Convergent CDR3 homology amongst Spike-specific antibody responses in convalescent COVID-19 subjects receiving the BNT162b2 vaccine

Wong, Matthew; Liu, Jun T; Budylowksi, Patrick; Yue, Feng Yun; Li, Zhijie; Rini, James M.; Carlyle, James R.; Zia, Amin; Ostrowski, Mario; Martín, Alberto

doi:10.1016/j.clim.2022.108963

Cited by 4 publications

(5 citation statements)

References 43 publications

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“…Previous studies revealed that different individuals generate antibody clones with the same or very similar CDR3s after stimulation from the same antigen ( 51 , 52 ), these shared CDR3s are known as public clones. Researchers later reported that functional public clones were also present in individuals without antigen exposure ( 16 , 53 , 54 ).…”

Section: Resultsmentioning

confidence: 99%

The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing

Zhu,

Tang,

Xie

et al. 2024

Sci. Adv.

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The extent to which AIRRs differ among and within individuals remains elusive. Via ultra-deep repertoire sequencing of 22 and 25 tissues in three cynomolgus macaques, respectively, we identified 84 and 114 novel IGHV and TRBV alleles, confirming 72 (85.71%) and 100 (87.72%) of them. The heterogeneous V gene usage patterns were influenced, in turn, by genetics, isotype (for BCRs only), tissue group, and tissue. A higher proportion of intragroup shared clones in the intestinal tissues than those in other tissues suggests a close intra-intestinal adaptive immunity network. Significantly higher mutation burdens in the public clones and the inter-tissue shared IgM and IgD clones indicate that they might target the shared antigens. This study reveals the extensive heterogeneity of the AIRRs at various levels and has broad fundamental and clinical implications. The data generated here will serve as an invaluable resource for future studies on adaptive immunity in health and diseases.

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Section: Resultsmentioning

confidence: 99%

The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing

Zhu,

Tang,

Xie

et al. 2024

Sci. Adv.

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“…We believe it is important to combine these two points to adequately reveal the response of the vaccination by BCR repertoire. Although some articles have reported changes in BCR repertoire after mRNA SARS-CoV-2 vaccination, [23][24][25] no report has clearly demonstrated an individual's vaccine response using a repertoire assay.…”

Section: Discussionmentioning

confidence: 99%

“…28 Recently, an ELISpot assay was developed to measure human IgG-secreting B cells stimulated with R-848 and IL-2 in vitro as a method to assess postinfection and vaccine B-cell response. 25 However, such ELISpot assays do not report real-time immune responses or provide additional information.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, the detection of non‐neutralizing antibodies is also a noteworthy indicator, given that the appearance of antibodies with non‐neutralizing activity has been associated with the severity of infection in infected patients 28 . Recently, an ELISpot assay was developed to measure human IgG‐secreting B cells stimulated with R‐848 and IL‐2 in vitro as a method to assess postinfection and vaccine B‐cell response 25 . However, such ELISpot assays do not report real‐time immune responses or provide additional information.…”

Section: Discussionmentioning

confidence: 99%

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Response to mRNA SARS‐CoV‐2 vaccination evaluated by B‐cell receptor repertoire after tixagevimab/cilgavimab administration

et al. 2023

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Summary The use of anti‐SARS‐CoV‐2 antibody products like tixagevimab/cilgavimab represents an important strategy to protect immunocompromised patients with haematological malignancies from COVID‐19. Although patients who receive these agents should still be vaccinated, the use of tixagevimab/cilgavimab can mask the production of anti‐spike antibody after vaccination, making it hard to assess vaccine response. We have newly established a quantification method to assess the response to SARS‐CoV‐2 vaccination at the mRNA level using B‐cell receptor (BCR) repertoire assay and the Coronavirus Antibody Database (CoV‐AbDab). Repeated blood samples before and after vaccination were analysed for the BCR repertoire, and BCR sequences were searched in the database. We analysed the number and percentage frequency of matched sequences. We found that the number of matched sequences increased 2 weeks after the first vaccination and quickly decreased. Meanwhile, the number of matched sequences more rapidly increased after the second vaccination. These results show that the postvaccine immune response can be assessed at the mRNA level by analysing the fluctuation in matching sequences. Finally, BCR repertoire analysis with CoV‐AbDab clearly demonstrated the response to mRNA SARS‐CoV‐2 vaccination even after tixagevimab/cilgavimab administration in haematological malignancy patients who underwent allogeneic haematopoietic stem cell transplantation.

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“…Ostmeyer et al (17), and by others (26,27). In addition, CDR3 AA sequence homology assessments have been applied in the SARS-CoV-2 and other viral settings (28,29), in cases of allergies (30), in Alzheimer's disease and in other neurological disorders (31,32). A key issue in this development is the focus on the CDR3 AA sequences in the big data setting.…”

Section: Discussionmentioning

confidence: 99%

Immune receptor CDR3 chemical features that preserve sequence information are highly efficient in reflecting survival distinctions: A pan‑cancer analysis

Mcbreairty

Chobrutskiy

et al. 2022

Biomed Rep

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Adaptive immune receptor (IR) chemical features have been used as signatures of an immune response for numerous medical conditions, raising the question of whether certain approaches to assessing the IR chemical features are more robust than others? In the cancer setting, a very large dataset of IR complementarity determining region-3 (CDR3) amino acid (AA) sequences has become available via the mining of cancer specimen and blood genomics files for IR recombination reads. The IR CDR3 AA sequences have been evaluated for chemical features, and survival rates have been correlated with distinct chemical features. Two common approaches have been i) to assign a single value to the CDR3, representing a chemical attribute, such as aromaticity; or ii) to reduce the actual CDR3 AA sequence to a chemical sequence motif, which merges similar CDR3 chemistries represented by distinct AA sequences but preserves potential functional aspects of the order of the AAs in the sequence. While a controlled comparison of the two approaches is not possible, the application of the two approaches to the same clinical datasets offers the opportunity to appreciate a trend with regard to the overall potential in distinguishing survival probabilities. We demonstrate that application of the chemical sequence motif approach is more likely to identify survival distinctions within cancer datasets, for both tumor specimen and blood sourced, adaptive IR CDR3 AA sequences.

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Convergent CDR3 homology amongst Spike-specific antibody responses in convalescent COVID-19 subjects receiving the BNT162b2 vaccine

Cited by 4 publications

References 43 publications

The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing

The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing

Response to mRNA SARS‐CoV‐2 vaccination evaluated by B‐cell receptor repertoire after tixagevimab/cilgavimab administration

Immune receptor CDR3 chemical features that preserve sequence information are highly efficient in reflecting survival distinctions: A pan‑cancer analysis

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