Patients
From July 6th, 2021 to January 13th, 2022, a total of 94 patients with congenital or acquired B-cell deficiency underwent screening at three study sites in Germany. A total of 54 patients received CoVac-1, 14 patients in the Phase I safety run-in, and 40 patients in the subsequent Phase II part of the trial. 28% of patients were female. Median patient age was 61.8 (range 37-90) years. 93% of study patients suffered from cancer-related, acquired B-cell deficiency, with chronic lymphocytic leukemia (CLL, 30%), mantle cell lymphoma (MCL, 24%) and follicular lymphoma (FL, 20%) as the most common diagnoses. Application of an approved COVID-19 vaccine prior to study inclusion was reported for 83% of patients with a median of two vaccinations per patient (Table S6). CD4+ T-cell counts in the study population ranged from 123-2,501/µl (median 458/µl). All patients received one dose of CoVac-1 on day 1 and were available for safety analyses until day 56 (Fig. 1). 49 patients were eligible for immunogenicity analysis until day 28. One major protocol violation occurred (missed study visit day 28). Analyses of follow-up safety and long-term immunogenicity data (until month 6) are ongoing. Demographic and clinical characteristics of the patients are provided in Table 1, S6 and S7.
Safety and reactogenicity
Data regarding solicited and unsolicited AEs were available for all patients from diary cards (for 28 days after CoVac-1 application) and safety visits (until day 56). No patient discontinued the trial because of an AE. No vaccine-related SAEs and no grade 4 AEs were reported. Until day 56 reactogenicity in terms of solicited AEs occurred in all trial patients (Fig. 2). Local events were normal to moderate (grade 0 to 2) in 87% of study patients. 94% of patients showed the expected formation of a granuloma/induration at the injection site, which persisted beyond day 56. Severe AEs (grade 3) comprised local erythema in 11% of patients. 4% of patients reported localized inguinal lymphadenopathy. Local skin ulceration at the injection site was reported by 2% of patients. No fever or other systemic inflammatory solicited AEs were reported. Other systemic solicited AEs occurred in 26% of patients. 93% of the reported systemic solicited AEs were mild, with transient fatigue being the most frequently reported (17% of patients). One patient suffered from unrelated (chemotherapy-induced) grade 4 neutropenia. In 36% of patients, acute phase reaction with elevated C-reactive protein was observed until day 56.
67 unsolicited AEs occurred, which were predominantly mild (79%, Extended Data Table 1). Of all unsolicited AEs, three were judged to be related to CoVac-1, comprising two viral reactivations (herpes simplex and varizella zoster virus) and one formation of a blister at injection site (grade 1). Of the unsolicited AEs, three were reported as SAE not related to CoVac-1 application (details in the Supplementary Appendix, Extended Data Table 1).
No immune-mediated AE was observed in any of the patients. Until day 56, two SARS-CoV-2 infections occurred, with reportedly mild disease course (detailed case narratives in the Supplementary Appendix) and resolved without sequel.
Immunogenicity
Immunogenicity was determined in terms of T-cell responses to the six SARS-CoV-2 HLA-DR CoVac-1 T-cell epitopes1,10,11 using ELISPOT assays. T-cell responses were assessed in all eligible patients at baseline (day 1), on day 7, day 14, and day 28 after CoVac-1 application. The immunogenicity endpoint was reached: CoVac-1-induced IFN-g T‑cell responses were documented in 86% of patients on day 28, with a 36‑fold increase (median positive calculated spot counts: 4 (day 1) to 144 (day 28)) from baseline (Fig. 3a). Vaccine-induced T‑cell responses were directed to multiple CoVac-1 peptides, with median 4/6 peptides recognized by patients` T cells on day 28 (Fig. 3b). The CoVac-1 peptide P6_ORF8 most frequently induced T-cell responses (75%), followed by P3_spi (69%), P5_mem and P4_env (both 52%, Extended Data Fig. 1). 12% and 44% of the study patients showed low-frequent pre-existing SARS-CoV-2 T‑cell responses ex vivo and after 12 days in vitro stimulation at baseline, respectively, in particular to the spike-derived peptide P3_spi (Extended Data Fig. 1 and 2). This may be explained by prior vaccination with approved COVID-19 vaccines as well as by cross-reactive T-cell responses to human common cold coronaviruses (HCoV-OC43, HCoV-229E, HCoV-NL63, HCoV-HKU1)10,17.
CoVac-1-induced CD4+ T cells displayed a multifunctional T-helper 1 (Th1) phenotype with positivity for IFN-g, tumor necrosis factor (TNF), interleukin-2 (IL-2), and CD107a (Fig. 3c). Frequency of functional CD4+ T cells was increased up to 38-fold after in vitro expansion (e.g. 0.03% (ex vivo) to 1.15% (median positive samples) CoVac-1-specific CD107a+CD4+ T cells), indicative of potent expandability of the induced T cells upon SARS-CoV‑2 exposure (Extended Data Fig. 3).
Subgroup analysis showed higher response rates and frequencies of CoVac-1-induced T cells on day 28 for patients with acquired B-cell deficiency (87% response rate, median calculated spot count 151) compared to patients with congenital B-cell deficiency (75% response rate, median calculated spot count 81), with highest frequencies of T cells observed in patients with FL and diffuse large B-cell lymphoma (DLBCL) (median calculated spot counts 401 and 663, respectively, Fig. 3d). No relevant difference in the frequency and intensity of CoVac-1-induced T-cell responses was observed between cancer patients with or without ongoing anti-CD20 therapy (85% vs 88% response, median calculated spot count 151 vs. 164, Fig. 3d).
Beyond T-cell responses, induction of low-level SARS-CoV-2 anti-spike IgG antibodies was observed on day 28 in 8 patients (Fig. 3e).
The intensity of CoVac-1-induced IFN‑g T-cell responses (median calculated spot count 144) exceeded spike-specific T-cell responses induced by approved mRNA-based vaccines (median calculated spot count 45) in B-cell deficient patients prior to CoVac-1 application (Fig. 4a, Table S6). Such pre-existing spike-specific T-cell responses after mRNA vaccination were boosted by CoVac-1, and expanded to various CoVac-1 peptides derived from other SARS-CoV-2 proteins (Fig. 4b, c). Notably, none of the variant-defining or associated mutations of the Omicron variants (BA.1, BA1.1, BA.2, BA.3, Fig. 4d, Table S8)22 affected any of the CoVac-1 peptides.
The intensity of CoVac-1-induced IFN-g T-cell responses in B-cell deficient patients at day 28 (B-CoVs, median calculated spot count 144) was similar or even higher than T-cell responses to CoVac-1 peptides (median calculated spot count 55), to SARS-CoV-2-specific (median calculated spot count 61) and to cross-reactive (median calculated spot count 105) T‑cell epitopes10,11 in immunocompetent HCs, with asymptomatic and mild disease1,10 (Fig. 4e, Table S5). The same held true for the comparison of CoVac-1-induced T-cell responses in B-cell deficient patients with a cohort of immunocompetent HCs10 with asymptomatic and mild disease that did not develop a humoral anti-spike IgG response upon infection (Fig. 4f), indicating that CoVac-1-induced T-cell responses in B-cell deficient patients might be sufficient to provide immunity against severe COVID-19 in this highly immunocompromised population.