Literature DB >> 35216664

SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses.

Debashree Chatterjee1, Alexandra Tauzin2, Lorie Marchitto2, Shang Yu Gong3, Marianne Boutin2, Catherine Bourassa1, Guillaume Beaudoin-Bussières2, Yuxia Bo4, Shilei Ding1, Annemarie Laumaea2, Dani Vézina2, Josée Perreault5, Laurie Gokool1, Chantal Morrisseau1, Pascale Arlotto1, Éric Fournier6, Aurélie Guilbault6, Benjamin Delisle6, Inès Levade6, Guillaume Goyette1, Gabrielle Gendron-Lepage1, Halima Medjahed1, Gaston De Serres7, Cécile Tremblay2, Valérie Martel-Laferrière2, Daniel E Kaufmann8, Renée Bazin5, Jérémie Prévost2, Sandrine Moreira6, Jonathan Richard9, Marceline Côté10, Andrés Finzi11.   

Abstract

Continuous emergence of SARS-CoV-2 variants of concern (VOCs) is fueling the COVID-19 pandemic. Omicron (B.1.1.529) rapidly spread worldwide. The large number of mutations in its Spike raise concerns about a major antigenic drift that could significantly decrease vaccine efficacy and infection-induced immunity. A long interval between BNT162b2 mRNA doses elicits antibodies that efficiently recognize Spikes from different VOCs. Here, we evaluate the recognition of Omicron Spike by plasma from a cohort of SARS-CoV-2 naive and previously infected individuals who received their BNT162b2 mRNA vaccine 16 weeks apart. Omicron Spike is recognized less efficiently than D614G, Alpha, Beta, Gamma, and Delta Spikes. We compare with plasma activity from participants receiving a short (4 weeks) interval regimen. Plasma from individuals of the long-interval cohort recognize and neutralize better the Omicron Spike compared with those who received a short interval. Whether this difference confers any clinical benefit against Omicron remains unknown.
Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  COVID-19; Coronavirus; Omicron; SARS-CoV-2; delayed mRNA vaccine regimen; humoral responses; neutralization; spike glycoproteins; variants of concern

Mesh:

Substances:

Year:  2022        PMID: 35216664      PMCID: PMC8823958          DOI: 10.1016/j.celrep.2022.110429

Source DB:  PubMed          Journal:  Cell Rep            Impact factor:   9.995


Introduction

SARS-CoV-2 variants are constantly evolving under immune selective pressure. Ongoing mutational events in the viral genome leads to the emergence of variants with unique properties, including increased transmission capabilities and resistance to antibodies elicited by both natural infection and vaccination. Based on transmission capabilities, virulence, and vaccine effectiveness, SARS-CoV-2 variants are classified as variants of concern (VOCs), variant of interest (VOIs), or variants under monitoring (VUMs) (WHO, 2021). In late 2020, the Alpha (B.1.1.7) variant emerged. The N501Y Spike mutation increased its affinity for the ACE2 receptor, leading to increased transmissibility (Davies et al., 2021; Prevost et al., 2021; Rambaut et al., 2020). The accumulation of E484K and K417N/T mutations along with N501Y in the receptor binding domain (RBD) led to the emergence of Beta (B.1.351) and Gamma (P.1) lineages, which rapidly spread worldwide (Amanat et al., 2021; ECDC, 2021; Tang et al., 2021). In April 2021, the Delta (B.1.617.2) variant emerged and quickly spread to most countries (Allen et al., 2022; Planas et al., 2021b), but is rapidly being replaced by Omicron (B.1.1.529). The World Health Organization designated Omicron as a VOC on November 26, 2021(WHO, 2021). Omicron accumulated more than 30 mutations in its Spike, raising concerns about a major antigenic drift that could significantly decrease vaccine efficacy. Here we evaluated the recognition of the Omicron Spike by plasma from a cohort of SARS-CoV-2 naive and previously infected individuals who received the two BNT162b2 mRNA vaccine doses 16 weeks apart. We compared these responses with those elicited in individuals receiving a short dose interval regimen (4 weeks). Plasma from vaccinated previously infected individuals recognized more efficiently all tested Spikes (D614G, Alpha, Beta, Gamma, Delta, and Omicron) than those from naive vaccinated individuals. Omicron Spike was recognized less efficiently than D614G, Alpha, Beta, Gamma, and Delta Spikes. However, plasma from individuals receiving a long interval recognized and neutralized better the Omicron Spike compared with those who received a short interval.

Results

Recognition of Spike variants by plasma from vaccinated individuals

The antigenic profile of D614G, Alpha, Beta, Gamma, Delta, and Omicron Spikes was assessed with plasma collected 3 weeks (V3) and 4 months (V4) after the second dose of the BNT162b2 mRNA vaccine administered with a 16-week interval between doses (Figure 1 A) (Tauzin et al., 2022). Briefly, 293T cells were transfected with plasmids coding for full-length Spike variants. Two days post-transfection, cells were incubated with the indicated plasmas followed by flow cytometry analysis, as described (Anand et al., 2021; Beaudoin-Bussieres et al., 2020; Gasser et al., 2021; Prevost et al., 2020; Tauzin et al., 2021, 2022). Spike expression levels of VOCs were normalized to the signal obtained with the conformationally independent anti-S2 neutralizing CV3-25 antibody (Li et al., 2021; Prevost et al., 2021; Ullah et al., 2021) that efficiently recognized and neutralized all VOCs Spike, including Omicron (Figure S1). Using plasma from previously infected individuals or from naive double-vaccinated individuals, we observed a significant increase of recognition of all tested Spikes upon vaccination (Figures 1B–1G), in agreement with previous observations (Stamatatos et al., 2021; Tauzin et al., 2021, 2022). In all cases, the Omicron Spike was significantly less recognized than all other Spikes, with the exception of the Beta variant (Figures 1D, 1H–1J). At V3 and V4, levels of plasma binding against Omicron Spike in previously infected individuals were similar to those against Delta Spike in naive individuals (Figure 1 I and 1J). In agreement with previous observations (Tauzin et al., 2022), Spike recognition declined more rapidly in the naive group compared with previously infected individuals.
Figure 1

Binding of vaccine-elicited antibodies to SARS-CoV-2 Spike variants

(A) SARS-CoV-2 vaccine cohort design.

(B–G) 293T cells were transfected with the indicated full-length Spike from different SARS-CoV-2 variants (D614G in B, Alpha in C, Beta in D, Gamma in E, Delta in F, and Omicron in G) and stained with the CV3-25 Ab or with plasma collected 3 weeks (V3) or 4 months (V4) after a second dose administered with a 16-week interval. Samples were analyzed by flow cytometry. The values represent the median fluorescence intensities (MFIs) normalized by CV3-25 Ab binding and presented as percentages of CV3-25 binding (B–G, left panels). Each curve represents the normalized MFIs obtained with the plasma of one donor at every time point. The mean of each group is represented by a bold line. In the right panels, plasma samples were grouped in different time points (V0, V3, and V4).

(H–J) Comparison of Spike recognition by plasma from naive and previously infected donors, represented by red and black points, respectively. Each symbol/points identifies one donor. Error bars indicate means ± SEM. For naive donors, n = 20 at V3 and V4. For previously infected donors vaccinated with two doses, n = 15 at V0 (H), V3 (I), and V4 (J). Statistical significance was tested using (B–G, left panels, (H, I, J) a Wilcoxon test, or (B–G, right panels) a Mann-Whitney test (∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001; ns, non-significant).

Binding of vaccine-elicited antibodies to SARS-CoV-2 Spike variants (A) SARS-CoV-2 vaccine cohort design. (B–G) 293T cells were transfected with the indicated full-length Spike from different SARS-CoV-2 variants (D614G in B, Alpha in C, Beta in D, Gamma in E, Delta in F, and Omicron in G) and stained with the CV3-25 Ab or with plasma collected 3 weeks (V3) or 4 months (V4) after a second dose administered with a 16-week interval. Samples were analyzed by flow cytometry. The values represent the median fluorescence intensities (MFIs) normalized by CV3-25 Ab binding and presented as percentages of CV3-25 binding (B–G, left panels). Each curve represents the normalized MFIs obtained with the plasma of one donor at every time point. The mean of each group is represented by a bold line. In the right panels, plasma samples were grouped in different time points (V0, V3, and V4). (H–J) Comparison of Spike recognition by plasma from naive and previously infected donors, represented by red and black points, respectively. Each symbol/points identifies one donor. Error bars indicate means ± SEM. For naive donors, n = 20 at V3 and V4. For previously infected donors vaccinated with two doses, n = 15 at V0 (H), V3 (I), and V4 (J). Statistical significance was tested using (B–G, left panels, (H, I, J) a Wilcoxon test, or (B–G, right panels) a Mann-Whitney test (∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001; ns, non-significant).

Impact of the interval between mRNA vaccine doses on Omicron Spike recognition and neutralization

Recent reports suggested that vaccine regimens with a delayed boost elicit stronger humoral responses than the approved, short interval, regimen (Grunau et al., 2021; Tauzin et al., 2022). The long regimen interval has been associated with good vaccine efficacy against different VOCs (Skowronski et al., 2021). We therefore compared the capacity of plasma from naive vaccinated individuals who received the second dose with an interval of 16 weeks (median [range]: 111 days [76–120 days]) with those obtained from 19 SARS-CoV-2 naive donors who received their two doses 4 weeks apart (median [range]: 29 days [22–34 days]) (Table 1 and Figure 2 A). As shown in Figure 2B, plasma from naive individuals who received a 16-week interval between the two doses recognized significantly better all tested Spikes, including Omicron, than plasma from individuals who received a short interval between doses (4 weeks). The 16-week interval regimen elicited significantly better neutralization activity against pseudoviral particles bearing the D614G, Beta, Delta, and Omicron Spikes (Figure 2C). Strikingly, this increased neutralization was more pronounced for the Omicron Spike (8.9-fold increase) compared with the other emerging variant Spikes (D614G, Beta, and Delta) (2.2- to 4.2-fold increase). This suggests that the delayed boosting in naive individuals facilitates antibody maturation resulting in enhanced breadth able to provide detectable levels of recognition and neutralization against Omicron.
Table 1

Characteristics of the vaccinated SARS-CoV-2 cohorts

SARS-CoV-2 naive
SARS-CoV-2 previously infected
Two dosesShort interval (n = 19)Two dosesLong interval (n = 25)Two dosesLong interval (n = 15)
Age39 (20–74)50 (21–62)47 (29–65)
Sex
 Male (n)121110
 Female (n)7145
Days between symptom onset and V0aN/AN/A191 (85–234)
Days between symptom onset and the 1st doseaN/AN/A274 (166–321)
Days between the 1st and 2nd dosea29 (22–34)111 (76–120)110 (90–134)
Days between the 2nd dose and V3a22 (12–53)21 (14–34)22 (13–51)
Days between the 2nd dose and V4aN/A112 (103–125)113 (90–127)

Values displayed are medians, with ranges in parentheses.

Figure 2

Omicron Spike recognition and neutralization with plasma from naive individuals who received a short versus a long mRNA vaccine dose interval

(A) SARS-CoV-2 vaccine cohort design.

(B) 293T cells were transfected with the full-length Spike from different SARS-CoV-2 variants (D614G, Beta, Delta, and Omicron) and stained with the CV3-25 Ab or with plasma from naive donors who received a short (4 weeks, yellow) or long (16 weeks, red) interval between doses collected 3 weeks after the second dose (V3) and analyzed by flow cytometry. The values represent the MFI normalized by CV3-25 Ab binding and presented as percentages of CV3-25 binding.

(C) Neutralizing activity was measured by incubating pseudoviruses bearing indicated SARS-CoV-2 Spikes (D614G, Beta, Delta, and Omicron), with serial dilutions of plasma for 1 h at 37°C before infecting 293T-ACE2 cells. Neutralization half-maximal inhibitory serum dilution (ID50) values were determined using a normalized non-linear regression using GraphPad Prism software. Undetectable measures are represented as white symbols, and limits of detection are plotted. Error bars indicate means ± SEM. For naive donors vaccinated with the short interval, n = 19. For naive donors vaccinated with the long interval, n = 25. Each symbol/points identifies one donor. Statistical significance was tested using a Mann-Whitney test (∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001).

Characteristics of the vaccinated SARS-CoV-2 cohorts Values displayed are medians, with ranges in parentheses. Omicron Spike recognition and neutralization with plasma from naive individuals who received a short versus a long mRNA vaccine dose interval (A) SARS-CoV-2 vaccine cohort design. (B) 293T cells were transfected with the full-length Spike from different SARS-CoV-2 variants (D614G, Beta, Delta, and Omicron) and stained with the CV3-25 Ab or with plasma from naive donors who received a short (4 weeks, yellow) or long (16 weeks, red) interval between doses collected 3 weeks after the second dose (V3) and analyzed by flow cytometry. The values represent the MFI normalized by CV3-25 Ab binding and presented as percentages of CV3-25 binding. (C) Neutralizing activity was measured by incubating pseudoviruses bearing indicated SARS-CoV-2 Spikes (D614G, Beta, Delta, and Omicron), with serial dilutions of plasma for 1 h at 37°C before infecting 293T-ACE2 cells. Neutralization half-maximal inhibitory serum dilution (ID50) values were determined using a normalized non-linear regression using GraphPad Prism software. Undetectable measures are represented as white symbols, and limits of detection are plotted. Error bars indicate means ± SEM. For naive donors vaccinated with the short interval, n = 19. For naive donors vaccinated with the long interval, n = 25. Each symbol/points identifies one donor. Statistical significance was tested using a Mann-Whitney test (∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001).

Discussion

In the province of Québec, Canada, like in other jurisdictions worldwide, the prevalence of Omicron increased dramatically from the first case detected on November 23 to being the dominant variant less than 1 month later. Compared with the reference Wuhan-Hu-1 strain, the Omicron variant carries more than 50 non-synonymous mutations within its genome, more than 30 of which are located in the gene coding for the Spike glycoprotein. Several of these mutations affecting the RBD, the N-terminal domain (NTD), and the furin cleavage domain were observed in other VOCs (Viana et al., 2021), which is consistent with positive selection of favorable mutations. Previous in vitro studies already showed the association of some of these mutations with increased infectivity, ACE2 interaction (N501Y, P681H) (Gong et al., 2021; Saito et al., 2021), or immune evasion (K417N, N440K, G446S, S477N, E484A/K, Q493R) (Baum et al., 2020; Clark et al., 2021; Greaney et al., 2021a, 2021b, 2021c; Liu et al., 2020; Rappazzo et al., 2021; Starr et al., 2021; Weisblum et al., 2020). This unprecedented accumulation of Spike mutations raised concern about a major antigenic drift that could significantly decrease the efficacy of current vaccines (Andrews et al., 2021; Khoury et al., 2021; Schmidt et al., 2021b). To get a better understanding of the antigenic profile, we compared the antigenicity of the Omicron Spike with those from D614G, Alpha, Beta, Gamma, and Delta VOCs. We used plasma from naive and previously infected individuals who received their two doses of the BNT162b2 mRNA vaccine 16 weeks apart. In agreement with previous observations, we found that previously infected vaccinated individuals recognized more efficiently all Spikes than naive individuals at the two timepoints analyzed (3 weeks and 4 months post second dose) (Stamatatos et al., 2021; Tauzin et al., 2021, 2022). Interestingly, we observed that recognition of all Spikes, including Omicron, decreased more rapidly in naive than previously infected individuals, as reported (Tauzin et al., 2022). The three antigenic exposures (infection +2 doses) of previously infected individuals compared with the two exposures in double-vaccinated naive individuals possibly explains their more sustained humoral response, suggesting that an additional exposition to the Spike antigen in the form of a third vaccine dose could elicit similar responses. Alternatively, if infection elicits a qualitatively broader humoral response linked to epitopes located outside the Spike glycoprotein, the effect of a third dose in naive individuals may remain qualitatively different. Independently of their infection history, all plasma recognized significantly less efficiently the Omicron Spike compared with Spikes from other VOCs (Figure 1). Of note, the sequence initially released for the Omicron Spike contained the Q493K substitution, but was then corrected to Q493R. Since initial studies on Omicron used the Q493K mutation, we verified whether the nature of the residue at 493 (either K or R) impacted plasma recognition or neutralization. We observed no significant differences among them (Figure S2). As indicated in the STAR methods section, all results generated in the current manuscript were done using the Q493R mutation. Since recent studies have shown that recognition of full-length Spikes at the surface of transfected 293T cells strongly correlates with recognition of primary airway epithelial cells infected with authentic viruses as well as with antibody-dependent cellular cytotoxicity (Ding et al., 2022), these results suggest that Fc-mediated effector functions against Omicron could also be affected. Of note, low Spike recognition translated into increased Omicron neutralization resistance (Figure 2C). In agreement with previous observations (Stamatatos et al., 2021; Tauzin et al., 2021, 2022), plasma from vaccinated previously infected individuals recognized more efficiently Omicron and all other VOCs than vaccinated naive individuals (Figure 1). As naive double-vaccinated individuals have been well protected against the Delta variant, the observation of similar levels of plasma binding against Delta Spike in naive individuals and those against Omicron Spike in previously infected individuals may be important. This suggests that the benefits of hybrid immunity also apply to Omicron but this hypothesis will need confirmation through vaccine effectiveness studies. Several reports (Cele et al., 2021; Garcia-Beltran et al., 2021; Planas et al., 2021a; Schmidt et al., 2021a; Zhang et al., 2021) have shown neutralization resistance using plasma from naive donors who received the approved regimen of the BNT162b2 mRNA vaccine (3- to 4-week vaccine interval). Strikingly, we observed that plasma from naive vaccinated donors who received their two doses according to the approved short 3- to 4-week interval, recognized and neutralized Omicron significantly less efficiently compared with the long 16-week interval. For all individuals, the level of Omicron Spike recognition remains lower than for the ancestral Spike, the antigen used in the current vaccines, and these levels decrease over time. Therefore, it will be important to determine in epidemiological studies if the vaccine interval advantage, as measured by these in vitro parameters, confers any clinical benefit against Omicron.

Limitations of the study

A limitation of our study is the relatively low number of individuals analyzed; however, we note that our results are in agreement with recent findings indicating that longer mRNA vaccine dosing intervals have improved immunogenicity (Grunau et al., 2021; Tauzin et al., 2022), which may have been associated with an optimized booster dose protection in Canada (Skowronski et al., 2021). Epidemiological studies will be required to establish the vaccine efficacy of the extended interval dosing against severe outcomes caused by Omicron.

STAR★Methods

Key resources table

Resource availability

Lead contact

Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Andrés Finzi (andres.finzi@umontreal.ca).

Materials availability

All unique reagents generated during this study are available from the lead contact without restriction.

Experimental model and subject details

Ethics statement

All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board. Blood samples were obtained from donors who consented to participate in this research project at CHUM (19.381) and from plasma donors who consented to participate in the Plasma Donor Biobank at Hema-Quebec (PLASCOV; REB-B-6-002-2021-003). Plasma was isolated by centrifugation, and samples stored at −80°C and in liquid nitrogen, respectively, until use.

Human subjects

The study was conducted in 25 SARS-CoV-2 naïve individuals (11 males and 14 females; age range: 21–62 years) vaccinated with a long interval, 19 SARS-CoV-2 naïve individuals (12 males and 7 females; age range: 20–74 years) vaccinated with a short interval and 15 SARS-CoV-2 previously-infected individuals (10 males and 5 females; age range: 29–65 years) vaccinated with a long interval. All this information is summarized in Table 1. No specific criteria such as number of patients (sample size), gender, clinical or demographic were used for inclusion, beyond PCR confirmed SARS-CoV-2 infection in adults.

Plasma and antibodies

Plasma from SARS-CoV-2 naïve and previously-infected donors were collected, heat-inactivated for 1 hour at 56°C and stored at −80°C until ready to use in subsequent experiments. The conformationally independent S2-specific monoclonal antibody CV3-25 (Gong et al., 2021; Jennewein et al., 2021; Li et al., 2021; Prevost et al., 2021; Ullah et al., 2021) was used as a positive control and to normalize Spike expression in our flow cytometry assays, as described (Gong et al., 2021; Tauzin et al., 2021, 2022). Alexa Fluor-647-conjugated goat anti-human Abs (Invitrogen) were used as secondary antibodies to detect plasma binding in flow cytometry experiments.

Cell lines

293T human embryonic kidney cells (obtained from ATCC) were maintained at 37°C under 5% CO2 in Dulbecco's modified Eagle's medium (DMEM) (Wisent) containing 5% fetal bovine serum (FBS) (VWR) and 100 μg/mL of penicillin-streptomycin (Wisent). The 293T-ACE2 cell line was previously reported (Prevost et al., 2020).

Method details

Plasmids

The plasmids encoding the SARS-CoV-2 Spike variants; D614G, B.1.1.7, B.1.351, P.1 and B.1.617.2 were previously described (Beaudoin-Bussieres et al., 2020; Gong et al., 2021; Li et al., 2021; Tauzin et al., 2021, 2022). The plasmids encoding the B.1.1.529 Spike was generated by overlapping PCR using a codon-optimized wild-type SARS-CoV-2 Spike gene (GeneArt, ThermoFisher) that was synthesized (Biobasic) and cloned in pCAGGS as a template. The B.1.1.529 Spike coding sequence was derived from the sequence ID EPI_ISL_6640919. This sequence initially contained the Q493K substitution, as previously reported (Cameroni et al., 2021; Schmidt et al., 2021a; Shah and Woo, 2021). The ECDC (European Centre for Disease Prevention and Control) later informed that Omicron spike actually have an R mutation at position 493. We therefore generated and used an Omicron Spike bearing the Q493R mutation for the full manuscript (Figures 1 and 2 and Figure S1). Nevertheless, we compared whether the nature of the residue (either K or R) at this position impacted plasma recognition and/or neutralization activity; no significant differences were observed (Figure S2).

Cell surface staining and flow cytometry analysis

293T were transfected with full-length SARS-CoV-2 Spikes and a green fluorescent protein (GFP) expressor (pIRES2-eGFP; Clontech) using the calcium-phosphate method. Two days post-transfection, Spike-expressing 293T cells were stained with the CV3-25 Ab (5 μg/mL) as control or plasma from vaccinated individuals (1:250 dilution) for 45 min at 37°C. AlexaFluor-647-conjugated goat anti-human IgG (1/1000 dilution) were used as secondary Abs. The percentage of Spike-expressing cells (GFP + cells) was determined by gating the living cell population based on viability dye staining (Aqua Vivid, Invitrogen). Samples were acquired on a LSR II cytometer (BD Biosciences), and data analysis was performed using FlowJo v10.7.1 (Tree Star). The conformationally-independent anti-S2 antibody CV3-25 was used to normalize Spike expression, as reported (Gong et al., 2021; Li et al., 2021; Prevost et al., 2021; Ullah et al., 2021). CV3-25 was shown to be effective against all Spike variants (Gong et al., 2021; Li et al., 2021; Prevost et al., 2021; Ullah et al., 2021) and (Figure S1). The Median Fluorescence intensities (MFI) obtained with plasma were normalized to the MFI obtained with CV3-25 (Gong et al., 2021; Li et al., 2021; Prevost et al., 2021; Ullah et al., 2021) and presented as percentage of CV3-25 binding.

Virus neutralization assay

To produce SARS-CoV-2 pseudoviruses, 293T cells were transfected with the lentiviral vector pNL4.3 R-E− Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated S glycoprotein (D614G, Alpha, Beta, Gamma, Delta or Omicron) at a ratio of 10:1. Two days post-transfection, cell supernatants were harvested and stored at −80°C until use. For the neutralization assay, 293T-ACE2 target cells were seeded at a density of 1×104 cells/well in 96-well luminometer-compatible tissue culture plates (PerkinElmer) 24h before infection. Pseudoviral particles were incubated with several plasma dilutions (1/50; 1/250; 1/1250; 1/6250; 1/31250) for 1h at 37°C and were then added to the target cells followed by incubation for 48h at 37°C. For CV3-25 neutralization, pseudoviral particles were incubated with increasing concentrations of CV3-25 (0.01, 0.0316, 0.1, 0.316, 1 and 3.16 μg/mL) for 1h at 37°C and were then added to the target cells followed by incubation for 48h at 37°C. Cells were lysed by the addition of 30 μL of passive lysis buffer (Promega) followed by one freeze-thaw cycle. An LB942 TriStar luminometer (Berthold Technologies) was used to measure the luciferase activity of each well after the addition of 100 μL of luciferin buffer (15mM MgSO4, 15mM KH2PO4 [pH 7.8], 1mM ATP, and 1mM dithiothreitol) and 50 μL of 1mM d-luciferin potassium salt (Prolume). The neutralization half-maximal inhibitory dilution (ID50) represents the plasma dilution to inhibit 50% of the infection of 293T-ACE2 cells by pseudoviruses.

Quantification and statistical analysis

Statistical analysis

Symbols represent biologically independent samples from SARS-CoV-2 naïve or PI individuals. Lines connect data from the same donor. Statistics were analyzed using GraphPad Prism version 8.0.1 (GraphPad, San Diego, CA). Every dataset was tested for statistical normality and this information was used to apply the appropriate (parametric or nonparametric) statistical test. p values < 0.05 were considered significant; significance values are indicated as ∗P <0.05, ∗∗P<0.01, ∗∗∗P<0.001, ∗∗∗∗ P<0.0001, ns, non-significant.
REAGENT or RESOURCESOURCEIDENTIFIER
Antibodies

LIVE-DEAD Fixable AquaVivid Cell StainThermo Fischer ScientificCat# P34957
CV3-25(Jennewein et al., 2021)N/A
Alexa Fluor 647 AffiniPure Goat Anti-Human IgA + IgG + IgM (H+L)Jackson ImmunoResearchCat # 109-605-064; RRID: AB_2337886
Goat anti-Human IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647InvitrogenCat # A-21445; RRID: AB_2535862

Biological samples

SARS-CoV-2 naïve donor blood samplesThis paperN/A
SARS-CoV-2 previously infected donor blood samplesThis paperN/A

Chemicals, peptides, and recombinant proteins

Dulbecco's Modified Eagle's medium (DMEM)WisentCat# 319-005-CL
Penicillin/StreptomycinWisentCat# 450-201-EL
Fetal Bovine Serum (FBS)VWRCat# 97068-085
Phosphate Buffered Saline (PBS)ThermoFischer ScientificCat# 10010023
Puromycin DihydrochlorideMillipore SigmaCat# P8833
Passive lysis bufferPromegaCat # E1941
D-Luciferin Potassium SaltProlumeCat # 306
Formaldehyde 37%Thermo Fischer ScientificCat# F79-500
Dimethyl sulfoxide (DMSO)Sigma-AldrichCat # D2650-5X5MLCAS: 67-68-5

Experimental models: cell lines

HEK293T cellsATCCCat# CRL-3216;RRID: CVCL_0063
293T-ACE2 cells(Prevost et al., 2020)N/A

Recombinant DNA

pNL4.3 R-E− LucNIH AIDS reagent programCat# 3418
pIRES2-EGFPClontechCat# 6029-1
pCG1-SARS-CoV-2 D614G-Spike(Beaudoin-Bussieres et al., 2020)N/A
pCDNA3.1-SARS-CoV-2-B.1.1.7 Spike(Tauzin et al., 2021)N/A
pcDNA3.1-SARS-CoV-2-B.1.351 Spike(Gong et al., 2021)N/A
pCAGGS-SARS-CoV-2-B.1.617.2 Spike(Gong et al., 2021)N/A
pcDNA3.1-SARS-CoV-2-P.1 Spike(Gong et al., 2021)N/A
pCAGGS-SARS-CoV-2 B.1.1.529 SpikeThis paperN/A

Software and algorithms

Flow Jo v10.7.1Flow Johttps://www.flowjo.com
GraphPad Prism v8.4.3GraphPadhttps://www.graphpad.com
Microsoft Excel v16Microsoft Officehttps://www.microsoft.com/en-ca/microsoft-365/excel

Others

BD LSRII Flow CytometerBD BiosciencesN/A
TriStar LB942 Microplate ReaderBerthold TechnologiesN/A
Nanodrop Spectrophotometer ND-1000ThermoFisher ScientificN/A
  40 in total

1.  High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape.

Authors:  Fabian Schmidt; Yiska Weisblum; Magdalena Rutkowska; Daniel Poston; Justin DaSilva; Fengwen Zhang; Eva Bednarski; Alice Cho; Dennis J Schaefer-Babajew; Christian Gaebler; Marina Caskey; Michel C Nussenzweig; Theodora Hatziioannou; Paul D Bieniasz
Journal:  Nature       Date:  2021-09-20       Impact factor: 69.504

2.  Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift.

Authors:  Elisabetta Cameroni; John E Bowen; Laura E Rosen; Christian Saliba; Samantha K Zepeda; Katja Culap; Dora Pinto; Laura A VanBlargan; Anna De Marco; Julia di Iulio; Fabrizia Zatta; Hannah Kaiser; Julia Noack; Nisar Farhat; Nadine Czudnochowski; Colin Havenar-Daughton; Kaitlin R Sprouse; Josh R Dillen; Abigail E Powell; Alex Chen; Cyrus Maher; Li Yin; David Sun; Leah Soriaga; Jessica Bassi; Chiara Silacci-Fregni; Claes Gustafsson; Nicholas M Franko; Jenni Logue; Najeeha Talat Iqbal; Ignacio Mazzitelli; Jorge Geffner; Renata Grifantini; Helen Chu; Andrea Gori; Agostino Riva; Olivier Giannini; Alessandro Ceschi; Paolo Ferrari; Pietro E Cippà; Alessandra Franzetti-Pellanda; Christian Garzoni; Peter J Halfmann; Yoshihiro Kawaoka; Christy Hebner; Lisa A Purcell; Luca Piccoli; Matteo Samuele Pizzuto; Alexandra C Walls; Michael S Diamond; Amalio Telenti; Herbert W Virgin; Antonio Lanzavecchia; Gyorgy Snell; David Veesler; Davide Corti
Journal:  Nature       Date:  2021-12-23       Impact factor: 69.504

3.  SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2.

Authors:  Fatima Amanat; Mahima Thapa; Tinting Lei; Shaza M Sayed Ahmed; Daniel C Adelsberg; Juan Manuel Carreño; Shirin Strohmeier; Aaron J Schmitz; Sarah Zafar; Julian Q Zhou; Willemijn Rijnink; Hala Alshammary; Nicholas Borcherding; Ana Gonzalez Reiche; Komal Srivastava; Emilia Mia Sordillo; Harm van Bakel; Jackson S Turner; Goran Bajic; Viviana Simon; Ali H Ellebedy; Florian Krammer
Journal:  Cell       Date:  2021-06-08       Impact factor: 66.850

4.  SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms.

Authors:  Sarah A Clark; Lars E Clark; Junhua Pan; Adrian Coscia; Lindsay G A McKay; Sundaresh Shankar; Rebecca I Johnson; Vesna Brusic; Manish C Choudhary; James Regan; Jonathan Z Li; Anthony Griffiths; Jonathan Abraham
Journal:  Cell       Date:  2021-03-16       Impact factor: 41.582

5.  Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies.

Authors:  Masaud Shah; Hyun Goo Woo
Journal:  Front Immunol       Date:  2022-01-24       Impact factor: 7.561

6.  Two-dose SARS-CoV-2 vaccine effectiveness with mixed schedules and extended dosing intervals: test-negative design studies from British Columbia and Quebec, Canada.

Authors:  Danuta M Skowronski; Yossi Febriani; Manale Ouakki; Solmaz Setayeshgar; Shiraz El Adam; Macy Zou; Denis Talbot; Natalie Prystajecky; John R Tyson; Rodica Gilca; Nicholas Brousseau; Geneviève Deceuninck; Eleni Galanis; Chris D Fjell; Hind Sbihi; Elise Fortin; Sapha Barkati; Chantal Sauvageau; Monika Naus; David M Patrick; Bonnie Henry; Linda M N Hoang; Philippe De Wals; Christophe Garenc; Alex Carignan; Mélanie Drolet; Agatha N Jassem; Manish Sadarangani; Marc Brisson; Mel Krajden; Gaston De Serres
Journal:  Clin Infect Dis       Date:  2022-04-19       Impact factor: 9.079

7.  Introduction of the South African SARS-CoV-2 variant 501Y.V2 into the UK.

Authors:  Julian W Tang; Oliver T R Toovey; Kirsty N Harvey; David D S Hui
Journal:  J Infect       Date:  2021-01-17       Impact factor: 6.072

8.  Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects.

Authors:  Madeleine F Jennewein; Anna J MacCamy; Nicholas R Akins; Junli Feng; Leah J Homad; Nicholas K Hurlburt; Emilie Seydoux; Yu-Hsin Wan; Andrew B Stuart; Venkata Viswanadh Edara; Katharine Floyd; Abigail Vanderheiden; John R Mascola; Nicole Doria-Rose; Lingshu Wang; Eun Sung Yang; Helen Y Chu; Jonathan L Torres; Gabriel Ozorowski; Andrew B Ward; Rachael E Whaley; Kristen W Cohen; Marie Pancera; M Juliana McElrath; Janet A Englund; Andrés Finzi; Mehul S Suthar; Andrew T McGuire; Leonidas Stamatatos
Journal:  Cell Rep       Date:  2021-06-22       Impact factor: 9.423

9.  SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells.

Authors:  Shilei Ding; Damien Adam; Guillaume Beaudoin-Bussières; Alexandra Tauzin; Shang Yu Gong; Romain Gasser; Annemarie Laumaea; Sai Priya Anand; Anik Privé; Catherine Bourassa; Halima Medjahed; Jérémie Prévost; Hugues Charest; Jonathan Richard; Emmanuelle Brochiero; Andrés Finzi
Journal:  Viruses       Date:  2021-12-21       Impact factor: 5.048

10.  Cross-Sectional Evaluation of Humoral Responses against SARS-CoV-2 Spike.

Authors:  Jérémie Prévost; Romain Gasser; Guillaume Beaudoin-Bussières; Jonathan Richard; Ralf Duerr; Annemarie Laumaea; Sai Priya Anand; Guillaume Goyette; Mehdi Benlarbi; Shilei Ding; Halima Medjahed; Antoine Lewin; Josée Perreault; Tony Tremblay; Gabrielle Gendron-Lepage; Nicolas Gauthier; Marc Carrier; Diane Marcoux; Alain Piché; Myriam Lavoie; Alexandre Benoit; Vilayvong Loungnarath; Gino Brochu; Elie Haddad; Hannah D Stacey; Matthew S Miller; Marc Desforges; Pierre J Talbot; Graham T Gould Maule; Marceline Côté; Christian Therrien; Bouchra Serhir; Renée Bazin; Michel Roger; Andrés Finzi
Journal:  Cell Rep Med       Date:  2020-09-30
View more
  15 in total

1.  Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients.

Authors:  Hye Kyung Lee; Ludwig Knabl; Mary Walter; Ludwig Knabl; Yuhai Dai; Magdalena Füßl; Yasemin Caf; Claudia Jeller; Philipp Knabl; Martina Obermoser; Christof Baurecht; Norbert Kaiser; August Zabernigg; Gernot M Wurdinger; Priscilla A Furth; Lothar Hennighausen
Journal:  Front Immunol       Date:  2022-06-15       Impact factor: 8.786

2.  VE607 stabilizes SARS-CoV-2 Spike in the "RBD-up" conformation and inhibits viral entry.

Authors:  Shilei Ding; Irfan Ullah; Shang Yu Gong; Jonathan R Grover; Mohammadjavad Mohammadi; Yaozong Chen; Dani Vézina; Guillaume Beaudoin-Bussières; Vijay Tailor Verma; Guillaume Goyette; Fleur Gaudette; Jonathan Richard; Derek Yang; Amos B Smith; Marzena Pazgier; Marceline Côté; Cameron Abrams; Priti Kumar; Walther Mothes; Pradeep D Uchil; Andrés Finzi; Christian Baron
Journal:  iScience       Date:  2022-06-03

3.  Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages.

Authors:  Jingwen Ai; Xun Wang; Xinyi He; Xiaoyu Zhao; Yi Zhang; Yuchao Jiang; Minghui Li; Yuchen Cui; Yanjia Chen; Rui Qiao; Lin Li; Lulu Yang; Yi Li; Zixin Hu; Wenhong Zhang; Pengfei Wang
Journal:  Cell Host Microbe       Date:  2022-05-08       Impact factor: 31.316

Review 4.  Instructing durable humoral immunity for COVID-19 and other vaccinable diseases.

Authors:  Deepta Bhattacharya
Journal:  Immunity       Date:  2022-05-10       Impact factor: 43.474

5.  Temporal associations of B and T cell immunity with robust vaccine responsiveness in a 16-week interval BNT162b2 regimen.

Authors:  Manon Nayrac; Mathieu Dubé; Gérémy Sannier; Alexandre Nicolas; Lorie Marchitto; Olivier Tastet; Alexandra Tauzin; Nathalie Brassard; Raphaël Lima-Barbosa; Guillaume Beaudoin-Bussières; Dani Vézina; Shang Yu Gong; Mehdi Benlarbi; Romain Gasser; Annemarie Laumaea; Jérémie Prévost; Catherine Bourassa; Gabrielle Gendron-Lepage; Halima Medjahed; Guillaume Goyette; Gloria-Gabrielle Ortega-Delgado; Mélanie Laporte; Julia Niessl; Laurie Gokool; Chantal Morrisseau; Pascale Arlotto; Jonathan Richard; Justin Bélair; Alexandre Prat; Cécile Tremblay; Valérie Martel-Laferrière; Andrés Finzi; Daniel E Kaufmann
Journal:  Cell Rep       Date:  2022-06-13       Impact factor: 9.995

6.  Long-Lived Immunity in SARS-CoV-2-Recovered Children and Its Neutralizing Capacity Against Omicron.

Authors:  Justyna Sieber; Margareta Mayer; Klara Schmidthaler; Sonja Kopanja; Jeremy V Camp; Amelie Popovitsch; Varsha Dwivedi; Jakub Hoz; Anja Schoof; Lukas Weseslindtner; Zsolt Szépfalusi; Karin Stiasny; Judith H Aberle
Journal:  Front Immunol       Date:  2022-05-17       Impact factor: 8.786

7.  Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine.

Authors:  Rishi R Goel; Mark M Painter; Kendall A Lundgreen; Sokratis A Apostolidis; Amy E Baxter; Josephine R Giles; Divij Mathew; Ajinkya Pattekar; Arnold Reynaldi; David S Khoury; Sigrid Gouma; Philip Hicks; Sarah Dysinger; Amanda Hicks; Harsh Sharma; Sarah Herring; Scott Korte; Wumesh Kc; Derek A Oldridge; Rachel I Erickson; Madison E Weirick; Christopher M McAllister; Moses Awofolaju; Nicole Tanenbaum; Jeanette Dougherty; Sherea Long; Kurt D'Andrea; Jacob T Hamilton; Maura McLaughlin; Justine C Williams; Sharon Adamski; Oliva Kuthuru; Elizabeth M Drapeau; Miles P Davenport; Scott E Hensley; Paul Bates; Allison R Greenplate; E John Wherry
Journal:  bioRxiv       Date:  2022-02-22

8.  Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine.

Authors:  Rishi R Goel; Mark M Painter; Kendall A Lundgreen; Sokratis A Apostolidis; Amy E Baxter; Josephine R Giles; Divij Mathew; Ajinkya Pattekar; Arnold Reynaldi; David S Khoury; Sigrid Gouma; Philip Hicks; Sarah Dysinger; Amanda Hicks; Harsh Sharma; Sarah Herring; Scott Korte; Wumesh Kc; Derek A Oldridge; Rachel I Erickson; Madison E Weirick; Christopher M McAllister; Moses Awofolaju; Nicole Tanenbaum; Jeanette Dougherty; Sherea Long; Kurt D'Andrea; Jacob T Hamilton; Maura McLaughlin; Justine C Williams; Sharon Adamski; Oliva Kuthuru; Elizabeth M Drapeau; Miles P Davenport; Scott E Hensley; Paul Bates; Allison R Greenplate; E John Wherry
Journal:  Cell       Date:  2022-04-08       Impact factor: 66.850

Review 9.  SARS-CoV-2 Omicron variant: recent progress and future perspectives.

Authors:  Yao Fan; Xiang Li; Lei Zhang; Shu Wan; Long Zhang; Fangfang Zhou
Journal:  Signal Transduct Target Ther       Date:  2022-04-28

10.  Evolution of Anti-RBD IgG Avidity following SARS-CoV-2 Infection.

Authors:  Alexandra Tauzin; Gabrielle Gendron-Lepage; Manon Nayrac; Sai Priya Anand; Catherine Bourassa; Halima Medjahed; Guillaume Goyette; Mathieu Dubé; Renée Bazin; Daniel E Kaufmann; Andrés Finzi
Journal:  Viruses       Date:  2022-03-04       Impact factor: 5.048

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.