key: cord-0933824-9urmdxu3 authors: Lee, Hye Kyung; Go, Jinyoung; Sung, Heungsup; Kim, Seong Who; Walter, Mary; Knabl, Ludwig; Furth, Priscilla; Hennighausen, Lothar; Huh, Jin Won title: Heterologous ChAdOx1-BNT162b2 vaccination in Korean cohort induces robust immune and antibody responses that includes Omicron date: 2022-05-26 journal: iScience DOI: 10.1016/j.isci.2022.104473 sha: 7e593375385acb665ea1be1389737bdf6f5e9db8 doc_id: 933824 cord_uid: 9urmdxu3 Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than BNT162b2-BNT162b2. Here we investigated the molecular transcriptome, germline allelic variants of immunoglobulin loci, and anti-Omicron antibody levels in 46 office and lab workers from the Republic of Korea following ChAdOx1-BNT162b2 vaccination. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml to 14,000 AU/ml to 142,000 AU/ml one, three and seven days following the second vaccination. Titers against VOC, including Omicron, were two- to three-fold lower, yet higher than those measured following BNT162b2-BNT162b2 vaccination. RNA-seq of peripheral immune cells demonstrated activation of interferon pathways with increased IGHV clonal transcripts encoding neutralizing antibodies. scRNA-seq revealed enriched B cell and CD4+ T cell responses in both ChAdOx1-BNT162b2 and BNT162b2-BNT162b2 recipients, but a stronger clonal expansion of memory B cells with ChAdOx1-BNT162b2. In summary, heterologous ChAdOx1-BNT162b2 provides an innate and adaptive immune response that exceeds homologous BNT162b2 vaccination. The ChAdOx1 nCoV-19 vector (AZD1222) and BNT162b2 mRNA vaccines (hereafter 42 referred to as ChAd and BNT, respectively) have been widely used and shown to induce protocol (Lee et al., 2022b) . Next, we directly compared anti-SARS-CoV-2 antibody titers 125 between the heterologous ChAd-BNT cohort and the homologous BNT-BNT reference 126 cohort within seven days after the second dose (II-D7) ( Figure 1F ). The anti-spike IgG 127 levels, including Omicron, were significantly higher in the heterologous cohort. However, 128 although median levels of antibody to variants were higher in the heterologous cohort, no 129 significant differences in ACE2 binding inhibition were observed ( Figure 1G) . Table S2 ). Functional enrichment analyses of common and 148 unique DEGs to each vaccination regimen revealed differences between the ChAd-BNT 149 and BNT-BNT regimens ( Figure S2 ). Expression of 308 genes was induced within two 150 days (I-D2) after the prime ChAd vaccination ( Figure S1A ). GSEA analyses linked them 151 to defense response pathways innate immune responses, including interferon and 152 cytokine signaling ( Figure S1B ). Specifically, genes regulated by the JAK-STAT pathway, 153 J o u r n a l P r e -p r o o f including STAT1 itself, interferon-induced (IFI) genes and the anti-viral OAS family were 154 activated within two days after the vaccination ( Figure S1C ). 155 Next, we analyzed the activation of genes induced in the heterologous group within 156 two days after the second dose ( Figure 3) . Expression of 318 genes was significantly 157 induced at day 2 as compared to day 0 ( Figure 3A) and levels of 84 genes remained 158 elevated at day 7 (Table S3 ). The 318 BNT-induced genes are enriched in IFN response, 159 complement and cytokine signaling ( Figure 3B ; Figure S2 ). Genes with elevated 160 expression at day 7 following the BNT vaccination are associated with proliferative 161 responses. To further investigate the impact of the heterologous vaccination regimen, we 162 compared its immune response with that of the homologous reference cohort (Lee et al., 163 2022b) after the second BNT dose ( Figure 3C ). While expression of 235 genes was 164 significantly higher in the heterologous group, 90 were selectively elevated in the 165 homologous reference group and 83 genes are significantly induced in both cohorts. 166 Thirty-one genes that were preferentially activated in the heterologous group are part of 167 interferon-activated pathways, including CXC chemokines and interferon induced genes 168 ( Figure 3D ). Fold change differences ranged from two to 90 (log21 ~ log26.5). Expression (two-way ANOVA followed by Tukey's multiple comparisons test, **P < 0.01, ***P < 0.001) 223 ( Figure 5C ). 224 To understand the difference between cell response to different vaccine regimen, 225 we performed DEG analysis on the B, CD4 T and CD8 T cells between two groups at day 226 2 after 2 nd dose ( Figure 5D : Table S4 The authors declare not competing interests. 313 We worked to ensure ethnic or other types of diversity in the recruitment of human 316 subjects. We worked to ensure that the study questionnaires were prepared in an 317 inclusive way. While citing references scientifically relevant for this work, we also actively 318 worked to promote gender balance in our reference list. The author list of this paper 319 includes contributors from the location where the research was conducted who 320 participated in the data collection, design, analysis, and/or interpretation of the work. 321 post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-428 human-subjects/). In addition, we followed the 'Sex and Gender Equity in Research -429 SAGERguidelines' and included sex and gender considerations where relevant. Whole blood was collected, PBMCs were isolated using density gradient medium, and 455 total RNA was extracted from PBMC and purified using the RNeasy Mini Kit (Qiagen, 456 #74104) according to the manufacturer's instructions. The concentration and quality of 457 RNA were assessed by an Agilent Bioanalyzer 2100 (Agilent Technologies, CA). 458 rearranged BCR/TCR genes were identified. The diversity of BCR/TCR genes was 485 investigated by the Chao1 index (Chao, 1984) . 486 Single-cell RNA sequencing (scRNA-seq) and data analysis 488 The isolated PBMCs were frozen in freezing media (Thermofisher) and stored at - cytokine levels between two groups, data were presented as standard deviation in each 510 group and were evaluated with a two-way ANOVA followed by Tukey's multiple 511 comparisons test using GraphPad PRISM (version 9.0). A value of *P < 0.05, **P < 0.01, 512 ***P < 0.001, ****P < 0.0001 was considered statistically significant. 513 MiXCR: software for comprehensive adaptive immunity 543 profiling Nonparametric estimation of the number of classes in a population CoV-2 Omicron variant following homologous and heterologous CoronaVac or BNT162b2 549 vaccination A 'mix and match' approach to SARS-CoV-2 551 vaccination STAR: ultrafast universal RNA-seq aligner Omicron thwarts some of the world's most-used COVID vaccines Heterologous ChAdOx1 and BNT162b2 prime-boost vaccination elicits potent neutralizing antibody responses 560 and T cell reactivity against prevalent SARS-CoV-2 variants Integrated analysis of multimodal single-564 cell data An 566 interferon-gamma-related cytokine storm in SARS patients Predictors of mortality in thrombotic 570 thrombocytopenia after adenoviral COVID-19 vaccination: the FAPIC score Safety and effectiveness of BNT162b2 mRNA Covid-19 vaccine in 574 adolescents Comparison of Antibody Response Elicited by ChAdOx1 and 577 BNT162b2 COVID-19 Vaccine A therapeutic neutralizing antibody targeting receptor binding 580 domain of SARS-CoV-2 spike protein Immune responses to the ChAdOx1 nCoV-19 and BNT162b2 584 vaccines and to natural COVID-19 infections over a three-month period BNT162b2 vaccination enhances interferon-588 CoV-2 Beta variant COVID-19 immune signature includes associations with poor prognosis JAK inhibitors dampen activation of 595 interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells Immune 599 transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying 600 the E484K escape mutation identifies a distinct gene module mRNA vaccination in 604 octogenarians 15 and 20 months after recovery from COVID-19 elicits robust immune 605 and antibody responses that include Omicron Immune transcriptomes of highly 609 exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from 610 the Ischgl community Serum Antibody Response Comparison and Adverse 613 Reaction Analysis in Healthcare Workers Vaccinated with the BNT162b2 or ChAdOx1 COVID-19 Vaccine. Vaccines (Basel) 9 Correlation between Reactogenicity and Immunogenicity 617 after the ChAdOx1 nCoV-19 and BNT162b2 mRNA Vaccination Comprehensive investigations revealed consistent pathophysiological 621 alterations after vaccination with COVID-19 vaccines Safety and 625 immunogenicity of heterologous versus homologous prime-boost schedules with an 626 adenoviral vectored and mRNA COVID-19 vaccine Moderated estimation of fold change and 629 dispersion for RNA-seq data with DESeq2 Neutralizing antibodies against 633 the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus 634 BNT162b2 booster vaccination Immunogenicity and 637 efficacy of heterologous ChAdOx1-BNT162b2 vaccination Normalization of RNA-seq data 640 using factor analysis of control genes or samples High genetic barrier to 644 SARS-CoV-2 polyclonal neutralizing antibody escape Immunogenicity and reactogenicity 648 of heterologous ChAdOx1 nCoV-19/mRNA vaccination Adjuvanted influenza-H1N1 vaccination 652 reveals lymphoid signatures of age-dependent early responses and of clinical adverse 653 events mRNA vaccination of 656 naive and COVID-19-recovered individuals elicits potent memory B cells that recognize 657 SARS-CoV-2 variants Single-cell profiling of T and B cell repertoires following SARS-CoV-660 2 mRNA vaccine Single-cell immunology of SARS-CoV-2 infection Ggplot2 : elegant graphics for data analysis Potent and protective IGHV3-53/3-66 public antibodies and 667 their shared escape mutant on the spike of SARS-CoV-2 Rapid isolation and profiling of a diverse 671 panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein mRNA sequencing (mRNA-seq) and data analysis. 460The Poly-A containing mRNA was purified by poly-T oligo hybridization from 1 mg of total 461 RNA and cDNA was synthesized using SuperScript III (Invitrogen, MA). Libraries for 462 sequencing were prepared according to the manufacturer's instructions with TruSeq 463 The raw data were subjected to QC analyses using the FastQC tool (version 0.11.9) 467 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). mRNA-seq read quality