scholarly journals Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution

2020 ◽  
Author(s):  
Huan Qi ◽  
Ming-liang Ma ◽  
Jeremy Jiang ◽  
Jian-ya Ling ◽  
Ling-yun Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleocapsid Protein ◽  
Epitope Mapping ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Therapeutic Antibodies ◽  
Igg Binding ◽  
Mapping Technology ◽  
Specific Proteins ◽  
Specific Igg

SARS-CoV-2 specific IgG responses play critical roles for patients to recover from COVID-19, in-depth dissecting of the IgG responses on systems level is of great interest. Herein, we adopted a newly developed high-throughput epitope mapping technology (AbMap), analyzed 55 COVID-19 convalescent sera and 226 antibody samples enriched by specific proteins or peptides from these sera. We revealed three areas that are rich of IgG epitopes, two are on Spike protein but outside of RBD, and one is on Nucleocapsid protein. We identified 29 significant epitopes on Spike protein, from two of these significant epitopes, two critical epitope residues were found, i. e., D936 and P1263, which are highly related to the infectivity of SARS-CoV-2. In summary, we provided the first global map of IgG binding epitopes for SARS-CoV-2 at single amino acid resolution. This map will facilitate the precise development of therapeutic antibodies and vaccines.

Covid-19 Mutations and How the Vaccine Enhances Immune Intelligence

2021 ◽  
Author(s):  
Xanya Sofra
Keyword(s):  
Amino Acid ◽  
Viral Entry ◽  
Open Reading Frames ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Immune Memory ◽  
Type I ◽  
Specific Amino Acid ◽  
Adaptive Efficiency ◽  
Acid Exchange

We traced the coronavirus classification and evolution, analyzed the Covid-19 composition and its distinguishing characteristics when compared to SARS-CoV and MERS-CoV. Despite their close kinship, SARS-CoV and Covid-19 display significant structural differences, including 380 amino acid substitutions, and variable homology between certain open reading frames that are bound to diversify the pathogenesis and virulence of the two viral compounds. A single amino acid substitution such as replacing Aspartate (D) with Glycine (G) composes the D614G mutation that is around 20% more infectious than its predecessor 614D. The B117 variant, that exhibits a 70% transmissibility rate, harbours 23 mutants, each reflecting one amino acid exchange. We examined several globally spreading mutations, 501.V2, B1351, P1, and others, with respect to the specific amino acid conversions involved. Unlike previous versions of coronavirus, where random mutations eventually precipitate extinction, the multiplicity of over 300,000 mutations appears to have rendered Covid-19 more contagious, facilitating its ability to evade detection, thus challenging the effectiveness of a large variety of emerging vaccines. Vaccination enhances immune memory and intelligence to combat or obstruct viral entry by generating antibodies that will prohibit the cellular binding and fusion with the Spike protein, ultimately debilitating the virus from releasing its contents into the cell. Developing antibodies during the innate response, appears to be the most compelling solution in light of the hypothesis that Covid-19 inhibits the production of Interferon type I, compromising adaptive efficiency to recognize the virus, possibly provoking a cytokine storm that injures vital organs. With respect to that perspective, the safety and effectiveness of different vaccines is evaluated and compared, including the Spike protein mRNA version, the Adenovirus DNA, Spike protein subunits, the deactivated virus genres, or, finally, the live attenuated coronavirus that appears to demonstrate the greatest effectiveness, yet, encompass a relatively higher risk.

scholarly journals Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Li Zhang ◽  
Zhimin Cui ◽  
Qianqian Li ◽  
Bo Wang ◽  
Yuanling Yu ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Receptor Binding ◽  
Immune Escape ◽  
Cathepsin L ◽  
Single Amino Acid ◽  
Receptor Binding Domain ◽  
Therapeutic Antibodies ◽  
Amino Acid Mutations ◽  
Better Than

AbstractEmerging mutations in SARS-CoV-2 cause several waves of COVID-19 pandemic. Here we investigate the infectivity and antigenicity of ten emerging SARS-CoV-2 variants—B.1.1.298, B.1.1.7(Alpha), B.1.351(Beta), P.1(Gamma), P.2(Zeta), B.1.429(Epsilon), B.1.525(Eta), B.1.526-1(Iota), B.1.526-2(Iota), B.1.1.318—and seven corresponding single amino acid mutations in the receptor-binding domain using SARS-CoV-2 pseudovirus. The results indicate that the pseudovirus of most of the SARS-CoV-2 variants (except B.1.1.298) display slightly increased infectivity in human and monkey cell lines, especially B.1.351, B.1.525 and B.1.526 in Calu-3 cells. The K417N/T, N501Y, or E484K-carrying variants exhibit significantly increased abilities to infect mouse ACE2-overexpressing cells. The activities of furin, TMPRSS2, and cathepsin L are increased against most of the variants. RBD amino acid mutations comprising K417T/N, L452R, Y453F, S477N, E484K, and N501Y cause significant immune escape from 11 of 13 monoclonal antibodies. However, the resistance to neutralization by convalescent serum or vaccines elicited serum is mainly caused by the E484K mutation. The convalescent serum from B.1.1.7- and B.1.351-infected patients neutralized the variants themselves better than other SARS-CoV-2 variants. Our study provides insights regarding therapeutic antibodies and vaccines, and highlights the importance of E484K mutation.

scholarly journals Two Trypanosome-Specific Proteins Are Essential Factors for 5S rRNA Abundance and Ribosomal Assembly in Trypanosoma brucei

2007 ◽  
Vol 6 (10) ◽  
pp. 1766-1772 ◽  
Author(s):  
Kristina M. Hellman ◽  
Martin Ciganda ◽  
Silvia V. Brown ◽  
Jinlei Li ◽  
William Ruyechan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Trypanosoma Brucei ◽  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
5S Rrna ◽  
Single Amino Acid ◽  
Ribosomal Subunits ◽  
Morphological Alterations ◽  
Specific Proteins

ABSTRACT We have previously identified and characterized two novel nuclear RNA binding proteins, p34 and p37, which have been shown to bind 5S rRNA in Trypanosoma brucei. These two proteins are nearly identical, with one major difference, an 18-amino-acid insert in the N-terminal region of p37, as well as three minor single-amino-acid differences. Homologues to p34 and p37 have been found only in other trypanosomatids, suggesting that these proteins are unique to this ancient family. We have employed RNA interference (RNAi) studies in order to gain further insight into the interaction between p34 and p37 with 5S rRNA in T. brucei. In our p34/p37 RNAi cells, decreased expression of the p34 and p37 proteins led to morphological alterations, including loss of cell shape and vacuolation, as well as to growth arrest and ultimately to cell death. Disruption of a higher-molecular-weight complex containing 5S rRNA occurs as well as a dramatic decrease in 5S rRNA levels, suggesting that p34 and p37 serve to stabilize 5S rRNA. In addition, an accumulation of 60S ribosomal subunits was observed, accompanied by a significant decrease in overall protein synthesis within p34/p37 RNAi cells. Thus, the loss of the trypanosomatid-specific proteins p34 and p37 correlates with a diminution in 5S rRNA levels as well as a decrease in ribosome activity and an alteration in ribosome biogenesis.

scholarly journals A Single Amino Acid Change within Antigenic Domain II of the Spike Protein of Bovine Coronavirus Confers Resistance to Virus Neutralization

2001 ◽  
Vol 8 (2) ◽  
pp. 297-302 ◽  
Author(s):  
Dongwan Yoo ◽  
Dirk Deregt
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Single Point Mutation ◽  
Bovine Coronavirus ◽  
Single Amino Acid Change ◽  
Group A ◽  
Escape Mutants ◽  
Group B

ABSTRACT The spike glycoprotein is a major neutralizing antigen of bovine coronavirus (BCV). Conformational neutralizing epitopes of group A and group B monoclonal antibodies (MAbs) have previously been mapped to two domains at amino acids 351 to 403 (domain I) and amino acids 517 to 621 (domain II). To further map antigenic sites, neutralization escape mutants of BCV were selected with a group A MAb which has both in vitro and in vivo virus-neutralizing ability. The escape mutants were demonstrated to be neutralization resistant to the selecting group A MAb and remained sensitive to neutralization by a group B MAb. In radioimmunoprecipitation assays, the spike proteins of neutralization escape mutants were shown to have lost their reactivities with the selecting group A MAb. Sequence analysis of the spike protein genes of the escape mutants identified a single nucleotide substitution of C to T at position 1583, resulting in the change of alanine to valine at amino acid position 528 (A528V). The mutation occurs in domain II and in a location which corresponds to the hypervariable region of the spike protein of the coronavirus mouse hepatitis virus. Experimental introduction of the A528V mutation into the wild-type spike protein resulted in the loss of MAb binding of the mutant protein, confirming that the single point mutation was responsible for the escape of BCV from immunological selective pressure.

scholarly journals Spike Protein of SARS-CoV-2: Impact of Single Amino Acid Mutation and Effect of Drug Binding to the Variant-in Silico Analysis

2020 ◽  
Author(s):  
Pratibha Manickavasagam
Keyword(s):  
Amino Acid ◽  
Host Cell ◽  
Drug Binding ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Wild Type ◽  
Amino Acid Mutation ◽  
S Protein ◽  
The Impact ◽  
Single Amino Acid Mutation

Novel SARS-CoV-2, a bat based virus originated in Wuhan, China that caused a global pandemic in December, 2019 belongs to the Betacorona virus family and contains single stranded genome of ~29Kbp. The host cell invasion of SARS-CoV-2 is facilitated by interaction of C-Terminal Domain (CTD) of Spike (S) protein of virus and host ACE2 receptor in the presence of TMPRSS seine protease secreted by the host cell. In this study the mutation hotspots of S-protein will be identified and the impact of such mutation in the binding affinity will be studied. Additionally, the lead molecule which can bind to the mutated protein also will be identified. Multiple sequence alignment of the spike protein sequence of SARS-CoV-2 shows the number of single amino acid mutation hotspots such as L5F, R214L, R408I, G476S, V483A, H519Q, A520S, T572I, D614G and H655Y. Among these mutations D614G has 57.5% occurrence and G476S, V483A has 7.5% occurrence. The mutated proteins were modelled based on wild type homolog and docked to ACE2 receptor. When the mutated S protein is docked, the ∆G (binding free energy) value is very minimal in mutated protein showed the stability of variants. By the drug repurposing method, 1000 FDA approved drugs were virtually screened for its binding to RBD of S1 domain. Among these drugs Digitoxin, Gliquidone and Zorubicin Hcl binds to spike proteins with higher docking score (lesser than -8.5 Kcal/mol) to both wild type and mutants.

scholarly journals Highly efficient SARS-CoV-2 infection of human cardiomyocytes: spike protein-mediated cell fusion and its inhibition

2021 ◽  
Author(s):  
Chanakha K. Navaratnarajah ◽  
David R. Pease ◽  
Peter Halfmann ◽  
Biruhalem Taye ◽  
Alison Barkhymer ◽  
...  
Keyword(s):  
Stem Cell ◽  
Amino Acid ◽  
Pluripotent Stem Cell ◽  
Cardiac Tissue ◽  
Induced Pluripotent Stem Cell ◽  
Cardiovascular Complications ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Cardiac Damage ◽  
Induced Pluripotent

Severe cardiovascular complications can occur in coronavirus disease of 2019 (COVID-19) patients. Cardiac damage is attributed mostly to the aberrant host response to acute respiratory infection. However, direct infection of cardiac tissue by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also occurs. We examined here the cardiac tropism of SARS-CoV-2 in spontaneously beating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). These cardiomyocytes express the angiotensin-converting enzyme 2 (ACE2) receptor but not the transmembrane protease serine 2 (TMPRSS2) that mediates spike protein cleavage in the lungs. Nevertheless, SARS-CoV-2 infection of hiPSC-CMs was prolific: viral transcripts accounted for about 88% of total mRNA. In the cytoplasm of infected hiPSC-CMs, smooth walled exocytic vesicles contained numerous 65-90 nm particles with canonical ribonucleocapsid structures, and virus-like particles with knob-like spikes covered the cell surface. To better understand how SARS-CoV-2 spreads in hiPSC-CMs we engineered an expression vector coding for the spike protein with a monomeric emerald-green fluorescent protein fused to its cytoplasmic tail (S-mEm). Proteolytic processing of S-mEm and the parental spike were equivalent. Live cell imaging tracked spread of S-mEm cell-to-cell and documented formation of syncytia. A cell-permeable, peptide-based molecule that blocks the catalytic site of furin and furin-like proteases abolished cell fusion. A spike mutant with the single amino acid change R682S that disrupts the multibasic furin cleavage motif was fusion inactive. Thus, SARS-CoV-2 replicates efficiently in hiPSC-CMs and furin and/or furin-like-protease activation of its spike protein is required for fusion-based cytopathology. This hiPSC-CM platform enables target-based drug discovery in cardiac COVID-19. Importance Cardiac complications frequently observed in COVID-19 patients are tentatively attributed to systemic inflammation and thrombosis, but viral replication has occasionally been confirmed in cardiac tissue autopsy materials. We developed an in vitro model of SARS-CoV-2 spread in myocardium using induced pluripotent stem cell-derived cardiomyocytes. In these highly differentiated cells, viral transcription levels exceeded those previously documented in permissive transformed cell lines. To better understand the mechanisms of SARS-CoV-2 spread, we expressed a fluorescent version of its spike protein that allowed us to characterize a fusion-based cytopathic effect. A mutant of the spike protein with a single amino acid mutation in the furin/furin-like protease cleavage site lost cytopathic function. Of note, the fusion activities of the spike protein of other coronaviruses correlated with the level of cardiovascular complications observed in infections with the respective viruses. These data indicate that SARS-CoV-2 may cause cardiac damage by fusing cardiomyocytes.

scholarly journals First identification of a single amino acid change in the spike protein region of feline coronavirus detected from a coronavirus-associated cutaneous nodule in a cat

2018 ◽  
Vol 4 (2) ◽  
pp. 205511691880138
Author(s):  
Takafumi Osumi ◽  
Ikki Mitsui ◽  
Christian M Leutenegger ◽  
Ryo Okabe ◽  
Kaori Ide ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Gene ◽  
Clinical Signs ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Molecular Diagnostic ◽  
Rt Pcr ◽  
Single Amino Acid Change ◽  
Cutaneous Nodule ◽  
Feline Coronavirus

Case summary A 32-month-old spayed female Singapura cat presented with a non-pruritic erythematous nodule on the upper lip. The cat also had multiple nodules in the liver but exhibited no other clinical signs consistent with classical feline infectious peritonitis (FIP), such as pleural effusion or ascites, uveitis or neurological symptoms. Histopathological and immunohistochemical analyses of the cutaneous nodule revealed pyogranulomatous dermatitis with intralesional macrophages laden with feline coronavirus (FCoV) antigen. Real-time reverse transcription (RT)-PCR of a cutaneous sample revealed a single nucleotide substitution in the spike protein gene of FCoV (mutation M1058L), which is consistent with an FCoV genotype commonly associated with FIP. The cat received a blood transfusion and supportive therapy, but the owner declined to continue the treatments owing to poor response. The cat was lost to follow-up 5 months after discharge. Relevance and novel information This report describes a case of a coronavirus-associated cutaneous nodule in which the evidence of amino acid changes in the spike protein gene identified by RT-PCR were consistent with an FCoV genotype commonly seen in cases of FIP. To the best of our knowledge, this is the first report of a case of cutaneous disease associated with the mutated FCoV that was confirmed by molecular diagnostic testing.

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