key: cord-1009589-rztljr05 authors: Shinde, Vivek; Bhikha, Sutika; Hoosain, Zaheer; Archary, Moherndran; Bhorat, Qasim; Fairlie, Lee; Lalloo, Umesh; Masilela, Mduduzi S. L.; Moodley, Dhayendre; Hanley, Sherika; Fouche, Leon; Louw, Cheryl; Tameris, Michele; Singh, Nishanta; Goga, Ameena; Dheda, Keertan; Grobbelaar, Coert; Kruger, Gertruida; Carrim-Ganey, Nazira; Baillie, Vicky; de Oliveira, Tulio; Koen, Anthonet Lombard; Lombaard, Johan J.; Mngqibisa, Rosie; Bhorat, As’ad Ebrahim; Benadé, Gabriella; Lalloo, Natasha; Pitsi, Annah; Vollgraaff, Pieter-Louis; Luabeya, Angelique; Esmail, Aliasgar; Petrick, Friedrich G.; Jose, Aylin Oommen; Foulkes, Sharne; Ahmed, Khatija; Thombrayil, Asha; Fries, Lou; Cloney-Clark, Shane; Zhu, Mingzhu; Bennett, Chijioke; Albert, Gary; Faust, Emmanuel; Plested, Joyce S.; Robertson, Andreana; Neal, Susan; Cho, Iksung; Glenn, Greg M.; Dubovsky, Filip; Madhi, Shabir A. title: Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant date: 2021-05-20 journal: N Engl J Med DOI: 10.1056/nejmoa2103055 sha: b4b18a5ea2bc1dd0130bae513362489028e074a4 doc_id: 1009589 cord_uid: rztljr05 BACKGROUND: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants threatens progress toward control of the Covid-19 pandemic. Evaluation of Covid-19 vaccine efficacy against SARS-CoV-2 variants is urgently needed to inform vaccine development and use. METHODS: In this phase 2a/b, multicenter, randomized, observer-blinded, placebo-controlled trial in South Africa, healthy human immunodeficiency virus (HIV)-negative adults (18 to 84 years) or medically stable people living with HIV (PLWH) (18 to 84 years) were randomized in a 1:1 ratio to receive two doses, administered 21 days apart, of either NVX-CoV2373 nanoparticle vaccine (5 μg recombinant spike protein with 50 μg Matrix-M1 adjuvant) or placebo. The primary endpoints were safety and vaccine efficacy ≥7 days following the second dose against laboratory-confirmed symptomatic Covid-19 in previously SARS-CoV-2 uninfected participants. RESULTS: A total of 4387 participants were randomized and dosed at least once, 2199 with NVX-CoV2373 and 2188 with placebo. Approximately 30% of participants were seropositive at baseline. Among 2684 baseline seronegative participants (94% HIV-negative; 6% PLWH), 15 and 29 predominantly mild to moderate Covid-19 cases were noted in NVX-CoV2373 and placebo recipients, respectively; vaccine efficacy was 49.4% (95% confidence interval [CI]: 6.1 to 72.8). Efficacy in HIV-negative participants was 60.1% (95% CI: 19.9 to 80.1) and did not differ by baseline serostatus; 38 (92.7%) of 41 sequenced cases were the B.1.351 variant. Post-hoc vaccine efficacy against B.1.351 was 51.0% (95% CI: −0.6 to 76.2) in HIV-negative participants. Preliminary local and systemic reactogenicity were primarily mild to moderate and transient, and higher with NVX-CoV2373; serious adverse events were rare in both groups. CONCLUSIONS: The NVX-CoV2373 vaccine was efficacious in preventing Covid-19, which was predominantly mild to moderate and due to the B.1.351 variant. to impair the quality of safety reporting). This study comprised two participant populations: 1) healthy HIV-negative adult male or nonpregnant female participants (Cohort 1) and 2) medically stable HIV-positive adult male or non-pregnant female participants (Cohort 2). Participants were randomly assigned in a blinded manner using the centralized Interactive Response Technology according to pre-generated randomization schedules. Safety oversight, including for specific vaccination pause rules, was performed by an independent Safety Monitoring Committee. NVX-CoV2373 is constructed from the full-length wild-type SARS-CoV-2 spike glycoprotein (GP) based upon the GenBank gene sequence MN908947, nucleotides 21563 to 25384, 1 and co-formulated with the saponin-based Matrix-M1 adjuvant. The recombinant spike protein is a type 1 trimeric GP of 1273 amino acids that is produced as an inactive S0 precursor 2 and is comprised of a full-length spike protein with amino acid substitutions in the S1/S2 cleavage domain furin cleavage site to confer protease resistance and also two proline substitutions (K986P and V987P) introduced in the heptad repeat 1 domain to produce a stable prefusion conformation. The gene for the recombinant spike protein, codon optimized for expression, was cloned using a baculovirus expression vector in Spodoptera frugiperda (Sf9) insect cells. 3, 4 The recombinant spike protein isolated from the Sf9 cell culture was solubilized and purified by several steps of chromatography and ultrafiltration. The saponin- The following supplies were used for vaccination in the study: Matrix-M1 is a saponin-based adjuvant, which is co-administered with an antigen to induce an enhanced immune response. 6 The mechanism of Matrix-M1 is not well defined, but it has been associated with a potent induction of leukocyte activation and migration into the draining lymph nodes. Even though there is no clear evidence of a specific pattern-recognition receptor being stimulated by Matrix-M1, it has been shown to induce a strong T-cell response in multiple virus vaccine models. 7 Matrix-M1, and closely related adjuvants, administered with diverse vaccine antigen targets, have been shown to be antigen dose-sparing, enhance antigen presentation/cross-presentation, expand the epitope repertoire, induce cross-neutralizing antibody responses, and boost induction of polyfunctional CD4+ and CD8+ T-cell responses. 7, [8] [9] [10] [11] Matrix-M1 is manufactured by mixing defined, partially purified extracts of the bark of the Quillaja saponaria Molina tree, termed Fraction-A and Fraction-C, with cholesterol and phosphatidylcholine in the presence of a detergent. 12 Safety data for the Matrix-M1 adjuvant from over 4200 participants in clinical studies with Ebola virus glycoprotein (EBOV GP), respiratory syncytial virus F, malaria, rabies, herpes simplex virus, and influenza vaccines with Matrix-M1, have been described. 13 The trial objectives and endpoints described below are a subset of those that pertain to the results described in this manuscript. For a description of the full set of the trial objectives and endpoints, please refer to the clinical study protocol provided with the manuscript at NEJM.org. The primary objectives of this trial were 1) to evaluate the efficacy of NVX-CoV2373 with Matrix-M1 adjuvant compared to placebo on the occurrence of symptomatic mild, moderate, or severe The primary endpoints of the trial were 1) positive (+) polymerase chain reaction (PCR)-confirmed SARS-CoV-2 illness with symptomatic mild, moderate, or severe Covid-19 in serologically naïve (to SARS-CoV-2) healthy HIV-negative and medically stable HIV-positive adult participants, analyzed overall, with a lower bound confidence interval (CI) of >0, from 7 days after the second vaccine dose (ie, Day 28) until the endpoint-driven efficacy analysis was triggered by the occurrence of a prespecified number of blinded endpoints across the two study vaccine arms and/or at prespecified time points; 2) numbers and percentages (with 95% CIs) of participants with solicited adverse events (local, systemic) for 7 days following each vaccination (Days 0 and 21) by severity score, duration, and peak intensity in healthy HIV-negative and medically stable HIV-positive adult participants, analyzed overall and separately, regardless of baseline serostatus and stratified by baseline serostatus. In the case of no toxicity, a score of zero (0) was applied; 3) numbers and percentages (with 95% CI) of participants with unsolicited adverse events (eg, treatment-emergent, serious, suspected unexpected serious, AESIs, MAAEs) through Day 35 by MedDRA classification, severity score, and relatedness in HIVnegative and medically stable HIV-positive adult participants, analyzed overall and separately, regardless of baseline serostatus and stratified by baseline serostatus. The intent-to-treat (ITT) analysis set included all participants who were randomly assigned to treatment, regardless of protocol violations or missing data. The ITT analysis sets were used for participant disposition summaries and analyzed according to the treatment arm in which the participant was randomly assigned to treatment. The full analysis set included all participants who were randomly assigned to treatment and received at least one dose study vaccine (NVX-CoV2373 with Matrix-M1 adjuvant or placebo), regardless of protocol violations or missing data. The full analysis set was used as a supportive analysis population for the immunogenicity and efficacy analyses and analyzed according to the study vaccine group as randomized. The safety analysis set included all participants who received at least 1 dose of study vaccine Analysis was performed to assess if immune responses differed between exposed and unexposed individuals (ie, whether prior exposure altered dosing regimen considerations in a pandemic response). The review and determination for exclusion from the per-protocol populations was carried out in a blinded fashion by a study clinician prior to unblinding for each interim evaluation based on all available information from the locked database. This study was designed to enroll a minimum of approximately 3200 to a maximum of approximately 4404 participants divided among two cohorts as follows: • At least 2960 to 4164 participants ≥18 to <85 years of age that included a minimum of approximately 1480 participants who received NVX-CoV2373 with Matrix-M1 adjuvant • 240 participants ≥18 to <65 years of age in Cohort 2 (HIV-positive) that included a minimum of approximately 120 participants who received NVX-CoV2373 with Matrix-M1 adjuvant The target sample size of 1480 actively immunized participants in Cohort 1 (HIV-negative) was sufficient to detect an adverse event rate of at least 1 in 625 participants (ie, background rates of 0.16%) with 90% probability. The target sample size of 120 actively immunized participants in Cohort 2 (HIV-positive) was sufficient to detect an adverse event rate of at least 1 in 53 participants (ie, background rates of 1.9%) with 90% probability. This study was designed as an event-driven statistical analysis. Power calculations were performed using the two-sided 95% CI to determine the target number of events needed for the desired power and the minimum vaccine efficacy (VE) needed to reject the null hypotheses (H0:VE ≤0%). The minimum target number of 23 primary endpoints in the overall population (HIV-negative and HIVpositive) was determined to provide approximately 90% power for the primary endpoint based on the following conservative assumptions. • A mild, moderate, or severe Covid-19 incident rate of 2% to 6% in the placebo group and a VE of 80% • 90% evaluability rate for the PP-EFF population (assuming 10% unevaluable due to attrition and/or baseline-seropositive participants) The upper limit of the target number of 50 primary endpoints was chosen so that the observed minimum VE of ~65% would result in rejecting the H0:VE ≤30%. Based on the above assumptions, the minimum target numbers of endpoints needed are 23 to 50 mild, moderate, or severe Covid-19 endpoints. The power calculations for the primary endpoint are summarized in the Table below The single primary efficacy endpoint, mild, moderate, or severe COVID-19, was analyzed on the PP-EFF population. Conclusions concerning declaration of attainment of the primary efficacy endpoint at the completion of the study was only based on the PP-EFF population. In addition, supportive analyses based on the full analysis set population, further excluding subjects with positive SARS-CoV-2 by qualitative PCR between Day 0 and Day 6 (inclusive), was also performed. The VE is defined as VE (%) = (1 -RR) × 100, where RR = relative risk of incidence rates between the two study vaccine groups (SARS-CoV-2 rS with Matrix-M1 adjuvant or placebo). The official (ie, event-driven) analysis for the primary objective in the PP-EFF population was carried out at an overall one-sided type I error rate of 0.025 for the single primary endpoint. The RR and its CI was estimated using Poisson regression with robust error variance. 14 The explanatory variables in the model included the study vaccine group. The dependent variable was the occurrence of the endpoint of interest. Hypothesis testing of the primary efficacy endpoint was carried out sequentially against the two prespecified null hypotheses: H0:VE ≤0% first and then H0:VE ≤30%. Rejection of the null hypothesis, H0:VE ≤0% demonstrates a statistically significant vaccine effect for the primary endpoint. If the primary endpoint meets the success criterion of the lower bound >0%, additional hierarchical testing of the primary endpoint against the more stringent success criterion of the lower bound >30% was to be carried out. Potential diagnostic threshold levels evaluated ranged from 200 (LLOQ) to 1500 EU/mL in increments of 100, with examinations of 50 EU/mL intervals near the peak. To further understand the performance characteristics of the proposed diagnostics threshold, PPVs and NPVs were generated using a resampling with replacement approach with 1000 simulation runs each for a sample size of 100. The unknown population prior COVID-19 infection rates evaluated were 5%, 10%, 20%, 30%, 40%, 50%, and 60%. The following table summarizes the sensitivity and specificity for the several candidate threshold levels in ELISA unit (EU/mL). The threshold of 500 EU/mL exhibits the best overall performance characteristics with the highest observed Youden's J statistic. It is the only threshold that simultaneously provides ~95% or higher sensitivity and specificity. Table S5 AND • Does not meet criteria for moderate or severe Moderate ≥1 of: • Fever (defined by subjective or objective measure, regardless of use of anti-pyretic medications) + any 2 Covid-19 symptoms in Table S5 for ≥3 days (need not be contiguous days) • High fever (≥38.4°C) for ≥ 3 days (need not be contiguous days) • Any evidence of significant LRTI: − Shortness of breath (or breathlessness or difficulty breathing) with or without exertion (greater than baseline) − Tachypnea: 20 to 29 breaths per minute at rest − SpO2: 94% to 95% on room air − Abnormal chest x-ray or chest CT consistent with pneumonia or LRTI − Adventitious sounds on lung auscultation (eg, crackles/rales, wheeze, rhonchi, pleural rub, stridor) AND • Does not meet criteria for severe disease Severe ≥1 of: • Tachypnea: ≥30 breaths per minute at rest • Resting heart rate ≥125 beats per minute • SpO2: ≤93% on room air or PAO2/FiO2 <300 • High flow oxygen therapy or NIV/NIPPV (eg, CPAP or BiPAP) • Mechanical ventilation or ECMO • One or more major organ system dysfunction or failure (eg, cardiac/circulatory, pulmonary, renal, hepatic, and/or neurological, to be defined by diagnostic testing/clinical syndrome/interventions), including any of the following: − ARDS − Acute renal failure − Acute hepatic failure − Acute right or left heart failure − Septic or cardiogenic shock (with shock defined as SBP <90 mm Hg OR DBP <60 mm Hg − Acute stroke (ischemic or hemorrhagic) − Acute thrombotic event: AMI, DVT, PE − Requirement for: vasopressors, systemic corticosteroids, or hemodialysis. • Lung exam (auscultation by qualified physician or nurse) • New medications? • Medical attention sought? • Collect nasal swab for SARS-CoV-2 PCR testing Every 1-weekly ACTIVE SURVEILLANCE calls to FOLLOW-UP until resolution of symptoms; then resume 2-weekly calls • Record any ongoing symptoms of suspected COVID-19 • Vital signs (including MightySat Fingertip Pulse Oximeter) • Lung exam (auscultation by qualified physician or nurse) • New medications? • Medical attention sought? • DO NOT COLLECT a second nasal swab for SARS-CoV-2 PCR testing • Record any ongoing symptoms of suspected COVID-19 • Vital signs (including MightySat Fingertip Pulse Oximeter) • Lung exam (auscultation by qualified physician or nurse) • New medications? • Medical attention sought? • COLLECT REPEAT nasal swab for SARS-CoV-2 PCR testing were used to generate paired-end fastq reads. 19 The bcftools 1.7-2 mpileup method was then used to filter out the low-quality mutations, and all the sequences were deposited in GISAID Solicited local adverse events were predominantly mild to moderate and transient, and more common in vaccine recipients (Table S8 ). In baseline seronegative participants, injection site pain and tenderness were the most frequently reported solicited local adverse events following first (37% and 15% for pain and 25% and 11% for tenderness in vaccine and placebo recipients, respectively) and second (37% and 10% for pain and 25% and 8% for tenderness, respectively), with no increased frequency of events following second vaccination (Table S9) . Similar results were seen in baseline seropositive participants. Severe local adverse events were infrequent but occurred more often in the vaccine group after second vaccination, but only in baseline seronegative participants. Solicited systemic adverse events were predominantly mild to moderate and transient, and generally more common in vaccine recipients (Table S8 ). In baseline seronegative participants, headache, muscle pain, and fatigue were the most frequently reported solicited systemic adverse events following first (25% and 21% for headache in vaccine and placebo recipients, respectively; 18% and 10% for muscle pain; and 16% and 12% for fatigue) and second (20% and 19% for headache; 17% and 9% for muscle pain; and 13% and 7% for fatigue) vaccination, with no increased frequency of events following second vaccination (Table S9) . Higher rates of systemic adverse events were generally reported in both vaccine and placebo recipients in baseline seropositive participants. Severe systemic adverse events were infrequent but generally occurred more often in the vaccine group after second vaccination. Fever was reported in few vaccine recipients. Medically attended adverse events and serious adverse events were infrequent but occurred slightly more often in the vaccine group, with no apparent clustering of specific adverse events by treatment group or system organ class (Table S10) . To date, no serious adverse events have been assessed as related to trial vaccine by study investigators. No prespecified vaccination pause rules were triggered (Table S11) . Genbank: Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome GenBank: MN908947 The spike protein of SARS-CoV-2-a target for vaccine and therapeutic development SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge Matrix-M adjuvant induces local recruitment, activation and maturation of central immune cells in absence of antigen Matrix-M adjuvant enhances antibody, cellular and protective immune responses of a Zaire Ebola/Makona virus glycoprotein (GP) nanoparticle vaccine in mice Matrix-M adjuvant: enhancing immune responses by 'setting the stage' for the antigen ISCOMATRIX adjuvant promotes epitope spreading and antibody affinity maturation of influenza A H7N9 virus like particle vaccine that correlate with virus neutralization in humans Adjuvants enhancing cross-presentation by dendritic cells: The key to more effective vaccines? Novel hemagglutinin nanoparticle influenza vaccine with Matrix-M™ adjuvant induces hemagglutination inhibition, neutralizing, and protective responses in ferrets against homologous and drifted A(H3N2) subtypes ISCOM technology-based Matrix M™ adjuvant: success in future vaccines relies on formulation Cov-2 Recombinant Spike Protein Nanoparticle Vaccine Investigator's Brochure A modified poisson regression approach to prospective studies with binary data Sensitive recovery of complete SARS-CoV-2 genomes from clinical samples by use of Swift Biosciences' SARS-CoV-2 multiplex amplicon sequencing panel nCoV-2019 sequencing protocol v3 (LoCost) Whole genome sequencing of SARS-CoV-2: adapting Illumina protocols for quick and accurate outbreak investigation during a pandemic NEBnext library construction and sequencing for SARS-CoV-2: Adapting COVID-19 ARTIC protocol Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa Priority List of Adverse Events of Special Interest: COVID-19 Division of AIDS (DAIDS), National Institutes of Health. DAIDS. Table for Grading the Severity of Adult and Pediatric Adverse Events. Version 2.1 Guidance for Industry: Toxicity Grading Scale for Healthy Adult and Adolescent Volunteers Enrolled in Preventive Vaccine Clinical Trials Hypertension Guideline Working Group. South African hypertension practice guideline 2014 South African Hypertension Society commentary on the American College of Cardiology/American Heart Association hypertension guidelines