ABSTRACT Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants raise concerns about decreased vaccine efficacy, vaccines continue to confer robust protection in humans, implying that immunity beyond neutralization contributes to vaccine efficacy. In addition to neutralization, antibodies can mediate various Fc-dependent effector functions, including antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP) and antibody-dependent cellular cytotoxicity (ADCC). However, the specific role of each Fc-mediated effector function in contributing to COVID-19 disease attenuation in human remains unclear. To fully define the potential immune correlates of Fc-mediated effector functions, we comprehensively analysed the above Fc-mediated effector functions in two study cohorts. In the CoronaVac vaccinee cohort, individuals without breakthrough infection exhibited higher levels of ADCP and ADNP activities with a greater degree of cross-reactivity compared to those who had breakthrough infection. A predictive model was established incorporating ADNP activity and IgG titre, achieving an area under the curve (AUC) of 0.837. In the COVID-19 patient cohort, BA.5-specific ADCP and ADNP responses were significantly reduced in COVID-19 patients with fatal outcomes compared to milder outcomes. The prognostic model incorporating WT, BA.5, and XBB.1.5 spike-specific ADNP demonstrated effective predictive ability, achieving an AUC of 0.890. Meanwhile, transcriptomic analysis of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients in the acute phases of infection highlighted remarkably upregulation of neutrophil activity and phagocytic function, further reinforcing the essential role of ADNP. Collectively, our findings underscored Fc-mediated effector activities, especially neutrophil phagocytosis, as significant antibody biomarkers for the risk of SARS-CoV-2 breakthrough infection and COVID-19 prognosis. KEYWORDS: COVID-19, vaccine, SARS-CoV-2, antibody-dependent neutrophil phagocytosis, Fc effector function Introduction The deployment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines has significantly reduced morbidity and mortality worldwide [[41]1,[42]2]. However, due to waning immunity and the emergence of viral variants that evade neutralizing antibodies (NAbs) induced by vaccines targeting the wild-type (WT) SARS-CoV-2 strain [[43]3,[44]4], breakthrough infections caused by variants of concern (VOCs) have increased globally among fully vaccinated individuals [[45]5]. Nevertheless, in cases where antibodies remain detectable, vaccine-mediated protection against severe disease and death has remained robust [[46]6,[47]7]. While NAbs have been associated with protection against infection across various vaccine trials [[48]8,[49]9], overall antibody-binding titres also strongly correlate with protective immunity [[50]10–12]. Additionally, emerging evidence from animal models suggests that antibody Fc-effector functions, including opsonophagocytosis, are linked to immune protection following natural infection [[51]13,[52]14], convalescent plasma therapy [[53]15] and monoclonal therapy [[54]16]. Yet, whether Fc profiles are directly associated with vaccine-mediated protection in humans remains unclear. Understanding this relationship could provide critical insights for guiding booster strategies and the design of next-generation, variant-specific vaccines. Real-world studies have indicated that breakthrough infections caused by new variants are associated with substantially lower rates of severe disease and mortality [[55]17,[56]18] even when prior vaccinations or infections involved earlier SARS-CoV-2 strains. These observations indicated that other immune responses beyond neutralization play an important role in protection. Emerging evidence showed that antibody Fc-mediated effector functions induced by different vaccine platforms play an important role in immunoprotection [[57]19]. Indeed, immune complexes can be recognized by Fc receptors (FcRs) located on the surface of various immune cells, such as natural killer (NK) cells, macrophages, and neutrophils, facilitating antimicrobial activities that function beyond neutralization. These activities include processes such as antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP) and antibody-dependent cellular cytotoxicity (ADCC). Early enrichment of FcγR-binding antibodies targeting the S2 domain, rather than specific IgG antibody levels, was identified as a biomarker of survival in COVID-19 [[58]20,[59]21]. Additionally, vaccination across different platforms elicited significant levels of antibody Fc-mediated effector functions with substantial cross-reactivity [[60]19,[61]22,[62]23] and durability [[63]23,[64]24], which confer robust protection in situations where neutralization is compromised by viral escape mutations [[65]22,[66]25]. Fc-dependent effector functions have been shown to be crucial for the therapeutic effectiveness of monoclonal antibodies in both mice and hamsters [[67]23]. Similarly, phagocytic cells play a key role in antibody-driven viral clearance during SARS-CoV infection. The activation of alveolar macrophages and ADCP are critical for Fc-mediated antibody protection in a mouse model of influenza A virus (IAV) infection [[68]26,[69]27]. In addition, the alternative immune responses, such as T-cell-mediated responses, might also contribute to vaccine protection against SARS-CoV-2 by identifying and eliminating infected cells, thereby offering long-term immunity beyond neutralization [[70]28]. Our previous study showed that the cross-reactive and durable Fc effector function of antibodies induced by vaccination with three-dose CoronaVac [[71]29]. Given the importance of Fc-effector functions, we aimed to comprehensively examine the potency of Fc-mediated effector functions, including ADCP, ADNP and ADCC, using cohorts of CoronaVac vaccine recipients and COVID-19 patients. In addition, we established two models using ADNP responses, which could effectively predict the risk of breakthrough infection and COVID-19 fatality. Our data highlighted that CoronaVac-induced antibody Fc-mediated effector functions, particularly ADNP activities, were strongly associated with the COVID-19 prevention and disease severity, which might serve as surrogate biomarkers for vaccine efficacy. Further studies will be performed to validate our prognosis models with ADNP activities, covering different vaccine platforms and emerging variants. Materials and methods Study cohort and sample collection We established two prospective study cohorts: the CoronaVac vaccinee cohort (cohort 1) and the COVID-19 patient cohort (cohort 2) in Nanjing Drum Tower Hospital, Nanjing, China ([72]Figure 1). Written informed consent was obtained from all participants before any study procedures were conducted. The study protocol was approved by the Nanjing Drum Tower Hospital Ethics Committee (2021-034-01). Figure 1. [73]Figure 1. [74]Open in a new tab Study design. (a) In the CoronaVac vaccinee cohort, 149 participants who received three doses CoronaVac vaccine were enrolled, in which 101 subjects experienced BA.5 breakthrough infection (BTI), while 48 subjects were not breakthrough infected (non-BTI) within one month during the Omicron BA.5 wave. Blood samples were collected 12 months after the third CoronaVac dose and two weeks before exposure to the Omicron wave. (b) In the COVID-19 patient cohort, there were 30 mild non-hospitalized patients and 139 hospitalized patients, including 40 patients with moderate disease, 54 patients with severe disease, and 45 patients with fatal outcomes. In the CoronaVac vaccinee cohort, 149 healthcare workers who had received 3-dose CoronaVac vaccine (Sinovac Biotech, Beijing, China) were enrolled. Due to the lift of the COVID Zero policy, the outbreak of Omicron breakthrough infection offers us an opportunity to evaluate the role of antibody Fc-mediated effector functions in COVID-19 disease resolution. Serum samples were collected in early December 2022, 12 months post last vaccination and prior to Omicron wave ([75]Figure 1(a)). An online questionnaire was used to collect data on COVID-19-related symptoms and infection status during 16 December 2022 and 16 January 2023. SARS-CoV-2 infection was confirmed by positive COVID-19 antigen or nucleic acid test in individuals who developed COVID-19-related symptoms. Based on breakthrough infection status, the 149 vaccinees were divided into non-breakthrough infected (non-BTI) subjects (n = 48) and breakthrough infected (BTI) subjects (n = 101). In the COVID-19 patient cohort, a total of 169 patients were enrolled, and serum samples were collected 7–15 days after the onset of symptoms ([76]Figure 1(b)). These serum samples were retrieved from routine biochemical or immunological testing and stored at −80°C for future analysis. The COVID-19 patient cohort was further categorized into non-hospitalized patients (mild, n = 30) and hospitalized patients (n = 139). The hospitalized COVID-19 patients were further stratified into 3 subgroups based on their disease severity and clinical outcomes, including moderate cases (n = 40), severe cases (n = 54) and fatal cases (n = 45). The severity of COVID-19 was evaluated based on the ninth version of the Diagnosis and Treatment guidance of COVID-19 [[77]22,[78]23]. Severe cases were defined as individuals meeting one of the following criteria: (1) Respiratory distress with respiratory rate over 30 per minute; (2) Hypoxia (oxygen saturation less than < 93% in the resting state); (3) Arterial blood oxygen partial pressure (PaO[2])/oxygen concentration (FiO[2]) less than 300 mm Hg; or (4) Severe disease complications including respiratory failure which requires mechanical ventilation, septic shock, or non-respiratory organ failure. The measurement of SARS-CoV-2 surrogate neutralizing antibodies (NAbs) The measurement of surrogate NAbs specific to the WT strain was conducted using a one-step immune-competition assay, as previously described [[79]30] with the iFlash3000-C Chemiluminescence Immunoassay Analyzer (Shenzhen Yhlo Biotech Co., Ltd, China). This assay detects total antibody levels in serum that compete with the SARS-CoV-2 spike protein receptor binding domain (RBD) for binding to its receptor, angiotensin-converting enzyme II (ACE2). The negative reference range for SARS-CoV-2 surrogate NAbs was 0–10 IU/mL. Serum SARS-CoV-2 spike-specific IgG antibody titre An in-house enzyme-linked immunosorbent test (ELISA) was used to evaluate antigen-specific serological antibodies against SARS-CoV-2 [[80]29]. WT, BA.5 and XBB.1.5 Spike proteins (Vazyme, Cat# CG202, CG246, CG27, Nanjing, China) were coated onto high-binding 96-well plates at a concentration of 500 ng/mL and incubated overnight at 4°C. After incubation, the plates were washed five times with phosphate-buffered saline (PBS) containing 0.1% Tween-20. Then, the plates were blocked by adding PBS with 5% Bovine Serum Albumin (BSA) and 0.5% Tween-20 and incubated at 37°C for 1 h. After blocking, rewash the plates and add serum samples from vaccinated or infected individuals, diluted in PBS containing 1% BSA and 0.5% Tween-20. The initial dilution was 1:500, followed by a five-step serial dilution using a 3-fold gradient. Incubate the plates at room temperature for 2 h. After incubation, the plates were washed five times, and horseradish peroxidase (HRP)-conjugated anti-IgG secondary antibody (Abcam, cat# ab6759, Cambridge, England) was added and incubated for 1 h at room temperature. After the second incubation, the plates were rewashed, tapped dry, and developed with tetramethylbenzidine (TMB) for 5 min. The reaction was stopped by adding 1M sulphuric acid. The optical density (OD) value was measured at 450 nm. The cut-off value was calculated by taking the average OD of 45 negative control healthy individuals. The greatest serum dilution that produced an OD value greater than the cut-off value of the healthy control group at the same dilution was used to determine the antibody endpoint titre. For the negative controls, the samples were collected from healthy individuals aged 18 to 60 years, with a similar gender ratio, prior to 2019. These individuals had neither been infected with SARS-CoV-2 nor received a COVID-19 vaccine. The demographic information of the healthy control group was summarized in Supplemental Table 4. Fc-mediated effector functional assays ADNP and ADCP assays were carried out as previously described [[81]29,[82]31]. All experiments were performed in triplicates to ensure the consistency of our results. To prepare the biotinylated SARS-CoV-2 spike protein, antigens were biotinylated using Sulfo-NHS-LC biotin (Thermo Fisher Scientific, cat# A39257, MA, USA) following the manufacturer’s protocol. Excess biotin was removed with a Zeba Spin desalting column (Thermo Fisher Scientific, cat# A44300, MA, USA). The biotinylated antigens were then mixed with 1 μm yellow-green fluorescent NeutrAvidin beads (Invitrogen, cat# F8776, MA, USA) in a 1:1 ratio and incubated overnight at 4°C in the dark. After incubation, the beads were washed with PBS at 16,000 g for 15 min and resuspended in PBS containing 0.5% BSA. For the ADNP assay, neutrophils were isolated from the whole blood of three healthy adults using a lysis method. In details, the serum was diluted 25-fold in sterile PBS containing 0.5% Tween-20 and 1% BSA, and incubated with antigen-coupled beads at 37°C for 2 h to form immune complexes. After incubation, sterile PBS was used to wash away unbound immunoglobulins. PBMCs were resuspended at a concentration of 2.5 × 10⁵ cells/ml in R10 media. A total of 25,000 cells per well were added to each well containing immune complexes, mixed by shaking and incubated for 1 h at 37°C, 5% CO[2]. After incubation, the PBMCs were washed with PBS and stained for CD66b + cells using APC-conjugated anti-CD66b antibody (BioLegend, cat# 17-0666-42, CA, USA) to identify neutrophils. The cells were then fixed with 4% paraformaldehyde (PFA) (Leagene, cat# DF0135, Beijing, China) for 30 min, followed by flow cytometry analysis. A blank control containing only beads and neutrophils was included as a negative control. The ADCP assay was performed as previously described [[83]29]. The diluted serum was used to prepare immune complexes following the same method described above. After washing to remove unbound immunoglobulins with sterile PBS, 25,000 THP-1 cells per well were added in R10 medium, mixed by shaking to ensure even distribution and incubated at 37°C with 5% CO[2] for 1 h. Following incubation, THP-1 cells were washed with PBS and then fixed with 4% PFA (Leagene, cat# DF0135, Beijing, China) for 30 min, followed by flow cytometry analysis. A blank control containing only beads and THP-1 cells was included as a negative control. The geometric mean fluorescent intensity (gMFI) of the phagocytosed beads (bead + THP-1 or neutrophils, classified as positive cells) (Figure S1) and the percentage of cells that had phagocytosed beads were determined using flow cytometry. Phagoscore = % positive cells × geometric mean fluorescent intensity of positive cells/1000,000. The corrected phagoscore was defined as the actual phagoscore derived from the sample minus phagoscore score derived from the blank control. If the phagoscore calculated was below zero, it would be set as zero. The BD Accuri^TM C6 Plus Flow Cytometer was used for flow cytometry, and FlowJo V10.8.1 was used for analysis. To assess the ADCC activity of serum antibodies, shake-cultured 293F cells stably expressing the spike protein of the original strain served as target cells. While Jurkat-FcγRIII-NFAT-Luc reporter cells (Vazyme, cat# DD1301-1, Nanjing, China) were used as effector cells. These cells contain a functional NFAT transcription factor, which regulates the expression of the Lucia luciferase gene. The Jurkat-FcγRIII-NFAT-Luc cells stably express the FcγRIIIa (CD16) receptor. When antibodies bind to the CD16 receptor, the NFAT pathway is activated, causing NFAT to translocate to the nucleus and bind to the promoter of the Lucia luciferase gene, thereby driving its expression. The ADCC levels were detected using luciferase activity assays as previously described [[84]32]. In details, serum samples diluted 1:60 in R10 medium were incubated with 25, 000 target 293F cells per well at 37°C and 5% CO₂ for 1 h. After incubation, 75, 000 Jurkat cells were added to each well, gently mixed, and incubated for 12 h under the same conditions. Following the incubation, luciferase substrate (Vazyme, cat# DD1204-03, Nanjing, China) was added, and the wells were shaken to ensure full reaction. Relative light units (RLU) were measured according to the PerkinElmer (Waltham, MA) instruction manual. Sera samples from healthy archived persons from 2019 were used as the unexposed and unvaccinated donors for the negative control experiment. ADCC was measured as the fold induction of Luciferase activity compared to the negative control sera. PBMC transcriptomic analysis PBMCs from forty volunteers were included in the transcriptomic analysis, collected 12 months after receiving three doses of the CoronaVac vaccine. Among them, twenty developed COVID-19-related symptoms and tested positive for SARS-CoV-2 antigen or nucleic acid within five days after sample collection, referring vaccinees during the acute phase of infection. As a negative control, twenty vaccinees who neither developed COVID-19 symptoms nor tested positive for SARS-CoV-2 antigen or nucleic acid were included as vaccinees without infection group. Total RNA was prepared and used for the RNA-seq library construction, and subsequently sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated [[85]33]. The human genome version of hg38 was used as reference. FeatureCounts vl.5.0-p3 was used to count the reads numbers mapped to each gene. Differential expression analysis of two groups was performed using the DESeq2R package (v 1.20.0). The resulting p values were adjusted using Benjamini and Hochberg's approach to control the false discovery rate (FDR). Genes with an adjusted p values < 0.05 found by DESeq2 were assigned as differentially expressed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using clusterProfiler package in R software and corrected p values less than 0.05 were considered significantly enriched by differentially expressed genes. Statistical analysis Single-variable comparisons between groups were performed using the Mann–Whitney U test. Multiple comparisons of ADCP, ADNP and ADCC responses were conducted using the Kruskal–Wallis test with FDR correction. Data were analysed using GraphPad Prism (version 9.0.1, La Jolla, California, USA). All statistical analyses were performed in a two-sided manner, and p values < 0.05 was considered statistically significant. * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001, **** indicates p < 0.0001, and ns indicates no significant difference. A partial least square discriminant analysis (PLS-DA) was used for the classification and visualization of immune parameters between the two groups. Selected immune features were ranked based on the Variable Importance in Projection (VIP) score and the first two latent variables (LVs) of the PLS-DA model were used for visualization. R package “ropls” (version 1.20.043) and “glmnet” (version 4.0.244) and the 27 systemseRology R package (version 1.1) ([86]https://github.com/LoosC/systemsseRology) were used for analysis. The predictive ability of the immunological index was evaluated using a receiver operating characteristic (ROC) curve. Variables based on the VIP score were selected for the multivariate models. A binary logistic regression analysis was used to combine multiple predictors. The area under the ROC curve (AUROC) was calculated. Data analysis was performed using Medcalc version 22.009 software (MedCalc Software Ltd, Belgium). Results Robust Fc-mediated phagocytosis activities induced by CoronaVac in non-breakthrough infected groups To evaluate humoral correlates of immunity against COVID-19, we performed a detailed profiling of the humoral immune response to WT, BA.5 and XBB.1.5 of SARS-CoV-2, including NAbs, spike-specific IgG titres, ADCP, ADNP and ADCC. Here, we characterized the antiviral effector function of antibodies in serum by assessing antibody-mediated phagocytosis in a prospective cohort of SARS-CoV-2 naïve healthcare workers ([87]Figure 1(a) and Supplemental Table 1). Although previous studies have confirmed the association between antibody-binding titres, neutralization and protection in phase 3 COVID-19 vaccine trials [[88]10,[89]34], comparable levels of IgG titres specific to WT and BA.5 spike proteins were observed between BTI patients and non-BTI patients. In contrast, serum samples from the non-BTI group exhibited significantly higher level of XBB.1.5 spike-specific IgG titres compared to the BTI group (p = 0.0002) ([90]Figure 2(a)). Interestingly, there was a trend indicating that the non-BTI group displayed a higher degree of cross-reactivity with the XBB.1.5 spike, but not with the BA.5 spike, compared to the BTI group ([91]Figure 2(b)). Additionally, compared to BTI individuals, non-BTI individuals had higher levels of ADCP activities specific to WT, BA.5 and XBB.1.5 spike proteins (p = 0.0001, 0.0013 and 0.0069 respectively) ([92]Figure 2(c)). However, sera from the BTI group exhibited slightly better cross-reactive ADCP activity against the XBB.1.5 spike protein compared to the non-BTI group ([93]Figure 2(d)). Moreover, the non-BTI group demonstrated a greater magnitude and higher degree of cross-reactive XBB.1.5 spike-specific ADNP activity compared to the BTI group (p < 0.0001) ([94]Figure 2(e,f)). Although minimal levels of ADCC activity were detected across the cohorts, sera from the non-BTI group exhibited higher ADCC activities compared to the BTI group (p = 0.0361) ([95]Figure 2(g)). In contrast, comparable levels of NAbs were observed between BTI and non-BTI group, possibly due to the relative low level of serum neutralization activities which could not confer disease prevention [[96]11] ([97]Figure 2(h)). Our data suggested that Fc-mediated effector functions were remarkably higher in non-BTI group than BTI group. Figure 2. [98]Figure 2. [99]Open in a new tab Baseline humoral immune responses between the vaccinees with breakthrough infection (BTI) and vaccinees without breakthrough infection (non-BTI). (a) The serum IgG, (c) antibody-dependent cellular phagocytosis (ADCP) and (e) antibody-dependent neutrophil phagocytosis (ADNP) specific to spike protein of WT, BA.5, and XBB.1.5 between the BTI and the non-BTI. Fold changes in (b) IgG titre, (d) ADCP and (f) ADNP responses specific to the Omicron BA.5 and XBB.1.5 subvariants spike proteins relative to those specific to the WT strain. The dotted line represents no fold change, and the solid lines indicate the median value. (g) WT spike-specific antibody-dependent cellular cytotoxicity (ADCC) response between the BTI and non-BTI groups. The Mann–Whitney U test was used for comparison between the two groups. * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001, **** indicates p < 0.0001. ns indicates no significant difference. Vaccine-elicited Fc effector biomarkers that differentiate BTI and non-BTI individuals Given the notable differences in binding antibody titres and Fc effector functions between the BTI and non-BTI groups, we aimed to determine whether Fc effector parameters might serve as potential biomarkers to differentiate BTI. To this end, a PLS-DA was performed, incorporating the tested humoral responses as well as sex and age across the two groups ([100]Figure 3(a)). This analysis distinguished BTI from non-BTI samples, indicating significant differences in humoral responses between the two groups. The top three biomarkers identified from VIP scores between the BTI and non-BTI groups were BA.5 spike-specific IgG, XBB.1.5 spike-specific ADNP and WT spike-specific ADNP ([101]Figure 3(b)). Given that these three biomarkers contribute most significantly to differentiating between BTI and non-BTI groups, the top three markers were adopted to establish a predictive model using logistic regression to assess the potential breakthrough infection risk. The predictive model equation is as follows: P[BTI] = 2.88776–0.085186*XBB.1.5 spike ADNP + 0.000068797*BA.5 spike IgG + 0.022264*WT spike ADNP. Figure 3. [102]Figure 3. [103]Open in a new tab Selected Fc-mediated function biomarkers and development of the risk prediction model for breakthrough infection. (a) A partial least squares discriminant analysis (PLS-DA) comparing BTI and non-BTI groups. (b) The top three indicators with the highest Variable Importance in Projection (VIP) scores, including BA.5 spike-specific IgG, WT spike-specific ADNP and XBB.1.5 spike-specific ADNP, were selected based on their VIP scores, which measure the contribution of each variable to the classification model in PLS-DA distinguishing between BTI and non-BTI groups. (c) Receiver operating characteristic (ROC) curves of the combined predictive model, using three biomarkers with the highest VIP scores, alongside the 3 individual top-performing indicators. (d) Area under the receiver operating characteristic curves (AUROCs) for eleven individual tested immune biomarker, as well as for the predictive model. The AUROC values provide a quantitative assessment of the model’s performance, highlighting its capacity to accurately classify individuals with breakthrough infection status. The vertical dotted line represents AUROC = 0.6. Curves with p values less than 0.05 are shown in red, while those with p values greater than 0.05 are shown in grey. To validate the performance of this predictive model, we generated receiver operating characteristic (ROC) plots to compare the predictive ability of each humoral antibody parameter. BA.5 spike-specific IgG, WT spike-specific ADNP, and WT spike-specific IgG yielded the modest predictive ability with AUC of 0.548, 0.552 and 0.552, respectively ([104]Figure 3(c,d)). To further assess the effectiveness of the combined parameters in predicting the risk of breakthrough infection, we applied the 3-indicator model to distinguish between BTI and non-BTI group. The AUROC of the model was 0.837 (95% confidence interval (CI): 0.767–0.892, sensitivity: 77.00%, specificity: 77.08%), demonstrating superior discriminatory ability in identifying COVID-19 patients with breakthrough infection ([105]Figure 3(c,d)). To further validate our findings, quartile ranges were set to establish the risk of breakthrough infection based on the magnitude of ADCP and ADNP activities specific to WT, BA.5 and XBB.1.5 spike protein ([106]Table 1). Specifically, participants with WT spike-specific ADCP responses in the third (Phagoscore: 145.23–225.37) and fourth (226.28–414.12) quartiles had 78.8% (p = 0.008, OR = 0.212, 95%CI:0.067–0.670) and 83.2% (p = 0.002, OR = 0.168, 95%CI:0.054–0.524) smaller odds respectively than those in the first quartile. Participants with XBB.1.5 spike-specific ADNP responses in the third (48.74–69.25) and fourth (71.21–168.50) quartiles had 82.4% (p = 0.013, OR = 0.176, 95%CI:0.045–0.694) and 94.9% (p < 0.0001, OR = 0.051, 95%CI:0.013–0.199) smaller odds respectively than those in the first quartile. Collectively, our data suggested that the high magnitude of Fc activities was associated with a relatively lower risk of breakthrough infection. Table 1. Risk of Omicron BA.5 variant infection within 1 month of blood sampling. Fc effector functions Quartile Phagocytosis score Infected Infection rate (%) WT spike ADCP Q1 (0–25%) <77.25 32/37 86.49 Q2 (25–50%) 79.25–144.51 27/37 72.97 Q3 (50–75%) 145.23–225.37 22/37 59.46 Q4 (75–100%) 226.28–414.12 19/37 51.35 BA.5 spike ADCP Q1 (0–25%) <16.39 28/37 75.68 Q2 (25–50%) 16.64–32.56 32/37 86.49 Q3 (50–75%) 32.79–67.36 21/37 56.76 Q4 (75–100%) 67.87–200.45 19/37 51.35 XBB.1.5 spike ADCP Q1 (0–25%) <24.85 31/37 83.78 Q2 (25–50%) 24.96–41.96 26/37 70.27 Q3 (50–75%) 42.15–65.79 22/37 59.46 Q4 (75–100%) 65.90–252.01 21/37 56.76 WT spike ADNP Q1 (0–25%) <59.74 25/37 67.57 Q2 (25–50%) 60.33–89.81 28/37 75.68 Q3 (50–75%) 90.13–134.27 27/37 72.97 Q4 (75–100%) 138.74–359.46 20/37 54.05 BA.5 spike ADNP Q1 (0–25%) <55.76 26/37 70.27 Q2 (25–50%) 56.67–79.43 29/37 78.38 Q3 (50–75%) 80.58–106.32 25/37 67.57 Q4 (75–100%) 107.44–232.67 20/37 54.05 XBB.1.5 spike ADNP Q1 (0–25%) <30.12 33/37 89.19 Q2 (25–50%) 31.07–48.69 29/37 78.38 Q3 (50–75%) 48.74–69.25 24/37 64.86 Q4 (75–100%) 71.21–168.50 14/37 37.84 [107]Open in a new tab Diminished Fc-mediated phagocytosis responses observed in COVID-19 patients with fatal outcomes compared to those with non-fatal outcomes To define the differences in Fc-mediated phagocytosis among COVID-19 patients and assess correlations with disease severity, we further analysed the Fc-mediated effector activities across patients with different clinical outcomes, including mild, moderate, severe and fatal cases ([108]Figure 1(b) and Supplemental Table 2). We found that non-hospitalized patients exhibited a higher magnitude of ADCP responses against the BA.5 subvariant compared to hospitalized patients (p < 0.0001), whereas no such effect was observed for the WT spike or XBB.1.5 spike ([109]Figure 4(a)). Specifically, COVID-19 patients with mild disease exhibited consistently higher levels of ADCP responses specific to WT, BA.5 and XBB.1.5 spike than patients with fatal outcomes (p = 0.018, p < 0.0001, and p = 0.0021 respectively). Furthermore, patients with severe COVID-19 showed elevated BA.5 spike-specific ADCP responses compared to those with moderate disease and fatal outcomes (p = 0.0361 and p = 0.002, respectively). Patients with fatal outcomes demonstrated significantly diminished levels of XBB.1.5 spike-specific ADCP responses compared to both with severe and moderate disease (p = 0.0021 and p = 0.0020, respectively). Different from ADCP, ADNP responses specific to WT spike, BA.5 spike and XBB.1.5 spike proteins were remarkably elevated in patients with mild disease compared to hospitalized patients (p = 0.0115, p < 0.0001, and p = 0.0006 respectively) ([110]Figure 4(b)). Specifically, BA.5 spike-specific ADNP responses were significantly higher in patients with mild disease than in those with severe and fatal disease (p < 0.0001, p < 0.0001, respectively), but not significantly different from patients with moderate disease (p = 0.3764). A similar trend was also observed for XBB.1.5 spike-specific ADNP responses. In addition, ADCC activities were significantly elevated in COVID-19 patients with mild disease, compared to hospitalized patients (p < 0.0001) and across all subgroups (p < 0.0001, p = 0.0002, and p < 0.0001, respectively) ([111]Figure 4(c)). A similar pattern was observed for patients with mild disease who had significantly higher NAbs compared to hospitalized patients (p < 0.0001) ([112]Figure 4(d)). However, there were no notable differences in either ADCC activities or NAb titres were observed among patients with moderate, severe, and fatal disease ([113]Figure 4(c,d)). Figure 4. [114]Figure 4. [115]Open in a new tab ADCP and ADNP responses among COVID-19 patients with different clinical outcomes. (a) ADCP and (b) ADNP specific to the WT, BA.5 and XBB.1.5 spike proteins among COVID-19 patients with varying clinical outcomes. (c) ADCC and (d) neutralizing antibody titres specific to the WT spike protein in COVID-19 patients with different clinical outcomes. (e-f) Cross-reactivity of ADCP and ADNP to WT, BA.5 and XBB.1.5 spike proteins in patients with different clinical outcomes, categorized as mild, moderate, severe, and fatal groups. The Mann–Whitney U test was used for two-group comparisons. While the Kruskal–Wallis test with FDR correction was applied for comparisons across four groups. * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001, **** indicates p < 0.0001. ns indicates no significant difference. The cross-reactivity of serum ADNP and ADCP activities was also assessed. Serum samples from patients with mild disease exhibited higher cross-reactivity in BA.5 spike-specific ADCP responses compared to those from patients with moderate disease (p = 0.0059). Meanwhile, serum from patients with fatal outcomes demonstrated greater cross-reactivity in BA.5 spike (p = 0.045 and 0.0002) and XBB.1.5 spike-specific ADCP (p = 0.0065 and 0.0065) responses compared to patients with severe and moderate disease ([116]Figure 4(e)). Interestingly, patients with fatal outcomes exhibited significantly reduced cross-reactivity in BA.5 spike-specific ADNP responses compared to those with severe and moderate disease (p = 0.0296 and 0.0191). Additionally, fatal COVID-19 patients showed markedly lower cross-reactivity in XBB.1.5 spike-specific ADNP responses compared to patients with severe, moderate and mild disease (p = 0.0293, 0.0001 and 0.0017) ([117]Figure 4(f)). Overall, serum from patients with mild disease displayed robust Fc-mediated effector functions, whereas patients with fatal outcomes exhibited only modest Fc-mediated effector functions, with a skew towards BA.5 spike-specific responses. ADNP accurately predicted the clinical outcomes in COVID-19 patients To determine whether Fc-mediated phagocytosis could serve as a biomarker to predict the disease progression of COVID-19, we further divided the hospitalized COVID-19 patients into two groups, including patients with fatal and non-fatal (including moderate and severe cases) outcomes. PLS-DA analysis was conducted to evaluate whether overall Fc-mediated effector functions differ between the two groups. As shown in [118]Figure 5(a), a partial separation between non-fatal and fatal COVID-19 patients was observed. Notably, the top 3 VIP scores from the PLS-DA analysis indicated that patients with non-fatal outcomes exhibited selective enrichment in XBB.1.5 spike-specific ADNP, WT spike-specific ADNP, and BA.5 spike-specific ADNP responses in their immune profiles ([119]Figure 5(b)). Similarly, we combined the three biomarkers into a predictive model to assess fatal outcomes. The prognosis model equation is as follows: P[fatality] = 0.95858–0.096526*XBB.1.5 spike ADNP +0.024837*BA.5 spike ADNP +0.0060758* WT spike ADNP. The AUROCs for predicting COVID-19 fatality were 0.851 (95% CI: 0.778–0.908), 0.807 (95% CI: 0.731–0.870), 0.708 (95% CI: 0.624–0.782) using XBB.1.5 spike-specific ADNP, WT spike-specific ADCP and XBB.1.5 spike-specific ADCP, respectively ([120]Figure 5(c)). Using the combined parameters with the top 3 VIP scores, the model achieved an AUC of 0.890 (95% CI:0.821–0.939), with 80.65% sensitivity and 82.80% specificity ([121]Figure 6(d)). Overall, the model incorporating the specific ADNP responses demonstrated strong performance in identifying the fatal outcomes of COVID-19 patients. Figure 5. [122]Figure 5. [123]Open in a new tab Selected Fc-mediated function biomarkers and the development of clinical prognosis model for COVID-19 fatality. (a) A PLS-DA was conducted to compare non-fatal versus fatal COVID-19 patients. (b) The top three indicators with the highest VIP scores, including WT, BA.5 and XBB.1.5 spike-specific ADNP, were selected based on their VIP scores, which measure the contribution of each variable to the classification model in PLS-DA distinguishing between fatal and non-fatal groups. (c) ROC curves of the prognosis model, using three biomarkers with the highest VIP scores, alongside the 3 individual top indicators. (d) AUROCs for 9 individual tested immune biomarker, as well as for the prognosis model. The AUROC values provide a quantitative assessment of the model’s performance, highlighting its capacity to accurately classify individuals with fatal COVID-19 outcomes. The vertical dotted line represents AUC = 0.6. Curves with p values less than 0.05 are shown in red, while those with p values greater than 0.05 are shown in grey. Figure 6. [124]Figure 6. [125]Open in a new tab Transcriptomic analysis of PBMCs from CoronaVac vaccinees during the acute phase of SARS-CoV-2 breakthrough infection and those without infection. (a) t-Distributed stochastic neighbour embedding (t-SNE) plot of PBMC transcriptomic data from twenty vaccinees in the acute phase of SARS-CoV-2 infection and twenty uninfected vaccinees. (b) Volcano plot showing differentially expressed genes in PBMCs of vaccinees at the acute phase of infection compared to uninfected vaccinees. The selection criteria are padj < 0.05 and an absolute log[2]fold change > 1 (c) Gene ontology (GO) and (d) Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of upregulated genes in vaccinees during the acute phase of infection compared to uninfected vaccinees. (e) Heatmap of significant differentially expressed genes comparing PBMC from vaccinees during the acute phase of SARS-CoV-2 infection versus vaccinees without breakthrough infection. Transcriptomic analysis revealed neutrophil activation in vaccinees during the acute phase of infection To further validate the protective role of Fc-mediated effector function in disease prevention and progression, we performed a transcriptomic analysis comparing blood samples from twenty vaccinees during the acute phase of breakthrough infection with twenty vaccinees without breakthrough infection ([126]Figure 6). The clinical and demographic information of the enrolled subjects was summarized in Supplemental Table 3. The principal component analysis showed that targeted transcriptomic profiles could effectively distinguish patients undergoing acute SARS-CoV-2 infection from uninfected vaccinees ([127]Figure 6(a)). 2209 genes were significantly upregulated whereas 4436 genes were downregulated in vaccinees in the acute phase of SARS-CoV-2 infection ([128]Figure 6(b)). Gene ontology (GO) analysis showed that the most strongly regulated biological process categories were associated with neutrophil activation, neutrophil activation involved in immune response, neutrophil degranulation and phagocytosis ([129]Figure 6(c)). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of gene expression profiles indicated a notable upregulation in Fcγ receptor-mediated phagocytosis, chemokine signalling pathway, neutrophil extracellular trap (NET) formation, and B cell receptor (BCR) signalling pathway ([130]Figure 6(d)). As shown in [131]Figure 6(e), compared to PBMCs from healthy control. Transcriptomic analysis of PBMCs from individuals in the acute phase of infection revealed upregulated gene expression related to neutrophil activation and regulation of neutrophil immune responses (TCN2, LILRA2, CD14, ANXA5, LILRB4, CCR1, CFD, BST2, FPR2, MNDA, MS4A3, SERPINB10, LRG1, C3AR1, PRTN3, LTF, GPR84, CLEC5A), Fcγ receptor-mediated phagocytosis (SYK, HCK, FCGR1A, LYN, FCGR2A, FCGR1CP, MARCKS, MYO10, DOCK1, FCGR3B) and B cell responses (FOS, LILRA1, LILRA6, BTK, IFITM2, LILRA5). Collectively, our data suggest that Fc-mediated neutrophil phagocytosis might play an essential role in the acute phase of infection and pathogen clearance, which may be associated with different disease outcomes. Discussion Neutralizing antibody responses are often employed to estimate protective efficacy in the context of COVID-19 vaccination [[132]35]. However, it is worth mentioning that even when neutralization is compromised in the setting of the SARS-CoV-2 variants and breakthrough infection, vaccine-induced protection against hospitalization remains relatively high [[133]36–38]. Antibodies that activate innate immune responses can both directly facilitate the rapid clearance of viral particles and eliminate infected cells by engaging the immune system [[134]39], suggesting that immune mechanisms beyond antibody-mediated virus neutralization may play an essential role in protecting against severe disease. There is increasing evidence suggesting that beyond neutralization, vaccine-induced antibodies are also capable of mediating an array of antibody effector functions that have been linked to protection against severe disease and death [[135]23] and monoclonal therapeutic activity [[136]24,[137]40]. Nevertheless, the protective role of Fc effector functions in preventing SARS-CoV-2 infection and limiting COVID-19 severity has not been well established. Previously, we profiled the Fc effector functions including ADCP and ADNP responses induced by 3-dose CoronaVac, in which Fc-mediated effector phagocytosis was cross-reactive with Omicron variants and long-lasting [[138]29], which provide a timely and comprehensive insight of the mechanism of vaccine efficacy. In contrast to NAbs, which are constrained to target a finite number of regions on the spike protein pertinent to attachment or fusion, antibodies mediating Fc-activity possess the capability to bind extensively across the entire antigenic surface. Fc-activity fundamentally necessitates the formation of immune complexes and the strategic arrangement of antibodies featuring Fc-domains that are readily accessible to local immune cells. Despite a diminished yet persistent binding affinity towards the Omicron spike antigen, IgG antibodies may persist in opsonizing both the virus and virally infected cells. Consequently, non-neutralizing antibodies that harness the potential of Fc-biology could play a pivotal role in expediting the elimination of infected cells immediately following the onset of infection. Here we further expanded our understanding of Fc-mediated effector functions elicited by CoronaVac, which might contribute to disease protection and clinical outcomes of SARS-CoV-2 infection. In our first cohort, since most participants received the last vaccination 12 months ago, the minimum level of serum neutralization activities was detected due to a pronounced loss of antibodies and the immune escape of Omicron variants. This also offered us a great opportunity to determine the preventive role of Fc-mediated activities to prevent the infection and disease control. We developed a model for predicting risk of BA.5 breakthrough infection which incorporated three parameters including two ADNP parameters (ADNP specific to XBB.1.5 and WT spike) and BA.5 spike IgG, achieved an AUC of 0.837 for predicting the risk of BA.5 breakthrough infection, with 77.08% specificity and 77.00% sensitivity. Meanwhile, the three-ADNP-indicator clinical prognosis model was established to distinguish COVID-19 patients with fatal and non-fatal outcomes achieved an AUC of 0.890, with 82.80% specificity and 80.65% sensitivity. For the first time, our models highlight the importance of Fc-mediated effector functions especially neutrophil-mediated phagocytosis that may contribute to the prevention of SARS-CoV-2 infection as well as disease control. Therefore, those at high risk of infection will be encouraged to boost with the updated COVID-19 vaccine. For individuals at high risk of COVID-19-related fatality, proactive clinical interventions such as the prompt administration of antiviral medications are strongly recommended. Neutrophils are the most abundant circulating leukocyte in the blood and can rapidly migrate to sites of infection and can mediate a range of effector responses [[139]41,[140]42]. FcγRs allow neutrophils to interact with virus particles and infected cells opsonized by specific IgG antibodies, leading to neutrophil activation, degranulation, phagocytosis, and the induction of neutrophil extracellular traps (NETs). Neutrophils express antibody receptors for IgG, including the activating high-affinity FcγRI and the low-affinity FcγRIIa and FcγRIIIb, as well as IgA, which binds to the low-affinity FcαRI. FcγRIIIb is the most abundantly expressed receptor on neutrophils and is exclusively expressed on these cells. which specifically binds to IgG1 and IgG3. In comparison, FcγRIIa is expressed at lower levels than FcγRIIIb on neutrophils, and similarly binds to IgG1 and IgG3. Although FcγRI is expressed at lower levels, it can bind IgG1, IgG3, and IgG4, making it a high-affinity receptor. These receptors distinguish neutrophils from their innate immune functions by endowing them with the ability to mount antigen-specific immune responses. In the context of COVID-19, the presence of FcγRIIIb-binding antibodies was found to be enriched in individuals who were protected against COVID-19 breakthrough, linked to neutrophil-mediated immune complex clearance [[141]43]. The protection against SARS-CoV-2 BA.5 infection in the upper respiratory airways correlated with binding, neutralizing, and ADNP activities of the serum antibody elicited by COVID-19 vaccine [[142]44]. Meanwhile, impairment of neutrophil functions, homeostasis, and inflammation was associated with COVID-19 disease severity [[143]45] and post-COVID-19 pulmonary sequelae [[144]39]. Similar mechanisms were also observed in alternative infectious diseases. Additionally, antibody specific for soluble glycoprotein (sGP) drives neutrophil-mediated phagocytosis and could predict vaccine-mediated protection. In Ebola vaccine, protective sGP-specific monoclonal antibodies have elevated neutrophil-mediated phagocytic activity compared with non-protective antibodies, highlighting the importance of sGP in vaccine protection and monoclonal antibody therapeutics against Ebola virus [[145]46]. Therefore, we and others pointed to a potential role of vaccine-induced, antibody-mediated neutrophil phagocytosis, as a surrogate of protection against COVID-19. As the first line of defense against pathogen, neutrophils play an important role during the acute phase of infection. To analyse the potential neutrophil activation during the acute phase of SARS-CoV-2 infection, comparative transcriptional analyses were performed using PBMC samples of infected individuals within five days upon disease onset versus uninfected individuals. Consistent with previous single-cell RNA-seq analysis, PBMC transcripts from infected individuals revealed remarkably elevated expression of genes related neutrophils activation, neutrophil degranulation, and neutrophil extracellular trap formation, along with increased FcγR-mediated phagocytosis, chemokine signalling and BCR signalling pathways, compared to non-infected individuals. The immune signatures associated with neutrophils and FcγR-mediated phagocytosis were also upregulated upon infection. Therefore, our transcriptional data further support that ADNP is a potential significant biomarker for disease prevention and control of COVID-19. We also observed that non-BTI group had a higher level of ADCP responses than that in BTI group, suggesting that ADCP might also play an important role in preventing infection. ADCP exerts a pivotal antibody-mediated immune mechanism, where phagocytic cells (e.g. macrophage, neutrophils, dendritic cells) actively engulf and destroy target cells or pathogens that are opsonized by antibodies. Previous studies have shown that the RBD-specific antibody-dependent monocyte phagocytosis was lower in deceased patients compared to survived patients [[146]21,[147]47], which is consistent with our observations. It was found that the uptake of SARS-CoV-2 by macrophage via ADCP did not lead to an aberrant cytokine production, possibly due to the small size of the virus-IgG immune complex [[148]46]. Furthermore, neutrophil and macrophage depletion resulted in the loss of protection from the convalescent plasma. It was observed that Fc-mediated effector functions of plasma with weak neutralizing activities could protect mice from lethality and severe disease better than a control treatment of plasma with weaker Fc activities [[149]47]. Furthermore, neutrophil and macrophage depletion resulted in the loss of protection from the convalescent plasma, which both validating the essential role of these innate effector cells via ADCC and ADCP protection [[150]39]. There are some limitations to our study. Firstly, in our study, our established predictive models were validated only among vaccine recipients who received inactivated COVID-19 vaccines and experienced breakthrough infections with Omicron BA.5 variants. It is important to further validate the protective role of vaccine-induced ADNP responses across different vaccine platforms and emerging variants. Secondly, antibody isotypes, glycosylation patterns, and FcR subtypes on multiple Fc effector functions could also regulate the neutrophil phagocytosis and confer disease attenuation, which were not dissected in this study. In summary, our study identified Fc-mediated neutrophil phagocytosis as a significant immunological correlate that contributes to disease attenuation in the absence of neutralization, which may provide key insights to guide effective pan-variant SARS-CoV-2 vaccine design. Supplementary Material Supplementary materials1116.docx [151]TEMI_A_2434567_SM5618.docx^ (378.5KB, docx) Funding Statement This work was supported by the National Key Research and development program [2023YFC2309100]; National Natural Science Foundation of China [92269118, 92269205, 92369117]; Nanjing Drum Tower Hospital Outstanding Youth Cultivation Fund [2024-JCYJ-YP-01]; Scientific Research Project of Jiangsu Health Commission [M2022013]; Project of Chinese Hospital Reform and Development Institute, Nanjing University, Aid project of Nanjing Drum Tower Hospital Health, Education &Research Foundation [NDYG2022003], and Postgraduate Research & Practice Innovation Program of Jiangsu Province [021093002704, JX22014156]. Disclosure statement No potential conflict of interest was reported by the author(s). References