of viral load (VL) after treatment with 3 different drugs approved in EU for the early treatment of patients with mild-moderate COVID-19. Method(s): Post-hoc analysis from MONET (EudraCT: 2021-004188-28), phase 4 open-label RCT to assess efficacy of 500 mg intravenous sotrovimab (SOT), 600 mg intramuscular tixagevimab/cilgavimab (TIX/CIL) and oral 5-days course of NMV/r 300/100 mg BID, in non-hospitalized high-risk patients (pts) with early COVID-19. Pts' features were analyzed as binary variables by Chi-squared test. SARS-Cov-2 VL in nasopharyngeal swabs was carried out at randomization (1d) and at day 7 (7d) by cycle threshold value (Ct). Variant sequencing was performed at 1d. Ct variation was assessed by mixed effect log-linear model including random intercept at pts' level, log of Ct as independent variable, time, arm, viral variant as dependent variables, and interaction between time and arm. Multiple comparisons were adjusted by Bonferroni. Result(s): Among the 320 pts included between 4 Mar and 16 Nov, 2022, 108 (33.75%) received NMV/r, 103 (32.19%) TIX/CIL, and 109 (34.06%) SOT. Main characteristics were balanced across arms. Most of the pts were infected either with BA.2 (N=194;60.63%) or BA.4/BA.5 (N=100;31.25%) (Fig1A). VL at 1d was similar across the arms. In contrast, mean 7d VL was significantly lower in pts receiving NMV/r than in those receiving TIX/ CIL or SOT (P< 0.001) No significant VL variation was observed between the mAb arms (Fig1B). The analysis of the impact of viral variants suggests that while VL was significantly affected by variants (P=0.034), the superior effect of NMV/r over mAbs was homogeneous across all variant groups (P=0.290 for interaction) (Fig1C). Conclusion(s): Our study provides for the first time strong in vivo evidence that, when used against Omicron lineages, NMV/r exerts a stronger antiviral effect than mAbs. These results confirm previous in vitro evidence suggesting that mAbs may not retain neutralizing activity against all Omicron sublineages and provide preliminary information on how to use VL variation as a surrogate marker of efficacy. Further studies are needed to investigate whether the superior virologic activity of NMV/r over mAbs is confirmed for newly emerging variants, including BQ.1.1 or XBB.
ABSTRACT
Background: Omicron subvariants questioned the efficacy of the approved therapies for the early COVID-19. In vitro data show that remdesivir (RDV), molnupiravir (MLN), and nirmatrelvir/ritonavir (NMV/r) all retained activity against all sub-lineages, while poor neutralizing activity was observed for Sotrovimab (SOT) and Tixagevimab/cilgavimab (TIX/CIL). No data about the risk of clinical failure or even in vivo antiviral activity are available. Method(s): Single-center observational comparison study enrolling all consecutive patients (pts) seen for care with a confirmed SARS-CoV-2 Omicron diagnosis and who met the AIFA criteria for eligibility for treatment with RDV, MLN, NMV/r, TIX/CIL, or SOT. Treatment allocation was subject to drug availability, time from symptoms onset, and comorbidities. Nasopharyngeal swab (NPS) VL was measured on day 1 (D1) and D7 and was expressed by log2 cycle threshold (CT) scale. Comparisons between treatment groups were made by Chi-square, and Wilcoxon paired tests. Primary endpoint was D1-D7 VL variation. Potential decrease in VL and average treatment effect (ATE) were calculated from fitting marginal linear regression models weighted for calendar month of drug initiation, duration of symptoms, and immunodeficiency using NMV/r as the comparator trial arm. Result(s): A total of 971 pts received treatments (SOT 321, MLN 231, NMV/r 211, TIX/CIL 70, and RDV 138): female 457 (47%), median age 67 yrs (IQR 56-78), 93% vaccinated;12% with negative baseline serology. At D1, median time from symptoms onset was 3 days (IQR 2,4). 379 (39%) pts were infected with BA.1, 215 (22%) with BA.2, 372 with BA.4/5 (38%), and 5 with BQ.1 (0,5%). D1 mean viral load was 4.02 log2. Adjusted analysis (ATE) showed that NMV/r significantly reduced VL compared to all the other drugs in pts infected with all sublineages, (Fig.1A-B) while less evidence for a difference vs. TIX/CIL was seen in those infected with BA.2 (p=0.05) (Fig.1 C-D). Conclusion(s): In this analysis of in vivo early VL reductions, NMV/r appears to be the drug showing the greatest antiviral activity, regardless of the underlying subvariant, perhaps with the exception of TIX/CIL in people infected with BA.2 for which there was less evidence for a difference. In the Omicron era, due to the high prevalence of vaccinated people and in absence of clinical events, VL is one of the possible alternative endpoints which guarantees adequate statistical power. Fig 1 SARS-CoV-2 RNA levels at D1 and D7 in patients treated with Nirmatrelvir/ ritonavir, Sotrovimab, Molnupiravir, Remdesivir, and Tixagevimab/cilgavimab. Dot-plots showing the comparison of viral loads detected at D1 and D7 and the variation of RNA levels observed between the two time-points by intervention in (A) all patients treated with Nirmatrelvir/ritonavir (n=211), Sotrovimab (n=321), or Molnupiravir (n=231), or Remdesivir (n=138), or Tixagevimab/ cilgavimab (n=136);(C) patients with Omicron BA.2 infection treated with Nirmatrelvir/ritonavir (n=58), Sotrovimab (n=81), or Molnupiravir (n=21), or Remdesivir (n=37), or Tixagevimab/cilgavimab (n=18);(D) patients with Omicron BA.4/5 infection treated with Nirmatrelvir/ritonavir (n=102), Sotrovimab (n=92), or Molnupiravir (n=110), or Remdesivir (n=16), or Tixagevimab/cilgavimab (n=52). Viral RNA levels are expressed as log2 CT values. The horizontal dashed line represents the limit of detection (CT: 40.0), values >=40 are considered negative. Mean of log2 CT values, and SD are shown in the graph. Statistical analysis of the differences in viral loads by intervention as compared to Nirmatrelvir/ritonavir was performed by Mann-Whitney test. Potential decrease in VL and average treatment effect (ATE) were calculated from fitting marginal linear regression models weighted for calendar month of drug initiation, duration of symptoms, and immunodeficiency using NMV/r as the comparator trial arm. Results are shown (B) for patients infected with all Omicron sublineages and (D) for those infected with Omicron BA.2 sublineage.
ABSTRACT
Background: Antivirals and monoclonal antibodies (mAbs) were approved for early treatment of COVID-19 based on data from trials conducted in unvaccinated people before the Omicron era. The comparative effectiveness of different treatments is unknown. We present the results of the interim analysis of MONET trial (EudraCT: 2021-004188-28). Method(s): In this ongoing multicenter, open-label, phase 4 trial, we randomly assigned, in a 1:1:1 ratio, non-hospitalized patients with early symptomatic Covid-19 (<=5 days after symptoms onset) and >=1 risk factor for disease progression, to receive 500 mg of intravenous sotrovimab (SOT) or 600 mg of intramuscular tixagevimab/cilgavimab (TIX/CIL) or oral 5-days course of NMV/r 300/100 mg BID. Primary outcome was hospitalization or death for any cause within 29 days after randomization, reported as cumulative incidence per 100 (95% CI), and P-value calculated by Fisher's exact test. Inflammatory marker (CRP, d-dimer, and neutrophils-to-lymphocytes ratio) and antibody level (serum anti-S IgG and anti-N IgG) analysed by mixed linear regression with random intercept and P-values for time trend calculated by ANOVA-style test with Bonferroni correction. Result(s): Prespecified interim analysis, including 400 patients (SOT =133, TIX/ CIL=130, NMV/r=137) enrolled from Mar 4 to Nov 16, 2022 (Fig.1A). Overall, 5 pts (3/5 immunosuppressed) had disease progression leading to hospitalization [1.25% (95% CI 0.4%-2.89%)], 1 in SOT (0.75%, 95% CI 0.01%-4.1%), 4 in TIX/CIL (3.08%, 95% CI 0.84%-7.69%) and none in NMV/r arm (P=0.030). No deaths or ICU admissions were observed. Among the hospitalized pts, 3 were infected with BA.2 (1 SOT, 2 TIX/CIL), one with BA.4/5, and one BQ.1.1 (both TIX/ CIL). No serious adverse events and no kidney or liver toxicity were reported. Temporal trend of inflammation markers was similar in the three arms, and their estimates are shown in Fig.1B. Kinetics of antibody was reported in Fig.1C. The plot shows a rapid increase of anti-S in both mAb arm and a linear increase of IgG in the NMV/r arm. Anti-N IgG kinetics was similar in the three arms. Conclusion(s): By these data the overall cumulative risk of clinical failure in mild Covid-19 occurring in the Omicron era is low. The hypothesis that differences in clinical progression among the three arms could be related to different activity against the Omicron subvariant observed in vitro should be further investigated. Type of treatment does not seem to influence the development of the natural antibody response.
ABSTRACT
Background: Early treatment for preventing severe outcome of COVID-19 in high-risk not-hospitalized patients (pts) by monoclonal antibodies or antivirals represented a high-priority approach. Real-world evidence (RWE) from observational studies could give information on clinical effectiveness and predictors of treatment failure. Method(s): Single-center observational study on SARS-CoV-2 pts, not requiring hospital admission but having high-risk of severe outcome from COVID-19. All were selected for early treatment with monoclonal antibodies or antivirals from March 2021 to November 2022. Participants were classified according to whether they were hospitalized due to severe COVID-19 or died by day 30 from starting treatment in the outpatient setting (baseline). We conducted a logistic regression analysis with this binary endpoint and 4 main exposures of interest measured at baseline: i) age ( >75 years old) ii) vaccination status iii) VoC, and iv) immunosuppression or having received immunosuppressive therapy. We built a separate model for each of these exposures, which included a specific set of potential confounders. Result(s): 3,491 pts, female 48.6%, median age 67 yrs (IQR 55-77), fully vaccinated 83.7%;previous infection 4.6%;CVD 52.2%;cancer 24.6%;immunodeficiency 40.6%. Prevalence of SARS-CoV-2 VoC: delta 8.7%, BA.1 16.9%, BA.2 6.8%, BA.4/5 12.2, BQ 0.1%, other 3.0% (Tab.1A). Treatment exposure was BAM/ETE 569 (16.5%), CAS/IMD 262 (7.6%), SOT 935 (27.1%), TIX/CIL 79 (2.3%), NMV/r 555 (16.1%), MLP 684 (19.8%), RDV 356 (10.3%). Primary endpoint occurred in 80/3,491 pts with a day-30 incident risk of 2.3% (95%CI 1.8-2.9). Tab.1B shows the unadjusted and adjusted odds ratios (OR) of hospitalization due to COVID-19 or death by day 30. After controlling for potential confounders, higher risk was observed for the unvaccinated (OR 1.95;95%CI 1.03-3.71) and for those affected by immunodeficiency [1.73;1.04-2.89). Having delta as reference variant, an increased risk was observed for BA.2 [2.08;1.00-2.34]. No evidence for a difference was seen by age or other comorbidities. Conclusion(s): In this RWE study, largely represented by vaccinated people and prevalently observed in the Omicron era, the estimated risk of clinical failure of early treatment was slightly higher than that recorded in the experimental arms of randomized studies. The analysis confirms that among those eligible for early treatment, the unvaccinated and those with severe immunodeficiency are at higher risk of developing severe COVID-19. Table 1 -A. Main characteristics of 3,491 not-hospitalized people with mildto-moderate COVID-19 at high risk of severe disease observed between March 2021 to November 2022 according to reaching (n=80) or not reaching (3,411) primary clinical endpoint. B. Odds ratios (OR) of having a COVID-19-related hospitalization or death by different exposure factors.
ABSTRACT
Background: In Italy in September 2021, administration of a booster shot (BS) of COVID-19 vaccine was approved for PLWH with advanced disease (current CD4 count<200 cell/mm3 and/or previous AIDS). The aim of this analysis was to investigate the degree of immunogenicity after BS by current CD4 count. Methods: In PLWH attending INMI Spallanzani Hospital in Rome, Italy and receiving a BS of BNT162b2 or mRNA-1273 >28 days after a complete mRNA vaccination cycle, immunogenicity was assessed at time of BS (T0) and at day 15 (T1) by anti-RBD CLIA, microneutralization assay [MNA90] and IFNγ production. Participants were stratified by CD4 count at T0 (severe immunodeficiency, SID: <200/mm3;minor immunodeficiency, MID: 200-500/mm3;no immunodeficiency, NID: >500/mm3). Immune response was defined: anti-RBD >7.1 BAU/mL, MNA90 titres >1:10 and IFNγ >12 pg/mL. A paired t-test was used to test overall changes (log2 scale) over T0-T1. ANOVA and truncated regression models were used to compare change in titers from T0 to T1, association between current CD4 count and the lack of immune response was determined by fitting a multivariable logistic regression adjusted for age, time from HIV diagnosis, CD4 nadir, cancer and HIV-RNA a T0. Results: We included 216 PLWH on ART (n=76 SID, n=96 MID, n=44 NID): median age 54 yrs (IQR 47-59), median CD4 nadir 45 cell/mm3 (20-122), 93% HIV-RNA <50 c/mL, 7yrs (3-12) since HIV diagnosis and 5yrs (2-8) since AIDS if diagnosed. Participants received BS after a median of 142 (132-156) days from second dose. Response rate was 95.5% in SID, 100% in MID, 100% in NID for anti-RBD (p=0.02);86.3%, 97.9% and 98.7% for nAbs (p=0.002), and 70%, 95.6% and 97.2% for IFNγ (p<0.0001). Overall we observed a significant increase of BS immunogenicity [anti RBD: mean Log2 4.5 (SD 1.9),p<0.0001;nAbs: 3.7 (2.2),p<0.0001;IFNγ: 0.77 (2.9),p=0.0003]. However, there was no evidence for a difference in mean change of humoral immunogenicity, anti-RBD, nAbs and IFNγ changes by CD4 count groups (Figure 1 A-C). A current CD4 count <200 cell/mm3 was not associated with the risk of failing to elicit neutralizing and cell-mediated response by logistic regression (Figure1D). Conclusion: A mRNA BS strongly boosted humoral response in PLWH with advanced disease, regardless of CD4 count at the time of booster. Although clinical implications of the observed immunological response remain uncertain, our data support the usefulness of BS in PLWH with immune dysregulation.
ABSTRACT
Background: Waning of vaccine protection against SARS-CoV-2 infection is currently a concern and durability of specific immunity after vaccination in PLWH is still unknown. The aim of this analysis was to evaluate persistence of immune response to mRNA vaccines in PLWH with advanced disease. Methods: PLWH with a CD4 count ≤200/mm3 and/or previous AIDS, enrolled in a SARS-CoV-2 vaccination program at INMI hospital in Rome, Italy, were evaluated >90 days after 2nd dose of BNT162b2 or mRNA-1273 (time T1). Anti-RBD by CLIA, neutralizing antibody (nAb) titers by microneutralization assay (MNA90) and IFNγ production were assessed and response defined as having anti-RBD >7.1 BAU/mL, nAbs ≥1:10, IFNγ >12 pg/mL. Participants were stratified by CD4 count (severe immunodeficiency, SID, ≤200/mm3;minor immunodeficiency, MID, 201-500/mm3;no immunodeficiency, NID, >500/mm3). Waning of immune response was evaluated in a subgroup of responders for whom two values post 2nd dose were available. Paired t-test was used to test the overall decline. ANOVA and logistic regression analysis controlling for age, viral load, CD4 nadir and cancer were used for comparisons by CD4 groups. Results: 221 pts were included (SID=47;MID=98;NID=76);81% male;median age 55 yrs (IQR 49-60);median time from HIV diagnosis 7 yrs (3-15);74% previous AIDS diagnosis;median CD4 nadir 44/mm3 (16-122). All pts receiving ART, 87% with HIV-RNA<50 cp/mL. After a median of 145 (133-157) days after 2nd dose, a detectable anti-RBD response was still present in 83% of SID, 96% of MID and 98% of NID (P=0.0009);nAbs in 38% of SID, 78% of MID and 88% of NID (P<0.0001);IFNγ in 67% of SID, 90% of MID and 92% of NID (P=0.0002). Magnitude of residual immune response at T1 was significantly lower in SID (Figure 1a). By logistic regression, risk of nAbs undetectability was higher in SID (aOR 5.03;95% CI 1.22-20.81) and in MID (aOR 3.77;11.4-12.48) vs NID, while no evidence for a difference was found for anti-RBD and IFNγ. A significant decline of immune response was observed for all immune parameters [mean log2 (SD):-2.66 (1.08), p<0.001, for anti-RBD;-1.23 (1.26), p<0.001, for nAbs;and-0.51 (2.3), p=0.05, for IFNγ], regardless of CD4 groups (Figure 1b/c). Conclusion: A high proportion of PLWH with advanced disease showed a lack of immune response after a median of 5 months from SARS-CoV-2 mRNA vaccination, suggesting an urgent need for a booster dose. A current CD4 ≤200/mm3 was associated with higher risk of vanishing of neutralizing activity.