BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection methods
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NAb evasion by BA.2.12.1, BA.4 and BA.5
To probe NAb evasion by the recently emerged Omicron sublineages, we performed pseudovirus-neutralization assays using D614G, BA.1, BA.1.1, BA.2, BA.3, BA.2.12.1, BA.2.13 and BA.4/BA.5 against plasma obtained from individuals who had received three doses of SARS-CoV-2 vaccine, vaccinated individuals who had recovered from BA.1 infection, and vaccinated individuals who had recovered from severe acute respiratory syndrome (SARS) (Supplementary Table ). Plasma samples were collected four weeks after the booster shot or four weeks after discharge from hospital following COVID-19 illness. In plasma from individuals who had received an inactivated virus (CoronaVac) or RBD protein (ZF2001) booster six months after two doses of CoronaVac, BA.1, BA.1.1 and BA.2 showed no significant difference in resistance to neutralization by plasma (Fig. ), concordant with previous reports,. However, we f...
NAb evasion by BA.2.12.1, BA.4 and BA.5
Omicron subvariants evaded most WT-stimulated group A, B and C NAbs, although a subset of these antibodies showed broad effectiveness against Omicron (Extended Data Fig. ). These broad NAbs were largely enriched by BA.1 stimulation, are generally encoded by similar heavy chain V genes compared with WT-stimulated antibodies and display higher convergence (Extended Data Fig. ). These broad ACE2-competing NAbs in groups A, B and C have been shown to be enriched in individuals who received a booster dose of mRNA vaccine, which probably accounts for the high neutralizing activity against Omicron variants in plasma of individuals who had received three doses of mRNA vaccine. Nevertheless, BA.1-stimulated group B and C NAbs were significantly evaded by BA.4 owing to F486V and L452R RBD mutations, concordant with results from DMS (Extended Data Fig. ), which explains the strong humoral immun...
Methods
Blood samples were obtained from 40 volunteers who had received 3 doses of CoronaVac, 39 individuals who had received 2 doses of CoronaVac and 1 booster dose of ZF2001, 54 individuals who had recovered from BA.1 infection who had previously received 3 doses of CoronaVac,, and 30 individuals who had recovered from SARS who had received 2 doses of CoronaVac and 1 dose of ZF2001. The volunteers' blood samples were obtained four weeks after the booster shot or four weeks after discharge from the hospital following BA.1 infection.COVID-19 disease severity was defined as asymptomatic, mild, moderate, severe or critical according to the WHO Living Guidance for Clinical Management of COVID-19. Relevant experiments with plasma from SARS convalescents and SARS-CoV-2 vaccinees were approved by the Beijing Ditan Hospital Capital Medical University (ethics committee archiving no. LL-2021-...
High-throughput antibody-escape mutation profiling
The magnetic-activated cell sorting-based antibody-escape mutation profiling system, was used to characterize mutation escape profile for NAbs. In brief, ACE2-binding mutants were induced overnight for RBD expression and washed followed with two rounds of Protein A antibody-based negative selection and MYC tag-based positive selection to enrich RBD-expressing cells. Protein A antibody-conjugated products were prepared following the protocol for Dynabeads Protein A (Thermo Fisher, 10008D) and incubated with induced yeast libraries at room temperature for 30 min with shaking. MYC tag-based positive selection was performed according to the manufacturer's instructions (Thermo Fisher, 88843).
ELISA
To detect the broad-spectrum binding of the antibodies among Sarbecovirus, we used a panel of 20 synthesized sarbecovirus RBDs (Sino Biological Technology) (Supplementary Table ). According to the sequence of 20 RBDs, a set of nested primers was designed. The coding sequences were obtained by the overlap PCR with a 6 × His tag sequence to facilitate protein purification. The purified PCR products were ligated to the secretory expression vector pCMV3 with CMV promoter, and then transformed into Escherichia coli XL1-blue competent cells. Monoclones with correct transformation were cultured and expanded, and plasmids were extracted. Healthy HEK293F cells were passaged into a new cell culture and grown in suspension at 37 °C, 120 RPM, 8% CO2 to logarithmic growth phase and transfected with the recombinant constructs by using liposomal vesicles as DNA carrier. After transfec...
ELISA
A panel of 21 sarbecovirus RBDs (Supplementary Table ) in PBS was pre-coated onto ELISA plates (NEST, 514201) at 4 °C overnight. The plates were washed and blocked. Then 1 µg ml -1 purified antibodies or serially diluted antibodies were added and incubated at room temperature for 20 min. Next, Peroxidase-conjugated AffiniPure Goat Anti-Human IgG (H+L) (JACKSON, 109-035-003) was applied and incubated at room temperature for 15 min. Tetramethylbenzidine (TMB) (Solarbio, 54827-17-7) was added onto the plates. The reaction was terminated with 2 M H 2 SO 4 after 10 min incubation. Absorbance was measured at 450 nm using Ensight Multimode Plate Reader (PerkinElmer, HH3400). ELISA A 450 measurements at different antibody concentrations for a particular antibody-antigen pair were fit to the model y = Ac n /( c...
Antibody and ACE2 competition for RBD
Omicron RBD (Sino Biological, 40592-V08H121) protein in PBS was immobilized on the ELISA plates at 4 °C overnight. The coating solution was removed and washed 3 times with PBST and the plates were then blocked for 2 h. After blocking, the plates were washed 5 times, and the mixture of ACE2-biotin (Sino Biological, 10108-H27B-B) and serially diluted competitor antibodies was added followed by 30 min incubation at room temperature. Peroxidase-conjugated Streptavidin (Jackson ImmunoResearch, 016-030-084) was added into each well for another 20 min incubation at room temperature. After washing the plates five times, TMB (Solarbio, 54827-17-7) was added into each well. After 10 min, the reaction was terminated with 2 M H 2 SO 4. Absorbancewas measured at 450 nm using Ensight Multimode Plate Reader (PerkinElmer, HH3400). The ACE2 competition c...
Biolayer interferometry
Biolayer interferometry assays were performed on Octet RED 384 Protein Analysis System (Fortebio) according to the manufacturer's instructions. To measure the binding affinities, monoclonal antibodies were immobilized onto Protein A biosensors (Fortebio) and the fourfold serial dilutions of Omicron S-trimer (BA.1 and BA.2) in PBS were used as analytes. Data were collected with Octet Acquisition 9.0 (Fortebio) and analysed by Octet Analysis 9.0 (Fortebio) and Octet Analysis Studio 12.2 (Fortebio).
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To probe NAb evasion by the recently emerged Omicron sublineages, we performed pseudovirus-neutralization assays using D614G, BA.1, BA.1.1, BA.2, BA.3, BA.2.12.1, BA.2.13 and BA.4/BA.5 against plasma obtained from individuals who had received three doses of SARS-CoV-2 vaccine, vaccinated individuals who had recovered from BA.1 infection, and vaccinated individuals who had recovered from severe acute respiratory syndrome (SARS) (Supplementary Table ). Plasma samples were collected four weeks after the booster shot or four weeks after discharge from hospital following COVID-19 illness. In plasma from individuals who had received an inactivated virus (CoronaVac) or RBD protein (ZF2001) booster six months after two doses of CoronaVac, BA.1, BA.1.1 and BA.2 showed no significant difference in resistance to neutralization by plasma (Fig. ), concordant with previous reports,. However, we found that BA.2 subvariants BA.2.13 and BA.2.12.1 showed increased immune-evasion capability over BA.2-with BA.2.12.1 exhibiting greater evasion than BA.2.13-and BA.4/BA.5 exhibiting even greater evasion (Fig. ). The decrease in neutralization was clearer in plasma obtained from individua...
Omicron subvariants evaded most WT-stimulated group A, B and C NAbs, although a subset of these antibodies showed broad effectiveness against Omicron (Extended Data Fig. ). These broad NAbs were largely enriched by BA.1 stimulation, are generally encoded by similar heavy chain V genes compared with WT-stimulated antibodies and display higher convergence (Extended Data Fig. ). These broad ACE2-competing NAbs in groups A, B and C have been shown to be enriched in individuals who received a booster dose of mRNA vaccine, which probably accounts for the high neutralizing activity against Omicron variants in plasma of individuals who had received three doses of mRNA vaccine. Nevertheless, BA.1-stimulated group B and C NAbs were significantly evaded by BA.4 owing to F486V and L452R RBD mutations, concordant with results from DMS (Extended Data Fig. ), which explains the strong humoral immune-evasion ability of BA.4/BA.5.
Blood samples were obtained from 40 volunteers who had received 3 doses of CoronaVac, 39 individuals who had received 2 doses of CoronaVac and 1 booster dose of ZF2001, 54 individuals who had recovered from BA.1 infection who had previously received 3 doses of CoronaVac,, and 30 individuals who had recovered from SARS who had received 2 doses of CoronaVac and 1 dose of ZF2001. The volunteers' blood samples were obtained four weeks after the booster shot or four weeks after discharge from the hospital following BA.1 infection.COVID-19 disease severity was defined as asymptomatic, mild, moderate, severe or critical according to the WHO Living Guidance for Clinical Management of COVID-19. Relevant experiments with plasma from SARS convalescents and SARS-CoV-2 vaccinees were approved by the Beijing Ditan Hospital Capital Medical University (ethics committee archiving no. LL-2021-024-02), the Tianjin Municipal Health Commission, and the ethics committee of Tianjin First Central Hospital (ethics committee archiving no. 2022N045KY). Written informed consent was obtained from each participant in accordance with the Declaration of Helsinki. All participants provided written info...
The magnetic-activated cell sorting-based antibody-escape mutation profiling system, was used to characterize mutation escape profile for NAbs. In brief, ACE2-binding mutants were induced overnight for RBD expression and washed followed with two rounds of Protein A antibody-based negative selection and MYC tag-based positive selection to enrich RBD-expressing cells. Protein A antibody-conjugated products were prepared following the protocol for Dynabeads Protein A (Thermo Fisher, 10008D) and incubated with induced yeast libraries at room temperature for 30 min with shaking. MYC tag-based positive selection was performed according to the manufacturer's instructions (Thermo Fisher, 88843).
To detect the broad-spectrum binding of the antibodies among Sarbecovirus, we used a panel of 20 synthesized sarbecovirus RBDs (Sino Biological Technology) (Supplementary Table ). According to the sequence of 20 RBDs, a set of nested primers was designed. The coding sequences were obtained by the overlap PCR with a 6 × His tag sequence to facilitate protein purification. The purified PCR products were ligated to the secretory expression vector pCMV3 with CMV promoter, and then transformed into Escherichia coli XL1-blue competent cells. Monoclones with correct transformation were cultured and expanded, and plasmids were extracted. Healthy HEK293F cells were passaged into a new cell culture and grown in suspension at 37 °C, 120 RPM, 8% CO2 to logarithmic growth phase and transfected with the recombinant constructs by using liposomal vesicles as DNA carrier. After transfection, the cell cultures were followed to assess the kinetics of cell growth and viability for 7 days. The cell expression supernatant was collected, and after centrifugation, passed through a Ni column for affinity purification. The molecular size and purity of eluted protein was confirmed by SDS...
A panel of 21 sarbecovirus RBDs (Supplementary Table ) in PBS was pre-coated onto ELISA plates (NEST, 514201) at 4 °C overnight. The plates were washed and blocked. Then 1 µg ml -1 purified antibodies or serially diluted antibodies were added and incubated at room temperature for 20 min. Next, Peroxidase-conjugated AffiniPure Goat Anti-Human IgG (H+L) (JACKSON, 109-035-003) was applied and incubated at room temperature for 15 min. Tetramethylbenzidine (TMB) (Solarbio, 54827-17-7) was added onto the plates. The reaction was terminated with 2 M H 2 SO 4 after 10 min incubation. Absorbance was measured at 450 nm using Ensight Multimode Plate Reader (PerkinElmer, HH3400). ELISA A 450 measurements at different antibody concentrations for a particular antibody-antigen pair were fit to the model y = Ac n /( c n + E n ) using the R package mosaic (v1.8.3), where y is the A 450 value and c is the corresponding antibody concentration. A, E and n are parameters, where E is the desired EC 50 value for the specific antibody and antigen.
Omicron RBD (Sino Biological, 40592-V08H121) protein in PBS was immobilized on the ELISA plates at 4 °C overnight. The coating solution was removed and washed 3 times with PBST and the plates were then blocked for 2 h. After blocking, the plates were washed 5 times, and the mixture of ACE2-biotin (Sino Biological, 10108-H27B-B) and serially diluted competitor antibodies was added followed by 30 min incubation at room temperature. Peroxidase-conjugated Streptavidin (Jackson ImmunoResearch, 016-030-084) was added into each well for another 20 min incubation at room temperature. After washing the plates five times, TMB (Solarbio, 54827-17-7) was added into each well. After 10 min, the reaction was terminated with 2 M H 2 SO 4. Absorbancewas measured at 450 nm using Ensight Multimode Plate Reader (PerkinElmer, HH3400). The ACE2 competition coefficient was calculated as ( B - A )/ B, where B is the A 450 value with 0.3 µg ml -1 antibody and A is the A 450 value with 6 µg ml -1 antibody.
Biolayer interferometry assays were performed on Octet RED 384 Protein Analysis System (Fortebio) according to the manufacturer's instructions. To measure the binding affinities, monoclonal antibodies were immobilized onto Protein A biosensors (Fortebio) and the fourfold serial dilutions of Omicron S-trimer (BA.1 and BA.2) in PBS were used as analytes. Data were collected with Octet Acquisition 9.0 (Fortebio) and analysed by Octet Analysis 9.0 (Fortebio) and Octet Analysis Studio 12.2 (Fortebio).
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"text": "To probe NAb evasion by the recently emerged Omicron sublineages, we performed pseudovirus-neutralization assays using D614G, BA.1, BA.1.1, BA.2, BA.3, BA.2.12.1, BA.2.13 and BA.4/BA.5 against plasma obtained from individuals who had received three doses of SARS-CoV-2 vaccine, vaccinated individuals who had recovered from BA.1 infection, and vaccinated individuals who had recovered from severe acute respiratory syndrome (SARS) (Supplementary Table ). Plasma samples were collected four weeks after the booster shot or four weeks after discharge from hospital following COVID-19 illness. In plasma from individuals who had received an inactivated virus (CoronaVac) or RBD protein (ZF2001) booster six months after two doses of CoronaVac, BA.1, BA.1.1 and BA.2 showed no significant difference in resistance to neutralization by plasma (Fig. ), concordant with previous reports,. However, we f..."
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"text": "Omicron subvariants evaded most WT-stimulated group A, B and C NAbs, although a subset of these antibodies showed broad effectiveness against Omicron (Extended Data Fig. ). These broad NAbs were largely enriched by BA.1 stimulation, are generally encoded by similar heavy chain V genes compared with WT-stimulated antibodies and display higher convergence (Extended Data Fig. ). These broad ACE2-competing NAbs in groups A, B and C have been shown to be enriched in individuals who received a booster dose of mRNA vaccine, which probably accounts for the high neutralizing activity against Omicron variants in plasma of individuals who had received three doses of mRNA vaccine. Nevertheless, BA.1-stimulated group B and C NAbs were significantly evaded by BA.4 owing to F486V and L452R RBD mutations, concordant with results from DMS (Extended Data Fig. ), which explains the strong humoral immun..."
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"text": "Blood samples were obtained from 40 volunteers who had received 3 doses of CoronaVac, 39 individuals who had received 2 doses of CoronaVac and 1 booster dose of ZF2001, 54 individuals who had recovered from BA.1 infection who had previously received 3 doses of CoronaVac,, and 30 individuals who had recovered from SARS who had received 2 doses of CoronaVac and 1 dose of ZF2001. The volunteers' blood samples were obtained four weeks after the booster shot or four weeks after discharge from the hospital following BA.1 infection.COVID-19 disease severity was defined as asymptomatic, mild, moderate, severe or critical according to the WHO Living Guidance for Clinical Management of COVID-19. Relevant experiments with plasma from SARS convalescents and SARS-CoV-2 vaccinees were approved by the Beijing Ditan Hospital Capital Medical University (ethics committee archiving no. LL-2021-..."
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"name": "Antibody and ACE2 competition for RBD",
"text": "Omicron RBD (Sino Biological, 40592-V08H121) protein in PBS was immobilized on the ELISA plates at 4 °C overnight. The coating solution was removed and washed 3 times with PBST and the plates were then blocked for 2 h. After blocking, the plates were washed 5 times, and the mixture of ACE2-biotin (Sino Biological, 10108-H27B-B) and serially diluted competitor antibodies was added followed by 30 min incubation at room temperature. Peroxidase-conjugated Streptavidin (Jackson ImmunoResearch, 016-030-084) was added into each well for another 20 min incubation at room temperature. After washing the plates five times, TMB (Solarbio, 54827-17-7) was added into each well. After 10 min, the reaction was terminated with 2 M H 2 SO 4. Absorbancewas measured at 450 nm using Ensight Multimode Plate Reader (PerkinElmer, HH3400). The ACE2 competition c..."
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"text": "Biolayer interferometry assays were performed on Octet RED 384 Protein Analysis System (Fortebio) according to the manufacturer's instructions. To measure the binding affinities, monoclonal antibodies were immobilized onto Protein A biosensors (Fortebio) and the fourfold serial dilutions of Omicron S-trimer (BA.1 and BA.2) in PBS were used as analytes. Data were collected with Octet Acquisition 9.0 (Fortebio) and analysed by Octet Analysis 9.0 (Fortebio) and Octet Analysis Studio 12.2 (Fortebio)."
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