Understanding the role of memory re-activation and cross-reactivity in the defense against SARS-CoV-2

Recent efforts in understanding the course and severity of SARS-CoV-2 infections have highlighted both potential beneficial as well as detrimental effects of cross-reactive antibodies derived from memory immunity. Specifically, due to a significant degree of sequence similarity between SARS-CoV-2 and other members of the coronavirus family, memory B-cells that emerged from previous infections with endemic human coronaviruses (HCoVs) could be re-activated upon encountering the newly emerged SARS-CoV-2, thus prompting the production of cross-reactive antibodies. Understanding the affinity and concentration of these potentially cross-reactive antibodies to the new SARS-CoV-2 antigens is therefore particularly important when assessing both existing immunity against common HCoVs and adverse effects like antibody-dependent enhancement (ADE) in COVID-19. However, these two fundamental parameters cannot easily be deconvoluted by surface-based assays like enzyme-linked immunosorbent assays (ELISAs) which are routinely used to assess cross-reactivity. Here, we have used microfluidic antibody-affinity profiling (MAAP) to quantitatively evaluate the humoral immune response in COVID-19 convalescent patients by determining both antibody affinity and concentration against spike antigens of SARS-CoV-2 directly in nine convalescent COVID-19 patient and three pre-pandemic sera that were seropositive for common HCoVs. All 12 sera contained low concentrations of high affinity antibodies against spike antigens of HCoV-NL63 and HCoV-HKU1, indicative of past exposure to these pathogens, while the affinity against the SARS-CoV-2 spike protein was lower. These results suggest that cross-reactivity as a consequence of memory re-activation upon an acute SARS-CoV-2 infection may not be a significant factor in generating immunity against SARS CoV-2.

Download Full-text

Cross-reactivity towards SARS-CoV-2: the potential role of low-pathogenic human coronaviruses

The Lancet Microbe ◽

10.1016/s2666-5247(20)30098-7 ◽

2020 ◽

Vol 1 (4) ◽

pp. e151 ◽

Cited By ~ 2

Author(s):

Zhongren Ma ◽

Pengfei Li ◽

Yuepeng Ji ◽

Aqsa Ikram ◽

Qiuwei Pan

Keyword(s):

Potential Role ◽

Cross Reactivity ◽

Human Coronaviruses

Download Full-text

Nitrite Transport Activity of the ABC-Type Cyanate Transporter of the Cyanobacterium Synechococcus elongatus

Journal of Bacteriology ◽

10.1128/jb.00013-09 ◽

2009 ◽

Vol 191 (10) ◽

pp. 3265-3272 ◽

Cited By ~ 19

Author(s):

Shin-ichi Maeda ◽

Tatsuo Omata

Keyword(s):

Nitrogen Deficiency ◽

Physiological Role ◽

Synechococcus Elongatus ◽

Transport Activity ◽

High Affinity ◽

Low Concentrations ◽

Cyanobacterial Species ◽

Relative Specificity ◽

Nitrite Transport

ABSTRACT In addition to the ATP-binding cassette (ABC)-type nitrate/nitrite-bispecific transporter, which has a high affinity for both substrates (Km , ∼1 μM), Synechococcus elongatus has an active nitrite transport system with an apparent Km (NO2 −) value of 20 μM. We found that this activity depends on the cynABD genes, which encode a putative cyanate (NCO−) ABC-type transporter. Accordingly, nitrite transport by CynABD was competitively inhibited by NCO− with a Ki value of 0.025 μM. The transporter was induced under conditions of nitrogen deficiency, and the induced cells showed a V max value of 11 to 13 μmol/mg of chlorophyll per h for cyanate or nitrite, which could supply ∼30% of the amount of nitrogen required for optimum growth. Its relative specificity for the substrates and regulation at transcriptional and posttranslational levels suggested that the physiological role of the bispecific cyanate/nitrite transporter in S. elongatus is to allow nitrogen-deficient cells to assimilate low concentrations of cyanate in the medium. Its contribution to nitrite assimilation was significant in a mutant lacking the ABC-type nitrate/nitrite transporter, suggesting a possible role for CynABD in nitrite assimilation by cyanobacterial species that lack another high-affinity mechanism(s) for nitrite transport.

Download Full-text

A Single, Engineered Protein Therapeutic Agent Neutralizes Exotoxins from Both Staphylococcus aureus and Streptococcus pyogenes

Clinical and Vaccine Immunology ◽

10.1128/cvi.00277-10 ◽

2010 ◽

Vol 17 (11) ◽

pp. 1781-1789 ◽

Cited By ~ 16

Author(s):

Ningyan Wang ◽

Daiva M. Mattis ◽

Eric J. Sundberg ◽

Patrick M. Schlievert ◽

David M. Kranz

Keyword(s):

Staphylococcus Aureus ◽

T Cell ◽

Streptococcus Pyogenes ◽

Sequence Similarity ◽

Large Fraction ◽

Cross Reactivity ◽

Structural Basis ◽

Cell Repertoire ◽

High Affinity ◽

The Cross

ABSTRACT Staphylococcus aureus and Streptococcus pyogenes secrete exotoxins that act as superantigens, proteins that cause hyperimmune reactions by binding the variable domain of the T-cell receptor beta chain (Vβ), leading to stimulation of a large fraction of the T-cell repertoire. To develop potential neutralizing agents, we engineered Vβ mutants with high affinity for the superantigens staphylococcal enterotoxin B (SEB), SEC3, and streptococcal pyrogenic exotoxin A (SpeA). Unexpectedly, the high-affinity Vβ mutants generated against SEB cross-reacted with SpeA to a greater extent than they did with SEC3, despite greater sequence similarity between SEB and SEC3. Likewise, the Vβ mutants generated against SpeA cross-reacted with SEB to a greater extent than with SEC3. The structural basis of the high affinity and cross-reactivity was examined by single-site mutational analyses. The cross-reactivity seems to involve only one or two toxin residues. Soluble forms of the cross-reactive Vβ regions neutralized both SEB and SpeA in vivo, suggesting structure-based strategies for generating high-affinity neutralizing agents that can cross-react with multiple exotoxins.

Download Full-text

Molecular basis for high ligand sensitivity and selectivity of strigolactone receptors in Striga

Plant Physiology ◽

10.1093/plphys/kiaa048 ◽

2021 ◽

Author(s):

Yupei Wang ◽

Ruifeng Yao ◽

Xiaoxi Du ◽

Lvjun Guo ◽

Li Chen ◽

...

Keyword(s):

Broad Spectrum ◽

Binding Pocket ◽

Striga Hermonthica ◽

High Affinity ◽

Low Concentrations ◽

Sensitivity And Selectivity ◽

F Box Protein ◽

High Ligand ◽

Spectrum Response

Abstract Seeds of the root parasitic plant Striga hermonthica can sense very low concentrations of strigolactones (SLs) exuded from host roots. The S. hermonthica HYPOSENSITIVE TO LIGHT (ShHTL) proteins are putative SL receptors, among which ShHTL7 reportedly confers sensitivity to picomolar levels of SL when expressed in Arabidopsis thaliana. However, the molecular mechanism underlying ShHTL7 sensitivity is unknown. Here we determined the ShHTL7 crystal structure and quantified its interactions with various SLs and key interacting proteins. We established that ShHTL7 has an active-site pocket with broad-spectrum response to different SLs and moderate affinity. However, in contrast to other ShHTLs, we observed particularly high affinity of ShHTL7 for F-box protein AtMAX2. Furthermore, ShHTL7 interacted with AtMAX2 and with transcriptional regulator AtSMAX1 in response to nanomolar SL concentration. ShHTL7 mutagenesis analyses identified surface residues that contribute to its high-affinity binding to AtMAX2 and residues in the ligand binding pocket that confer broad-spectrum response to SLs with various structures. Crucially, yeast-three hybrid experiments showed that AtMAX2 confers responsiveness of the ShHTL7–AtSMAX1 interaction to picomolar levels of SL, in line with the previously reported physiological sensitivity. These findings highlight the key role of SL-induced MAX2-ShHTL7-SMAX1 complex formation in determining the sensitivity to SL. Moreover, these data suggest a strategy to screen for compounds that could promote suicidal seed germination at physiologically relevant levels.

Download Full-text

Going beyond clinical routine in SARS-CoV-2 antibody testing - A multiplex corona virus antibody test for the evaluation of cross-reactivity to endemic coronavirus antigens

10.1101/2020.07.17.20156000 ◽

2020 ◽

Cited By ~ 3

Author(s):

Matthias Becker ◽

Monika Strengert ◽

Daniel Junker ◽

Tobias Kerrinnes ◽

Philipp D. Kaiser ◽

...

Keyword(s):

Vaccine Development ◽

Antibody Test ◽

Cross Reactivity ◽

Antibody Testing ◽

N Protein ◽

Humoral Immune ◽

In Vitro Diagnostic ◽

Human Coronaviruses ◽

Multiplexed Immunoassay

Given the importance of the humoral immune response to SARS-CoV-2 as a global benchmark for immunity, a detailed analysis is needed to (i) monitor seroconversion in the general population, (ii) understand manifestation and progression of the disease, and (iii) predict the outcome of vaccine development. Currently available serological assays utilize single analyte technologies such as ELISA to measure antibodies against SARS-CoV-2 antigens including spike (S) or nucleocapsid (N) protein. To measure individual antibody (IgG and IgA) responses against SARS-CoV-2 and the endemic human coronaviruses (hCoVs) NL63, 229E, OC43, and HKU1, we developed a multiplexed immunoassay (CoVi-plex), for which we included S and N proteins of these coronaviruses in an expanded antigen panel. Compared to commercial in vitro diagnostic (IVD) tests our CoVi-plex achieved the highest sensitivity and specificity when analyzing 310 SARS-CoV-2 infected and 866 uninfected individuals. Simultaneously we see high IgG responses against hCoVs throughout all samples, whereas no consistent cross reactive IgG response patterns can be defined. In summary, our CoVi-plex is highly suited to monitor vaccination studies and will facilitate epidemiologic screenings for the humoral immunity toward pandemic as well as endemic coronaviruses.

Download Full-text

HLA-dependent variation in SARS-CoV-2 CD8+ T cell cross-reactivity with human coronaviruses

10.1101/2021.07.17.452778 ◽

2021 ◽

Author(s):

Paul Buckley ◽

Chloe Hyun-jung Lee ◽

Mariana Pereira Pinho ◽

Rosana Ottakandathil Babu ◽

Jeongmin Woo ◽

...

Keyword(s):

T Cell ◽

Sequence Similarity ◽

Cross Reactivity ◽

Skewed Distribution ◽

Prior Exposure ◽

High Sequence Similarity ◽

Protein Coding ◽

Cell Immunity ◽

Immunogenic Peptides ◽

Human Coronaviruses

Pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure to SARS-CoV-2 has been reported in several studies. While emerging evidence hints toward prior exposure to common-cold human coronaviruses (HCoV), the extent of- and conditions for- cross-protective immunity between SARS-CoV-2 and HCoVs remain open. Here, by leveraging a comprehensive pool of publicly available functionally evaluated SARS-CoV-2 peptides, we report 126 immunogenic SARS-CoV-2 peptides with high sequence similarity to 285 MHC-presented target peptides from at least one of four HCoV, thus providing a map describing the landscape of SARS-CoV-2 shared and private immunogenic peptides with functionally validated T cell responses. Using this map, we show that while SARS-CoV-2 immunogenic peptides in general exhibit higher level of dissimilarity to both self-proteome and -microbiomes, there exist several SARS-CoV-2 immunogenic peptides with high similarity to various human protein coding genes, some of which have been reported to have elevated expression in severe COVID-19 patients. We then combine our map with a SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls and show that whereas the public repertoire for the majority of convalescent patients are dominated by TCRs cognate to private SARS-CoV-2 peptides, for a subset of patients, more than 50% of their public repertoires that show reactivity to SARS-CoV-2, consist of TCRs cognate to shared SARS-CoV-2-HCoV peptides. Further analyses suggest that the skewed distribution of TCRs cognate to shared and private peptides in COVID-19 patients is likely to be HLA-dependent. Finally, by utilising the global prevalence of HLA alleles, we provide 10 peptides with known cognate TCRs that are conserved across SARS-CoV-2 and multiple human coronaviruses and are predicted to be recognised by a high proportion of the global population. Overall, our work indicates the potential for HCoV-SARS-CoV-2 reactive CD8+ T cells, which is likely dependent on differences in HLA-coding genes among individuals. These findings may have important implications for COVID-19 heterogeneity and vaccine-induced immune responses as well as robustness of immunity to SARS-CoV-2 and its variants.

Download Full-text

Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses

10.1101/2020.08.13.249953 ◽

2020 ◽

Author(s):

Nischay Mishra ◽

Xi Huang ◽

Shreyas Joshi ◽

Cheng Guo ◽

James Ng ◽

...

Keyword(s):

Immune Responses ◽

Cross Reactivity ◽

Humoral Immune ◽

Humoral Immune Responses ◽

Human Coronaviruses ◽

Peptide Maps

AbstractSerodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity to the human coronaviruses (HCoV) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 and other HCoV peptides that can be used to detect asymptomatic, mild and, severe SARS-CoV-2 infections, and may enable the discovery of biomarkers for immunity following infection or vaccination.

Download Full-text

Antibody Responses to SARS-CoV-2 Antigens in Humans and Animals

Vaccines ◽

10.3390/vaccines8040684 ◽

2020 ◽

Vol 8 (4) ◽

pp. 684

Author(s):

Hyunsuh Kim ◽

Patrick Seiler ◽

Jeremy C. Jones ◽

Granger Ridout ◽

Kristi P. Camp ◽

...

Keyword(s):

Immune Responses ◽

Cross Reactivity ◽

Serum Samples ◽

Public Health Response ◽

The Public ◽

Humoral Immune ◽

Humoral Immune Responses ◽

Health Response ◽

Seroepidemiologic Studies ◽

Human Coronaviruses

To optimize the public health response to coronavirus disease 2019 (COVID-19), we must first understand the antibody response to individual proteins on the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the antibody’s cross reactivity to other coronaviruses. Using a panel of 37 convalescent COVID-19 human serum samples, we showed that the magnitude and specificity of responses varied across individuals, independent of their reactivity to seasonal human coronaviruses (HCoVs). These data suggest that COVID-19 vaccines will elicit primary humoral immune responses in naïve individuals and variable responses in those previously exposed to SARS-CoV-2. Unlike the limited cross-coronavirus reactivities in humans, serum samples from 96 dogs and 10 cats showed SARS-CoV-2 protein-specific responses focused on non–S1 proteins. The correlation of this response with those to other coronaviruses suggests that the antibodies are cross-reactive and generated to endemic viruses within these hosts, which must be considered in seroepidemiologic studies. We conclude that substantial variation in antibody generation against coronavirus proteins will influence interpretations of serologic data in the clinical and veterinary settings.

Download Full-text

Generation of High Affinity Anti-Peptide Polyclonal Antibodies Recognizing Goat αs1-Casein

Molecules ◽

10.3390/molecules25112622 ◽

2020 ◽

Vol 25 (11) ◽

pp. 2622

Author(s):

Aliah Zannierah Mohsin ◽

Rashidah Sukor ◽

Jinap Selamat ◽

Anis Shobirin Meor Hussin ◽

Intan Hakimah Ismail ◽

...

Keyword(s):

Binding Affinity ◽

Analytical Methods ◽

Polyclonal Antibodies ◽

Sequence Similarity ◽

High Specificity ◽

Cross Reactivity ◽

Enzyme Linked Immunosorbent Assay ◽

High Sequence Similarity ◽

High Affinity

The chemical, technological and allergy properties of goat’s milk are significantly affected by the level of αs1-casein. Detection and quantification of αs1-casein requires high-specificity methods to overcome high-sequence similarity between this protein and others in the casein family. Unavailability of antibodies with high affinity and specificity towards goat αs1-casein hinders the development of immuno-based analytical methods such as enzyme-linked immunosorbent assay (ELISA) and biosensors. Here, we report the generation of polyclonal antibodies (or immunoglobulins, IgGs) raised towards goat αs1-casein N- (Nter) and C-terminal (Cter) peptide sequences. The Nter and Cter peptides of goat αs1-casein were immunized in rabbits for the generation of antisera, which were purified using protein G affinity chromatography. The binding affinity of the antisera and purified IgGs were tested and compared using indirect ELISA, where peptide-BSA conjugates and goat αs1-casein were used as the coating antigens. The Nter antiserum displayed higher titer than Cter antiserum, at 1/64,000 and 1/32,000 dilutions, respectively. The purification step further yielded 0.5 mg/mL of purified IgGs from 3 mL of antisera. The purified Nter IgG showed a significantly (p < 0.05) higher binding affinity towards peptide-BSA and goat αs1-casein, with lower Kd value at 5.063 × 10−3 μM compared to 9.046 × 10−3 μM for the Cter IgG. A cross-reactivity test showed that there was no binding in neither Nter nor Cter IgGs towards protein extracts from the milk of cow, buffalo, horse and camel. High-quality antibodies generated will allow further development of immuno-based analytical methods and future in vitro studies to be conducted on goat αs1-casein.

Download Full-text

Identification and Characterization of Heparin Binding Regions of the Fim2 Subunit of Bordetella pertussis

Infection and Immunity ◽

10.1128/iai.66.5.2256-2263.1998 ◽

1998 ◽

Vol 66 (5) ◽

pp. 2256-2263 ◽

Cited By ~ 19

Author(s):

Cecile A. W. Geuijen ◽

Rob J. L. Willems ◽

Peter Hoogerhout ◽

Wouter C. Puijk ◽

Rob H. Meloen ◽

...

Keyword(s):

Amino Acids ◽

Bordetella Pertussis ◽

Sequence Similarity ◽

Basic Amino Acid ◽

Cross Reactivity ◽

Site Directed Mutagenesis ◽

Heparin Binding ◽

Basic Amino Acids ◽

Binding Regions

ABSTRACT Bordetella pertussis fimbriae bind to sulfated sugars such as heparin through the major subunit Fim2. The Fim2 subunit contains two regions, designated H1 and H2, which show sequence similarity with heparin binding regions of fibronectin, and the role of these regions in heparin binding was investigated with maltose binding protein (MBP)-Fim2 fusion proteins. Deletion derivatives of MBP-Fim2 showed that both regions are important for binding to heparin. The role of H2 in heparin binding was confirmed by site-directed mutagenesis in which basic amino acids were replaced by alanine. These studies revealed that Lys-186 and Lys-187 are important for heparin binding of MBP-Fim2, whereas Arg-179 is not required. Peptides derived from H1 and H2 (pepH1 and pepH2) also showed heparin binding activity. Using a series of peptides, in each of which a different basic amino acid was substituted for alanine, we demonstrated that the structural requirements for heparin binding differ significantly among pepH1 and pepH2 peptides. A Pepscan analysis of Fim2 revealed regions outside H1 and H2 which bind heparin and showed that not only basic amino acids but also tyrosines may be important for binding to sulfated sugars. A comparison of the heparin binding regions of Fim2 with homologous regions of Fim3 and FimX, two closely related but antigenically distinct fimbrial subunits, showed that basic amino acids and tyrosines are generally conserved. The major heparin binding regions identified in Fim2 are part of epitopes recognized by human antibodies, suggesting that the heparin binding regions are exposed at the fimbrial surface and are immunodominant. Since B. pertussis fimbriae show weak serological cross-reactivity, the differences in primary structure in the heparin binding regions of Fim2, Fim3, and FimX may affect antibody binding but not heparin binding, allowing the bacteria to evade antibody-mediated immunity by switching the fimbrial gene expressed.

Download Full-text