key: cord-0976137-k6e0jdht authors: Ercanoglu, Meryem Seda; Gieselmann, Lutz; Dähling, Sabrina; Poopalasingam, Nareshkumar; Detmer, Susanne; Koch, Manuel; Korenkov, Michael; Halwe, Sandro; Klüver, Michael; Di Cristanziano, Veronica; Janicki, Hanna; Schlotz, Maike; Worczinski, Johanna; Gathof, Birgit; Gruell, Henning; Zehner, Matthias; Becker, Stephan; Vanshylla, Kanika; Kreer, Christoph; Klein, Florian title: No substantial pre-existing B cell immunity against SARS-CoV-2 in healthy adults date: 2022-02-19 journal: iScience DOI: 10.1016/j.isci.2022.103951 sha: e383130cbc1d7a6d6d49b6d0f812f0811758e4ee doc_id: 976137 cord_uid: k6e0jdht Pre-existing immunity against SARS-CoV-2 may have critical implications for our understanding of COVID-19 susceptibility and severity. The presence and clinical relevance of a pre-existing B cell immunity remains to be fully elucidated. Here, we provide a detailed analysis of the B cell response to SARS-CoV-2 in unexposed individuals. To this end, we extensively investigated SARS-CoV-2 humoral immunity in 150 adults sampled pre-pandemically. Comprehensive screening of donor plasma and purified IgG samples for binding and neutralization in various functional assays revealed no substantial activity against SARS-CoV-2 but broad reactivity to endemic betacoronaviruses. Moreover, we analyzed antibody sequences of 8,174 putatively SARS-CoV-2-reactive B cells at a single cell level and generated and tested 158 monoclonal antibodies. None of these antibodies displayed relevant binding or neutralizing activity against SARS-CoV-2. Taken together, our results show no evidence of competent pre-existing antibody and B cell immunity against SARS-CoV-2 in unexposed adults. The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 40 represents a global health emergency that challenges health care systems throughout the (Barnes et al., 2020a; Hurlburt et al., 2020; Shi et al., 2020; Wu et al., 2020; Yuan et al., 2020) , 71 are restricted to specific heavy chain V genes (Brouwer et al., 2020; Cao et al., 2020; Ju et al., 72 2020; Robbiani et al., 2020; Rogers et al., 2020; Seydoux et al., 2020; Wu et al., 2020; Zost et 73 al., 2020) , or exhibit a low degree of somatic mutations (Barnes et al., 2020b; 2020a; Robbiani et al., 2020; Seydoux et al., 2020) . This suggests that near-germline B cell 75 receptor (BCR) sequences with close similarity to SARS-CoV-2-reactive antibodies might 76 already be encoded in the naïve B cell repertoire and can be readily selected to mount a potent 77 B cell response without further affinity maturation. In line with this, we previously identified 78 potential heavy and/or light-chain precursor sequences of SARS-CoV-2 binding as well as 79 neutralizing antibodies by deep sequencing of naïve B cell receptor repertoires sampled before 80 the SARS-CoV-2 pandemic (Kreer et al., 2020a) . Cross-reactive immune responses to endemic HCoVs may also account for a potential pre-82 existing humoral immunity against SARS-CoV-2. Recent studies provide controversial results 83 regarding the frequency of cross-reactive antibodies in the sera of unexposed individuals 84 (Anderson et al., 2021; Ng et al., 2020; Nguyen-Contant et al., 2020a; Poston et al., 2020; 85 Shrock et al., 2020; Song et al., 2021) and their association with protection from disease 86 severity or hospitalization (Anderson et al., 2021; Gombar et al., 2021; Sagar et al., 2021) . Whereas one study found SARS-CoV-2 reactive antibodies in a considerable number of 88 unexposed individuals -particularly amongst children, adolescents and pregnant women (Ng 89 et al., 2020 )other studies did not find comparable evidence (Anderson et al., 2021; Nguyen-90 Contant et al., 2020a; Poston et al., 2020; Song et al., 2021; Chau et al., 2021) . Most studies 91 to date depended on the investigation of SARS-CoV-2 reactivity in serum/plasma or affinity-92 enriched or secreted IgG fractions of unexposed individuals (Anderson et al., 2021; Ng et al., 93 2020; Nguyen-Contant et al., 2020a; Poston et al., 2020; Shrock et al., 2020; Song et al., In order to detremine the presence of a relevant pre-existing SARS-CoV-2 B cell immunity, we 98 investigated plasma samples, single B cells, and monoclonal antibodies isolated from 150 99 SARS-CoV-2 unexposed individuals. We found no evidence of a competent pre-existing B cell We previously identified unpaired rare heavy and light chain variable regions of pre-pandemic 105 naive B cells that closely resembled near-germline SARS-CoV-2-reactive antibodies by 106 performing NGS analyses on healthy individuals (Kreer et al., 2020a) (Figure S1 ). Some of 107 these heavy and light chains derived from naïve B cells can replace the original one of SARS-108 CoV-2-reactive antibodies without altering their functionality (Figure S1 B) . These findings 109 complement previous observations that some SARS-CoV-2-reactive antibodies exhibit their 110 activity by germline-encoded sequence features (Barnes et al., 2020b; Hurlburt et al., 2020; 111 Robbiani et al., 2020; Seydoux et al., 2020) . To investigate how these findings translate to 112 plasma responses and whether SARS-CoV-2-reactive antibodies are already present in the 113 plasma of unexposed individuals, we investigated pre-pandemic blood samples from 150 114 donors. Samples were collected between August and November 2019 and were studied for 115 binding and neutralizing activity against SARS-CoV-2 ( Figure 1A and B; Table S1 ). Donors 116 were between 18 and 66 years of age (with a mean/median age of 30.6/27 years) ( Figure 1A 117 and Table S1 ). 49.3 % of donors were male and 50.7 % female ( Figure 1A and Table S1 ). With regard to previously published conflicting results we decided to use different assays in 119 parallel as a stringent search for pre-existing SARS-CoV-2-reactive antibodies. Initially, plasma 120 samples of all 150 donors were tested for binding to the soluble full trimeric SARS-CoV-2 S 121 ectodomain (S1/S2) or the S1 subunit (S1) by commercially available (com. IA) and in-house in the assay, all other samples did not reveal any binding activity ( Figure 1C and Figure S2 ). of 50 -60 % was found in two plasma and six pIgG samples, respectively. However, 142 neutralizing activity of these samples could not be confirmed by testing serial dilutions ( Figure 143 1C and Figure S3 ). In summary, none of the pre-pandemic samples obtained from 150 adults displayed reactivity 145 against SARS-CoV-2 in more than one of the various assays applied. Thus, based on the 146 parallel application of the various assays we found no convincing evidence of SARS-CoV-2-147 reactive antibodies in the pre-pandemic blood samples examined. The lack of binding or neutralization activity against SARS-CoV-2 on plasma level does not and Figure S4 ) were investigated. Using the same analysis gate as for COVID-19 156 convalescent donors, frequencies of SARS-CoV-2-reactive IgG + and IgG -B cells isolated from 157 pre-pandemic blood samples were significantly lower (p-value < 0.0001). For COVID-19 158 convalescent donors, frequencies ranged from 0.002 to 0.065 % for IgG + (median 0.02 %) and 159 0.007 to 0.39 % for IgG -(median 0.031 %) B cells (Figure 2A ). Applying the same analysis 160 gate of the COVID-19 convalescent samples to our pre-pandemic samples, frequencies 161 ranged from 0 to 0.0013 % for IgG + (median 0.0001 %) and from 0 to 0.016 for IgG -(median 162 0.003 %) B cells (Figure 2A and Figure S4 ). Therefore, we conclude that, if present at all, 163 SARS-CoV-2-reactive B cells have a significantly lower frequency in pre-pandemic samples. We reasoned that gate settings applied for COVID-19 convalescent samples may exclude 165 reactive B cells with low spike affinity which may be present in individuals unexposed to SARS-166 CoV-2. To assure that such cells do not remain undetected, we adjusted the actual sorting 167 gate (Figure 2A) to isolate a total of 8,174 putatively SARS-CoV-2-reactive single B cells, of 168 which 3,852 were IgG + and 4,322 IgGcells. Of those, we amplified a total of 5,432 productive 169 heavy chain sequences, of which 2,789 sequences accounted for IgG and 2,643 for IgM heavy 170 chains, respectively ( Figure 2B) . Sequence analyses showed that in each individual 0 to 58 171 % of the sequences were clonally related with a mean clone number of 8.1 clones per individual 172 and a mean clone size of 2.9 members per clone ( Figure 2B ). Heavy chain variable (VH) gene 173 segment distribution, heavy chain complementarity-determining region 3 (CDRH3) length and naïve IgM repertoire data set (Kreer et al., 2020a) (Figure 2C ). We conclude that pre-pandemic 176 samples of healthy adults lack high-reactive B cells against SARS-CoV-2. Monoclonal antibodies isolated from pre-pandemic samples are not reactive 178 To confirm the absence of SARS-CoV-2-reactive B cells in pre-pandemic samples on a strategies (Imkeller and Wardemann, 2018; Niu et al., 2020; Schultheiß et al., 2020) . Although 204 various studies already provide evidence for pre-existing T cell immunity against SARS-CoV-Recently published studies that investigated a pre-existing B cell immunity in unexposed 208 individuals provide partially conflicting results. For instance, some studies based on the 209 examination of serum samples reported detection of SARS-CoV-2 cross-reactive antibodies 210 and pre-existing humoral immunity in uninfected individuals (Ng et al., 2020; Majdoubi et al., 211 2021; Sagar et al., 2021; Woudenberg et al., 2021) . Cross-reactive humoral immune 212 responses were mainly observed against S protein structures within the S2 subunit, the N 213 protein or against ORF polypeptides such as non-structural proteins protein 2 (NSP2) and 15 214 (NSP15) that are relatively conserved among endemic HCoVs and SARS-CoV-2. However, 215 the frequency of cross-reactive serum responses varies greatly between the individual studies. For instance, whereas some of these studies report an overall seroprevalence of cross-217 reactive serum responses in 10% to 20% in unexposed subjects (Ng et al., 2020; Nguyen-218 Contant et al., 2020b; Woudenberg et al., 2021) another study determined antibody responses 219 in more than 90% of all samples analyzed (Majdoubi et al., 2021) . Varying frequency of cross-220 reactive serum responses between these studies are attributed to differences in cohort 221 composition and heterogeneous sensitivities of applied diagnostic assays. Furthermore, in the 222 described studies the extent to which prior immunity against HCoVs may modify COVID-19 223 disease severity and susceptibility as well as seasonal and geographical transmission patterns 224 is controversially discussed (Ng et al., 2020; Sagar et al., 2021; Woudenberg et al., 2021) . In In our study, we cover not only an extensive examination of plasma and IgG fractions but reach 238 out further to investigate the presence of SARS-CoV-2-reactive B cell precursors, memory B 239 cells and the characterization of respective monoclonal antibodies. We recently isolated SARS-CoV-2-reactive antibodies from convalescent individuals and 241 identified highly similar heavy and/or light chain sequences in naive B cell receptor repertoires maturation. This finding supports previous observations that the readily detected antibody 245 response in some individuals might use existing antibody heavy or light chains with distinct 246 CDR3 recombination patterns or germline encoded sequence features (Barnes et al., 2020b (Barnes et al., , 247 2020a Hurlburt et al., 2020; Kreer et al., 2020a; Robbiani et al., 2020) . In line with this, SARS- CoV-2 neutralizing antibodies were successfully isolated from the human naïve B cell 249 compartment using antigen-specific single B cell sorts or phage display (Bertoglio et al., 2021; 250 Feldman et al., 2021) . Feldman et al. sequentially applied diverse SARS-CoV-2 spike protein 251 subdomains as antigen probes for the isolation of single SARS-CoV-2 and sarbecovirus-252 reactive naïve B cells. Following this approach, they report a median frequency of 0.0025% for 253 RBM-reactive naïve B cells. BCR sequence analyses revealed a diverse and polyclonal gene 254 usage for heavy and light chains but an increase in the mean repertoire frequency of 20% for 255 the heavy chain v gene IGHV3-9 (Feldman et al., 2021) . Finally, monoclonal antibodies were 256 isolated from naïve B cell precursors that exhibited binding and neutralization activity against 257 circulating SARS-CoV-2 variants of concern and bat-derived coronarviruses. Bertoglio et al. applied phage display to isolate antibody candidate STE73-2E9 from naïve B cell libraries that 259 targets the ACE2-RBD interface without cross-reactivity to other coronaviruses and neutralizes 260 authentic SARS-CoV-2 wildtype virus with an IC50 of 0.43 nM. However, since phage display 261 relies on random sequence recombination this study does not provide evidence that SARS- CoV-2-reactive antibodies naturally occur in the naïve B cell repertoire. Using various immunological and functional assays assessing SARS-CoV-2 binding and 264 neutralization activity as well as cross-reactivity to endemic beta coronaviruses, we found no 265 evidence of significant plasma or IgG reactivity against SARS-CoV-2 in pre-pandemic 266 samples. We comprehensively investigated plasma binding activity of IgG, IgM and IgA 267 immunoglobulin isotypes against diverse beta coronavirus S proteins (SARS-CoV-2 S1 and 268 S1/S2, HCoV-HKU1 and HCoV-OC43 S) by in house and commercially available ELISAs. Moreover, we validated our ELISA results against cell-surface-expressed S protein using flow 270 cytometry and by applying SARS-CoV-2 pseudo-as well as wildtype neutralization assays. Our results are consistent with recently published studies that disagreed on a broad pre-272 existing B cell background immunity (Anderson et al., 2021; Chau et al., 2021; Nguyen-Contant 273 et al., 2020a; Poston et al., 2020; Shrock et al., 2020; Song et al., 2021) . These studies report 274 an overall prevalence of cross-reactive serum responses against the SARS-CoV-2 S protein 275 or the S1 subdomain below 5%. In line with this, only 3% of analyzed plasma samples (5/150) 276 in our study displayed some binding activity against the SARS-CoV-2 S protein. (Anderson et al., 2021; Poston et al., 2020) . Consistent with these samples. However, the findings of our plasma screening may not be directly comparable to the 282 recent studies that indeed reported pre-existing humoral immunity due to cohort composition 283 or differences in experimental assays. For example, Ng et al. detected serum neutralization 284 activity in unexposed children, adolescents, and pregnant women since who are not included 285 in our study cohort (Ng et al., 2020) . To investigate potential pre-existing immunity on a molecular level, we applied antigen-specific (Barnes et al., 2020b (Barnes et al., , 2020a Robbiani et al., 2020) . Furthermore, we detected no relevant reactivity of 158 recombinantly produced monoclonal 305 antibodies against SARS-CoV-2 and endemic HCoV S proteins. In the presented study, we could not detect cross-reactivity of pre-pandemic serum samples 308 between endemic HCoVs HKU1 or OC43 and SARS-CoV-2 S proteins. However, individuals 309 involved in the cohort were not investigated for recent HCoV infections or a documented history 310 of infection prior to blood sampling. Therefore, this study cannot rule out that recent HCoV 311 infections may be important determinants for the detection of serum cross-reactivity to SARS-312 CoV-2. In this light, recent HCoV infections may for example elicit a transient serum cross-313 reactivity against SARS-CoV-2 that is not detected in our study. Moreover, HCoV infections 314 appear with higher prevalence in children and young adolescents who were not included in the For single cell sorts, we could only express and functionally characterize a small proportion 317 (n=158) of amplified BCR sequences (n=5,223) due to the limited scalability of antibody 318 isolation protocols. Although we applied defined criteria for selection of BCR sequences for 319 downstream antibody production, we cannot rule out that SARS-CoV-2-reactive BCR 320 sequences were indeed present among isolated sequences amplified but omitted by the bio-321 informatical approach. CoV-2 and endemic HCoVs (HKU1 and OC43) S proteins or SARS-CoV-2 authentic wildtype 337 (WT) and pseudovirus (PSV Wu_01), respectively (see also Figure S2 and 3). Immunoassays 338 were performed in duplicates and the AUCs are presented as geometric mean of duplicates. Neutralizing activity was first determined for single sample concentrations. Samples that 340 displayed neutralization activity of ≥ 50% are indicated as (x) and were repeatedly investigated 341 in serial dilutions (see also Figure S3 ). Samples were tested in duplicates. The average of 342 neutralization is presented and each row represents one donor. Generation of cDNA and amplification of antibody heavy and light chain genes from sorted 475 single cells was performed as previously described (Gieselmann et al., 2021; PCRs using optimized V gene-specific primer mixes (Kreer et al., 2020b) and Platinum Taq 487 DNA Polymerase or Platinum Taq Green Hot Start Polymerase (Thermo Fisher Scientific) as 488 previously described (Kreer et al., 2020a; Schommers et al., 2020; Kreer et al., 2020b; 489 Gieselmann et al., 2021) . PCR products were analyzed by agarose gel electrophoresis for 490 correct product size and subsequently send for Sanger sequencing. Only chromatograms with 491 a mean Phred score of 28 and sequences with a minimal length of 240 nucleotides were 492 selected for downstream sequence analyses. Filtered sequences were annotated with IgBlast 493 (Ye et al., 2013) according to the IMGT system (Lefranc et al., 2009 ) and only the variable 494 region from FWR1 to the end of the J gene was extracted. Base calls within the variable region 495 with a Phred score below 16 were masked and sequences with more than 15 masked 496 nucleotides, stop codons, or frameshifts were excluded from further analyses. Sequence 497 analyses to inform on sequence clonality were performed separately for each study participant. All productive heavy chain sequences were grouped by identical VH/JH gene pairs and the 499 pairwise Levenshtein distance for their CDRH3s was determined. Starting from a random 500 sequence, clone groups were assigned to sequences with a minimal CDRH3 amino acid 501 identity of at least 75 % (with respect to the shortest CDRH3). 100 rounds of input sequence 502 randomization and clonal assignment were performed and the result with the lowest number 503 of remaining unassigned (non-clonal) sequences was selected for downstream analyses. All 504 clones were cross-validated by the investigators taking shared mutations and light chain 505 information into account. Antibody selection for cloning was was performed with an in-house python script (Python 508 v3.6.8) by two approaches. First, a similarity search was performed against 868 and 52 SARS- and Kreer et al., 2020 (Kreer et al., 2020a , respectively. To this end, SARS-CoV-2 antibodies 511 were annotated with IgBLAST (Ye et al., 2013) . Annotations and sequence information from 512 published antibodies and sequences from this study were loaded with the pandas module 513 (McKinney, 2010) into data frames. Both data frames were grouped by their V/J gene 514 combination (ignoring any allele information). For all V/J groups that were found in both data with the python-Levenshtein package. Sequences from this study, where the Levenshtein 518 distance was ≤ 3 AA in comparison to at least one SARS-CoV-2-binding antibody, were 519 selected as similar and produced (18 antibodies in total). Second, a random selection was performed with the python random module (Python standard 521 library) on clonal and non-clonal sequences from each individual (determined as described in 522 "B cell receptor amplification and sequence analysis") to select at least 3 different clones and 523 at least 3 non-clonal sequences. If less than 3 clones were available for an individual, random 524 non-clonal sequences were used to fill up the selection to yield at least 6 antibodies per 525 individual. Heavy and light chain variable regions of selected antibodies were cloned into expression 528 vectors by sequence and ligation independent cloning (SLIC) (von Boehmer et al., 2016) as 529 previously described (Tiller et al., 2008; Schommers et al., 2020; Kreer et al., 2020a; 530 Gieselmann et al., 2021) . 1 st PCR product was amplified using Q5 Hot Start High Fidelity DNA 531 Polymerase (New England Biolabs) and specific forward and reverse primers including adaptor 532 sequences which are homologous to the restriction sites of the antibody expression vector 533 (IgG1, IgL, IgK (Tiller et al., 2008) . Forward primers were designed according to 2 nd PCR 534 primers (Kreer et al., 2020b) and encode for the complete native leader sequence of all heavy 535 and light chain V genes, whereas reverse primers bind to the conserved sequence motifs at Anti-SARS-CoV-2 S1/S2 IgG and IgM antibody titers of plasma samples were also assessed 590 using the automated DiaSorin's LIAISON® SARS-CoV-2 S1/S2 protein ELISA kit according to For testing neutralization at a single dilution, polyclonal IgG samples at a concentration of 1000 610 µg/ml, plasma samples at a dilution of 1:10, or mAbs at a concentration of 50 µg/ml, were co-611 incubated with pseudovirus supernatants for 1 h at 37°C, following which 293T-ACE-2 cells 612 were added. After a 48 h incubation at 37 °C and 5 % CO2, luciferase activity was determined 613 using the luciferin/lysis buffer. After subtracting background RLUs of non-infected cells, % of 614 neutralization was calculated and the mean value was used for reporting. Each sample was 615 tested in duplicates. To determine IC50 values for mAbs a dilution series of the antibody was performed starting with 617 50 µg/ml. IC50 values were calculated as the antibody concentration causing a 50 % reduction 618 in signal compared the virus-only controls using a dose-response curve in GraphPad Prism. Authentic virus neutralization was tested using a virus previously grown out from an oro-/naso-622 pharyngeal swab using VeroE6 cells (Vanshylla et al., 2021) . For testing neutralization, plasma 623 samples at a single dilution of 1:10 were co-incubated with the 200 TCID50 virus for 1 h at 37°C, 624 following which VeroE6 cells were added. After 4 days, cytopathic effects (CPE) were analysed 625 under a bright-field microscope and neutralization was determined as the absence of CPE. Cells without any virus served as reference for lack of CPE and cells with virus only served as 627 reference for positive CPE. Flow cytometry analyses and quantification were performed using FlowJo10 software. 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