A phase I/II clinical trial of intradermal, controllable self-replicating RNA vaccine EXG 5003 against SARS-CoV-2 (preprint)

mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have played a key role in reducing morbidity and mortality from coronavirus disease 2019 (COVID 19). We conducted a double-blind, placebo-controlled phase I/II trial to evaluate the safety, tolerability, and immunogenicity of EXG 5003, a two-dose, controllable self-replicating RNA vaccine against SARS-CoV-2. EXG 5003 encodes the receptor binding domain (RBD) of SARS-CoV-2 and was administered intradermally without lipid nanoparticles (LNP). The participants were followed for 12 months. Forty healthy participants were enrolled in Cohort 1 (5 g per dose, n = 16; placebo, n = 4) and Cohort 2 (25 g per dose, n = 16; placebo, n = 4). No safety concerns were observed with EXG 5003 administration. SARS-CoV-2 RBD antibody titers and neutralizing antibody titers were not elevated in either cohort. Elicitation of antigen-specific cellular immunity was observed in the EXG 5003 recipients in Cohort 2. At the 12-month follow-up, participants who had received an approved mRNA vaccine (BNT162b2 or mRNA-1273) >1 month after receiving the second dose of EXG 5003 showed higher cellular responses compared to equivalently vaccinated participants in the placebo group. The findings suggest a priming effect by EXG-5003 on the long-term cellular immunity of approved SARS-CoV-2 mRNA vaccines.

Efficacy and Safety of 5-Day Oral Ensitrelvir for Patients With Mild-to-Moderate COVID-19: The SCORPIO-SR Randomized Clinical Trial (preprint)

IMPORTANCE Treatment options for coronavirus disease 2019 (COVID-19) that can be used irrespective of risk factors for severe disease are warranted. OBJECTIVE To assess the efficacy and safety of ensitrelvir in patients with mild-to-moderate COVID-19. DESIGN The phase 3 part of a phase 2/3, double-blind, randomized, placebo controlled study conducted from February 10 to July 10, 2022. SETTING A multicenter study conducted at 92 institutions in Japan, Vietnam, and South Korea. PARTICIPANTS Patients (aged 12 to <70 years) with mild-to-moderate COVID-19 within 120 hours of positive viral testing. INTERVENTIONS Patients were randomized (1:1:1) to receive once-daily ensitrelvir 125 mg (375 mg on day 1), 250 mg (750 mg on day 1), or placebo for 5 days. Among 1821 randomized patients, 1030 (347, 340, and 343 in the ensitrelvir 125-mg, ensitrelvir 250-mg, and placebo groups, respectively) were randomized in less than 72 hours of disease onset and assessed as the primary analysis population. MAIN OUTCOMES AND MEASURES The primary end point was the time to resolution of five COVID-19 symptoms (stuffy or runny nose, sore throat, cough, feeling hot or feverish, and low energy or tiredness). Other end points included virologic efficacy and safety. RESULTS The mean age was 35.7, 35.3, and 34.7 years, and 193 (55.6%), 185 (54.4%), and 174 (50.7%) patients were men in the ensitrelvir 125-mg, ensitrelvir 250-mg, and placebo groups, respectively (intention-to-treat, primary analysis population). A significant difference (P=.04 with a Peto-Prentice generalized Wilcoxon test stratified by vaccination history) was observed in the primary end point between ensitrelvir 125 mg and placebo in the primary analysis population (difference in median, -24.3 hours; 95% confidence interval, -78.7 to 11.7). Viral RNA levels on day 4 and time to negative viral titer demonstrated significant reduction vs placebo. The incidence of adverse events was 44.2%, 53.6%, and 24.8% in the ensitrelvir 125-mg, ensitrelvir 250-mg, and placebo groups, respectively. No treatment-related serious adverse events were reported. CONCLUSIONS AND RELEVANCE Treatment with ensitrelvir 125 mg demonstrated clinical and antiviral efficacy without new safety concerns. Generalizability to non-Asian populations should be confirmed. TRIAL REGISTRATION Japan Registry of Clinical Trials identifier: jRCT2031210350.

Efficacy and safety of ensitrelvir in patients with mild-to-moderate COVID-19: A protocol for a multicenter, randomized, double-blind, placebo-controlled, phase 3 study (the SCORPIO-SR trial) (preprint)

BackgroundMost antiviral treatments are targeted toward patients with severe or moderate-to-severe illness or those at high risk of developing severe Coronavirus disease 2019 (COVID-19). Limited options exist for patients with mild-to-moderate COVID-19, irrespective of vaccination history or risk status. Ensitrelvir is a novel oral SARS-CoV-2 3C-like protease inhibitor. The phase 2 studies of ensitrelvir have demonstrated promising results in mild-to-moderate COVID-19, whereas the challenge to evaluate the clinical efficacy due to shifting vaccinated status and the emergence of the Omicron variant has been suggested. Here, we describe the protocol for a phase 3 study designed to evaluate the efficacy and safety of ensitrelvir in patients with mild-to-moderate COVID-19, regardless of risk status or vaccination history. MethodsThis is a multicenter, randomized, double-blind, placebo-controlled, phase 3 study. Patients with mild-to-moderate COVID-19 within 120 hours from onset will be randomized in a 1:1:1 ratio into 3 treatment arms--ensitrelvir 125 mg (375 mg as loading dose on Day 1), ensitrelvir 250 mg (750 mg as loading dose on Day 1), or placebo. The study interventions will be administered orally once daily for 5 days. The primary endpoint will be the time to resolution of the 5 symptoms of COVID-19 (stuffy or runny nose, sore throat, cough, feeling hot or feverish, low energy or tiredness), and the primary population will be patients with <72 hours from COVID-19 onset to randomization in ensitrelvir 125 mg group. The key secondary endpoints include the change from baseline on Day 4 in the amount of SARS-CoV-2 viral RNA and the time to the first negative SARS-CoV-2 viral titer. Closed testing procedure will be used for the primary and key secondary endpoints in both the primary and entire patient population. All safety assessments and adverse events will be reported. DiscussionTime to resolution of the 5 COVID-19 symptoms is a suitable endpoint to assess antiviral treatment in patients infected with the Omicron variant. In the phase 2 studies, ensitrelvir has demonstrated antiviral efficacy against SARS-CoV-2 and a trend toward reducing time to resolution of symptoms in patients with mild-to-moderate COVID-19. Through this study, we will seek to validate and establish the clinical efficacy and safety of ensitrelvir in patients with mild-to-moderate COVID-19. Trial registrationJapan Registry of Clinical Trials (https://jrct.niph.go.jp): jRCT2031210350.

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 (preprint)

This phase 2b part of a randomized phase 2/3 study assessed the efficacy and safety of ensitrelvir for mild-to-moderate coronavirus disease 2019 (COVID-19). Patients were randomized (1:1:1) to orally receive ensitrelvir fumaric acid 125 mg (375 mg on day 1; n=140) or 250 mg (750 mg on day 1; n=140) or placebo (n=141) once daily for 5 days. Compared with placebo, the change from baseline in severe acute respiratory syndrome coronavirus 2 titer (measured as log10 50% tissue-culture infectious dose) on day 4 was significantly greater with ensitrelvir 125 mg and 250 mg (differences from placebo: -0.41, P<0.0001 for both). The total score of predefined 12 COVID-19 symptoms showed an improving trend with ensitrelvir treatment without a significant intergroup difference. Most adverse events were mild in severity. Ensitrelvir treatment demonstrated a favorable antiviral efficacy and potential clinical benefit with an acceptable safety profile. (Japan Registry of Clinical Trials identifier: jRCT2031210350)

A Randomized Phase 2/3 Study of Ensitrelvir, a Novel Oral SARS-CoV-2 3C-like Protease Inhibitor, in Japanese Patients With Mild-to-Moderate COVID-19 or Asymptomatic SARS-CoV-2 Infection: Results of the Phase 2a Part (preprint)

For the treatment of coronavirus disease 2019 (COVID-19), antiviral agents that can achieve rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reduction are warranted. This double-blind, phase 2a part of a phase 2/3 study assessed the efficacy and safety of ensitrelvir, a novel oral SARS-CoV-2 3C-like protease inhibitor, in Japanese patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection. Sixty-nine patients enrolled from 56 sites were randomized (1:1:1) to orally receive 5-day ensitrelvir fumaric acid (375 mg on day 1 followed by 125 mg daily or 750 mg on day 1 followed by 250 mg daily) or placebo and followed up until day 28. The primary outcome was change from baseline in SARS-CoV-2 viral titer. A total of 16, 14, and 17 patients in the ensitrelvir 125 mg, ensitrelvir 250 mg, and placebo groups, respectively, were included in the intention-to-treat population (mean age: 38.8, 40.4, and 38.0 years, respectively). On day 4, the change from baseline in SARS-CoV-2 viral titer (log10 50% tissue culture infectious dose/mL) in patients with positive viral titer and viral RNA at baseline was greater with ensitrelvir 125 mg (mean [standard deviation], -2.42 [1.42]; P = 0.0712) and 250 mg (-2.81 [1.21]; P = 0.0083) versus placebo (-1.54 [0.74]), and ensitrelvir treatment reduced SARS-CoV-2 RNA by -1.4 to -1.5 log10 copies/mL versus placebo. All adverse events were mild to moderate. Ensitrelvir treatment demonstrated rapid SARS-CoV-2 clearance and was well tolerated in patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection (Japan Registry of Clinical Trials identifier: jRCT2031210350).

An Early Return-to-Work Program for COVID-19 Close Contacts in Healthcare During the Omicron Wave in Japan (preprint)

During the coronavirus disease 2019 (COVID-19) pandemic, maintaining adequate staffing in healthcare facilities is important to provide a safe work environment for healthcare workers (HCWs). Japanese early return-to-work (RTW) program may be a rational strategy at a time when there is an increased demand for the services of HCWs. We assessed whether the early RTW program for HCWs who have been in close contact with a COVID-19 case in our hospital was justified. Close contacts were identified according to the guidance of the World Health Organization. Between January and March 2022, 256 HCWs were identified as close contacts (median age, 35 years; 192 female). Thirty-seven (14%) secondary attack cases of COVID-19 were detected. Among 141 HCWs who applied to the early RTW program, nurses and doctors comprised about three-quarters of participants, with a higher participation rate by doctors (78%) than nurses (59%). Eighteen HCWs tested positive for COVID-19 by the sixth day after starting the early RTW program. No COVID-19 infection clusters were reported during the observation period. These findings suggest that the early RTW program for COVID-19 close contacts was a reasonable strategy for HCWs during the Omicron wave.

Machine Learning Supports Clinical Decision in Optimized Treatment for COVID-19 Patients (preprint)

Background: It has been difficult to distinguish between mild, moderate, and severe cases at an early stage for COVID-19 patients, making it challenging to decide an optimized treatment for each patient. This machine learning system could predict the clinical course and be used to develop a novel method to provide optimal treatment based on risk. Method: We applied machine learning techniques to international clinical data from a large cohort of patients with COVID-19 at 15 hospitals in Japan and three hospitals in New York City from January 1, 2020 to March 30, 2021. We analyzed clinical information of over 2000 COVID-19 patients comprising various races and ethnicities and built a severity and mortality prediction model. Furthermore, using a severity index with machine learning allowed early detection of patients most at-risk for developing severe illness to support the decision for the patient to receive optimized therapy. Findings: We developed an international COVID-19 early prediction model for use at the time of hospital admission that predicts disease severity and mortality with high accuracy, 0.88 (AUC). Using the novel method of severity-matched analysis to assess treatment effectiveness, in the high-risk group, the Kaplan–Meier estimates of mortality by Day 30 were 26% in the dexamethasone treatment group and 63% in the non-treatment group. The Kaplan–Meier estimates of mortality were low at 3% with remdesivir and dexamethasone in combination and 49% with no remdesivir and dexamethasone treatment by Day 30. There may be an add-on effect of remdesivir to conventional dexamethasone. Interpretation: The severity prediction index can be calculated, which can assist with an optimized treatment for COVID-19 patients in each risk group. The severity-matched treatment system could support the recommendation of optimized treatments, such as dexamethasone, remdesivir, or heparin, in high-risk groups by calculating the severity index predicted at the time of the first visit.Trial Registration Details: The trial registration number was 2020142NI. Funding Information: K.T., K.I., and Y.D. received funding from the Japan Agency for Medical Research and Development (AMED) (19fk0108153h0001). K.T. received funding from AMED (19jm0610015h0001). K.T. received funding from the Healthy Longevity Global Grand Challenge, Catalyst Award.Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: The study protocol was centrally reviewed by the Institutional Review Board of Tokyo University. The requirement for consent was waived given the retrospective and non-interventional nature of the study.

Comparative analysis of antigen-specific anti-SARS-CoV-2 antibody isotypes in COVID-19 patients (preprint)

Serological tests for detection of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in blood are expected to identify individuals who have acquired immunity against SARS-CoV-2 and indication of seroprevalence of SARS-CoV-2 infection. Many serological tests have been developed to detect antibodies against SARS-CoV-2. However, these tests have considerable variations in their specificity and sensitivity, and whether they can predict levels of neutralizing activity is yet to be determined. This study aimed to investigate the kinetics and neutralizing activity of various antigen-specific antibody isotypes against SARS-CoV-2 in serum of coronavirus disease 2019 (COVID-19) patients confirmed via polymerase chain reaction test. We developed IgG, IgM and IgA measurement assays for each antigen, including receptor-binding domain (RBD) of spike (S) protein, S1 domain, full length S protein, S trimer and nucleocapsid (N) domain, based on enzyme-linked immunosorbent assay. The assays of the S protein for all isotypes showed high specificity, while the assays for all isotypes against N protein showed lower specificity. The sensitivity of all antigen-specific antibody isotypes depended on the timing of the serum collection and all of them, except for IgM against N protein, reached more than 90% at 15-21 days post-symptom onset. The best correlation with virus neutralizing activity was found for IgG against RBD (RBD-IgG), and levels of RBD-IgG in sera from four severe COVID-19 patients increased concordantly with neutralizing activity. Our results provide valuable information regarding the selection of serological test for seroprevalence and vaccine evaluation studies.

Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide (preprint)

Cell penetration after recognition of the SARS-CoV-2 virus by the ACE2 receptor, and the fusion of its viral envelope membrane with cellular membranes, are the early steps of infectivity. A region of the Spike protein (S) of the virus, identified as the "fusion peptide" (FP), is liberated at its N-terminal site by a specific cleavage occurring in concert with the interaction of the receptor binding domain of the Spike. Studies have shown that penetration is enhanced by the required binding of Ca2+ ions to the FPs of corona viruses, but the mechanisms of membrane insertion and destabilization remain unclear. We have predicted the preferred positions of Ca2+ binding to the SARS-CoV-2-FP, the role of Ca2+ ions in mediating peptide-membrane interactions, the preferred mode of insertion of the Ca2+-bound SARS-CoV-2-FP and consequent effects on the lipid bilayer from extensive atomistic molecular dynamics (MD) simulations and trajectory analyses. In a systematic sampling of the interactions of the Ca2+-bound peptide models with lipid membranes SARS-CoV-2-FP penetrated the bilayer and disrupted its organization only in two modes involving different structural domains. In one, the hydrophobic residues F833/I834 from the middle region of the peptide are inserted. In the other, more prevalent mode, the penetration involves residues L822/F823 from the LLF motif which is conserved in CoV-2-like viruses, and is achieved by the binding of Ca2+ ions to the D830/D839 and E819/D820 residue pairs. FP penetration is shown to modify the molecular organization in specific areas of the bilayer, and the extent of membrane binding of the SARS-CoV-2 FP is significantly reduced in the absence of Ca2+ ions. These findings provide novel mechanistic insights regarding the role of Ca2+ in mediating SARS-CoV-2 fusion and provide a detailed structural platform to aid the ongoing efforts in rational design of compounds to inhibit SARS-CoV-2 cell entry. STATEMENT OF SIGNIFICANCESARS-CoV-2, the cause of the COVID-19 pandemic, penetrates host cell membranes and uses viral-to-cellular membrane fusion to release its genetic material for replication. Experiments had identified a region termed "fusion peptide" (FP) in the Spike proteins of coronaviruses, as the spearhead in these initial processes, and suggested that Ca2+ is needed to support both functions. Absent structure and dynamics-based mechanistic information these FP functions could not be targeted for therapeutic interventions. We describe the development and determination of the missing information from analysis of extensive MD simulation trajectories, and propose specific Ca2+-dependent mechanisms of SARS-CoV-2-FP membrane insertion and destabilization. These results offer a structure-specific platform to aid the ongoing efforts to use this target for the discovery and/or of inhibitors.

Dry loop mediated isothermal amplification assay for detection of SARS-CoV-2 from clinical specimens (preprint)

Coronavirus disease 2019 (COVID-19) has had a major disease burden on many countries around the world. The spread of COVID-19 is anticipated to have a major impact on developing countries including African nations. To establish a point-of-care test for COVID-19, we developed a dry loop mediated isothermal amplification (LAMP) method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. We carried out reverse transcription (RT)-LAMP using the Loopamp SARS-CoV-2 Detection kit (Eiken Chemical, Tokyo, Japan). The entire mixture except for the primers is dried and immobilized inside the tube lid. To determine the specificity of the kit, 22 viral genomes associated with respiratory infections, including the SARS coronavirus, were tested. No LAMP product was detected in reactions performed with RNA from these pathogens. The sensitivity of this assay, determined by either a real-time turbidity assay or colorimetric change of the reaction mixture, as evaluated by the naked eye or under illumination with ultraviolet light, was 10 copies/reaction. After the initial validation analysis, we analyzed 24 nasopharyngeal swab specimens collected from patients suspected to have COVID-19. Nineteen (79.2%) of the 24 samples were positive for SARS-CoV-2 RNA, as determined by real-time RT-PCR analysis. Using the Loopamp SARS-CoV-2 Detection kit, we detected SARS-CoV-2 RNA in 15 (62.5%) of the 24 samples. Thus, the sensitivity, specificity, positive predictive value, and negative predictive value of the Loopamp 2019-CoV-2 detection reagent kit were 94.0%, 96.0%, 95.9%, and 94.1%, respectively. The dry LAMP method for detection of SARS-CoV-2 RNA was fast and easy to use, solves the cold chain problem, and therefore represents a promising tool for diagnosis of COVID-19 in developing countries.

Reliability of serological tests for COVID-19: Comparison of three immunochromatography test kits for SARS-CoV-2 antibodies. (preprint)

Background: Several immunochromatographic serological test kits have been developed to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibodies, but their relative performance and potential clinical utility is unclear. Methods: Three commercially available serological test kits were evaluated using 99 serum samples collected from 29 patients diagnosed with coronavirus disease 2019 (COVID-19). Results: The IgM antibody-positive rates of the three serological test kits for samples taken at the early stage of the disease (0-6 days after onset) were 19.0%, 23.8%, and 19.0%, respectively. The IgM antibody-positive rates over the entire period were 21.2%, 60.6%, and 15.2%, respectively. The IgG antibody-positive rates for samples taken after 13 days of onset were 100.0%, 97.6%, and 97.6%, respectively. Conclusion: There were large differences among the results of the three test kits. Only few cases showed positive results for IgM in the early stage of disease and the IgM antibody-positive rates over the entire period were low, suggesting that the kits used in this study were unsuitable for diagnosis of COVID-19. The IgG antibody was positive in almost all samples after 13 days of onset, suggesting that it may be useful for determining infections in the recent past.