scholarly journals SARS-CoV-2 and ORF3a: Non-Synonymous Mutations and Polyproline Regions

Author(s):  
Elio Issa ◽  
Georgi Merhi ◽  
Balig Panossian ◽  
Tamara Salloum ◽  
Sima Tokajian

AbstractThe effect of the rapid accumulation of non-synonymous mutations on the pathogenesis of SARS-CoV-2 is not yet known. To predict the impact of non-synonymous mutations and polyproline regions identified in ORF3a on the formation of B-cell epitopes and their role in evading the immune response, nucleotide and protein sequences of 537 available SARS-CoV-2 genomes were analyzed for the presence of non-synonymous mutations and polyproline regions. Mutations were correlated with changes in epitope formation. A total of 19 different non-synonymous amino acids substitutions were detected in ORF3a among 537 SARS-CoV-2 strains. G251V was the most common and identified in 9.9% (n=53) of the strains and was predicted to lead to the loss of a B-cell like epitope in ORF3a. Polyproline regions were detected in two strains (EPI_ISL_410486, France and EPI_ISL_407079, Finland) and affected epitopes formation. The accumulation of non-synonymous mutations and detected polyproline regions in ORF3a of SARS-CoV-2 could be driving the evasion of the host immune response thus favoring viral spread. Rapid mutations accumulating in ORF3a should be closely monitored throughout the COVID-19 pandemic.ImportanceAt the surge of the COVID-19 pandemic and after three months of the identification of SARS-CoV-2 as the disease-causing pathogen, nucleic acid changes due to host-pathogen interactions are insightful into the evolution of this virus. In this paper, we have identified a set of non-synonymous mutations in ORF3a and predicted their impact on B-cell like epitope formation. The accumulation of non-synonymous mutations in ORF3a could be driving protein changes that mediate immune evasion and favoring viral spread.

2021 ◽  
Author(s):  
Deepa Kumari ◽  
Namrata Kumari ◽  
Sudhir Kumar ◽  
Prabhat Kumar Sinha ◽  
Shivendra Kumar Shahi ◽  
...  

SARS-CoV-2, the causative agent of COVID-19 has mutated rapidly which enabled them to adapt and evade the immune system of the host. Emerging SARS-CoV-2 variants with crucial mutations pose a global challenge in context of therapeutic drugs and vaccines being developed globally. There are currently no specific therapeutics or vaccines available to combat SARS-CoV-2 devastation. In view of this, the current study aimed to identify and characterize the mutations found in the Nsp13 of SARS-CoV-2 in Indian isolates. Non-structural protein, Nsp13 protein sequences from Indian isolates were analyzed by comparing with the first reported Severe acute respiratory syndrome Corona Virus-2 (SARS-CoV-2) protein sequence from Wuhan, China. Out of 825 Nsp13 protein sequences, a total of 38 mutations were observed among Indian isolates. Our data show that mutations in Nsp13 at various positions (H164Y, A237T, T214I, C309Y, S236I, P419S, V305E, G54S, H290Y, P53S, A308Y, and A308Y) have a significant impact on the protein's stability and flexibility. Also, the impact of Nsp13 mutations on the protein function were predicted based on PROVEAN score that includes 15 mutants as neutral and 23 mutants as deleterious effect. Furthermore, B-cell epitopes contributed by Nsp13 were identified using various predictive immunoinformatic tools. Immunological Parameters of Nsp13 such as antigenicity, allergenicity and toxicity were evaluated to predict the potential B-cell epitopes. The predicted peptide sequences were correlated with the observed mutants. Our predicted data showed that there are seven high rank linear epitopes as well as 18 discontinuous B-cell epitopes based on immunoinformatic tools. Moreover, it was observed that out of total 38 identified mutations among Indian SARS-CoV-2 Nsp13 protein, four mutant residues at position 142 (E142), 245 (H245), 247 (V247) and 419 (P419) are localised in the predicted B cell epitopic region. Altogether, the results of the present in-silico study might help to understand the impact of the identified mutations in Nsp13 protein on its stability, flexibility and function.


2018 ◽  
Vol 11 (1) ◽  
Author(s):  
Mario Hidalgo-Ruiz ◽  
Carlos E. Suarez ◽  
Miguel A. Mercado-Uriostegui ◽  
Ruben Hernandez-Ortiz ◽  
Juan Alberto Ramos ◽  
...  

2018 ◽  
Vol 49 (4) ◽  
pp. 1600-1614 ◽  
Author(s):  
Shudong He ◽  
Jinlong Zhao ◽  
Walid Elfalleh ◽  
Mohamed Jemaà ◽  
Hanju  Sun ◽  
...  

Background/Aims: The incidence of lectin allergic disease is increasing in recent decades, and definitive treatment is still lacking. Identification of B and T-cell epitopes of allergen will be useful in understanding the allergen antibody responses as well as aiding in the development of new diagnostics and therapy regimens for lectin poisoning. In the current study, we mainly addressed these questions. Methods: Three-dimensional structure of the lectin from black turtle bean (Phaseolus vulgaris L.) was modeled using the structural template of Phytohemagglutinin from P. vulgaris (PHA-E, PDB ID: 3wcs.1.A) with high identity. The B and T-cell epitopes were screened and identified by immunoinformatics and subsequently validated by ELISA, lymphocyte proliferation and cytokine profile analyses. Results: Seven potential B-cell epitopes (B1 to B7) were identified by sequence and structure based methods, while three T-cell epitopes (T1 to T3) were identified by the predictions of binding score and inhibitory concentration. The epitope peptides were synthesized. Significant IgE binding capability was found in B-cell epitopes (B2, B5, B6 and B7) and T2 (a cryptic B-cell epitope). T1 and T2 induced significant lymphoproliferation, and the release of IL-4 and IL-5 cytokine confirmed the validity of T-cell epitope prediction. Abundant hydrophobic amino acids were found in B-cell epitope and T-cell epitope regions by amino acid analysis. Positively charged amino acids, such as His residue, might be more favored for B-cell epitope. Conclusion: The present approach can be applied for the identification of epitopes in novel allergen proteins and thus for designing diagnostics and therapies in lectin allergy.


Virology ◽  
1994 ◽  
Vol 200 (1) ◽  
pp. 98-104 ◽  
Author(s):  
Lata M. Chandrachud ◽  
Brian W. O'Neil ◽  
William F.H. Jarrett ◽  
G.Joan Grindlay ◽  
Gail M. McGarvie ◽  
...  

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1101-1101
Author(s):  
Philip M Zakas ◽  
Kristine Vanijcharoenkarn ◽  
Rebecca Markovitz ◽  
Shannon L. Meeks ◽  
Christopher B Doering

Abstract Approximately 20-30% of severe hemophilia A patients develop inhibitors (anti-fVIII antibodies) to human fVIII (hfVIII) with the primary targets being the A2 and C2 domains. Studies of A2 domain-specific murine monoclonal antibodies (MAbs) targeting hfVIII identified 8 distinct groups of inhibitory MAbs displaying varying inhibitor titers and kinetics, with groups A, D, and E possessing the greatest inhibitory activity. Furthermore within the C2 domain, we previously characterized 5 distinct groups, whereby group BC antibodies were the most common and displayed the highest specific inhibitory activity. At present, a recombinant porcine fVIII (pfVIII) product (OBI-1, Baxter International) is being investigated within a pivotal clinical trial for persons with acquired hemophilia A. The rational for a recombinant pfVIII product stems from the limited cross reactivity of pfVIII, and potentially other fVIII orthologs, with antibodies developed against hfVIII and the prior clinical success of plasma-derived pfVIII. We have described the biochemical characterization of both pfVIII and, more recently, ovine fVIII (ofVIII) and now investigate their antigenic properties to define/refine key inhibitory epitopes and determine the amino acid differences that confer reduced antigenicity. Using an ELISA-based assay, 15 A2 and 12 C2 MAbs spanning all inhibitory groups were screened against B-domain deleted (BDD) pfVIII and ofVIII. Only 4 A2 domain targeting MAbs representing groups B, C, DE, and E were found to bind pfVIII and all displayed reduced cross-reactivity (Figure 1). Additionally, 3 MAbs within groups B, C, or E also bound ofVIII. No group A or D MAbs screened bound either ortholog. Of the C2 domain targeting MAbs tested, 3 MAbs (I109, D102, and ESH-8) from groups AB, B and C, respectively, bound pfVIII to lesser degrees. Nine of the 12 C2 targeting MAbs bound ofVIII, albeit at reduced signal strength, suggesting divergence in C2 epitopes between pfVIII and hfVIII as well as between pfVIII and ofVIII. Using these data and previous literature defining the specific epitopes of these MAbs, we suggest that species-specific amino acid sequence differences may be responsible for the differential binding. MAb413, a well characterized A2 group A inhibitor, was found not to bind either ortholog. Alanine scanning mutagenesis within the 484 – 508 epitope demonstrated that single point mutations at R484, Y487, R489, or P492 could each inhibit binding of MAb413 to below 10%. In addition, P485 or S488 mutations each reduced binding to approximately 40% (Lubin et al J Biol Chem 272:48). Both pfVIII and ofVIII share substitutions R484S, Y487H, R489G, and pfVIII contains unique substitutions P485A, S488P, and P492L. Since all but two A2 group A MAbs have been mapped to residues 484-508, and because all group A MAbs compete with each other for their epitope, we hypothesize that these substitutions are responsible for diminished binding of group A MAbs. Group D inhibitory antibodies have been mapped to residues 604-740. Within this region, there are 12 shared amino acid substitutions and 7 amino acids altered in either ortholog but not both. As it was demonstrated that the orthologs display differential cross reactivity, this suggests disparate amino acids alter inhibitor-epitope recognition. Walter et al. (J Biol Chem 2013 288:14) used small angle x-ray scattering (SAXS) to isolate the epitope of MAb 3E6, a C2 MAb group A inhibitor, to exposed loops R2209-S2216 and L2178-D2187. Our data show that this MAb is not cross reactive and both orthologs contain S2216T and S2182N substitutions. Finally, ESH-8, a well-studied C2 group C MAb, binds ofVIII and pfVIII equivalently at 29% of the hfVIII level. The epitope for ESH-8 contains amino acids 2248-2285 and within this region there is only one conserved substitution, F2275L. Therefore, we predict that substitution of this residue could restore or further diminish ESH-8 binding. These data provide evidence that the lack of A2 group A and D epitopes, as well as the C2 domain group BC epitopes within these orthologs may be responsible for the residual procoagulant activity in the context of inhibitor plasma. Furthermore, these data also suggest that 1) B-cell epitopes can be defined or refined through this approach, 2) less antigenic residues can be identified and 3) the information obtained can be utilized to rationally design recombinant fVIII products with reduced antigenicity. Disclosures: No relevant conflicts of interest to declare.


2006 ◽  
Vol 04 (02) ◽  
pp. 389-402 ◽  
Author(s):  
ELENA SVIRSHCHEVSKAYA ◽  
LUDMILA ALEKSEEVA ◽  
ALEXEI MARCHENKO ◽  
SERGEI BENEVOLENSKII ◽  
VALENTINA M. BERZHEC ◽  
...  

Sub-unit vaccines are synthetic or recombinant peptides representing T- or B-cell epitopes of major protein antigens from a particular pathogen. Epitope selection requires the synthesis of peptides that overlap the protein sequences and screening for the most effective ones. In this study a new method of immunogenic peptide selection based on the analysis of information structure of protein sequences is suggested. The analysis of known B-cell epitope location in the information structure of Aspergillus fumigatus proteins Asp f 2 and Asp f 3 has shown that epitopes are scattered along the sequences of proteins for the exception of sites with Increased Degree Information Coordination (IDIC). Based on these results peptides from different allergens such as Asp f 2, Der p 1, and Fel d 1 were selected and produced in a recombinant form in the context of yeast virus-like particles (VLPs). Immunization of mice with VLPs containing peptides form allergens has induced the production of IgG able to recognize full-length antigens. This result suggests that the analysis of information structure of proteins can be used for the selection of peptides possessing cryptic B-cell epitope activity.


2017 ◽  
Vol 16 (11) ◽  
pp. 4093-4103 ◽  
Author(s):  
Saúl G. Martínez-Arzate ◽  
Esvieta Tenorio-Borroto ◽  
Alberto Barbabosa Pliego ◽  
Héctor M. Díaz-Albiter ◽  
Juan C. Vázquez-Chagoyán ◽  
...  

2021 ◽  
Author(s):  
Jiaoyu He ◽  
Qiufu Li ◽  
Yuning Chen ◽  
Jianying Peng ◽  
Shiyu Ma ◽  
...  

Abstract Background:Cervical cancer is one of the malignant tumors threatening women's health worldwide, only second to breast cancer. 99.7% cervical cancer was found to be associated with high-risk HPV (HR-HPV) persistent infections. HPV68 is a common HR-HPV, closely related to cervical cancer.Methods:Cell samples were collected by cervical scraped for HPV detecting and typing, and HPV 68 positive samples were selected out. Important E6, E7 genes of HPV 68 were sequenced and analyzed for the study of HPV 68 genetic polymorphisms. Phylogenetic tree of E6-E7 was constructed by Maximum likelihood method of MEGA v7.0 software. The selection pressure sites of HPV68 E6, E7 were predicted by codeml in the PAML 4.8. The secondary structure and three-dimensional structure of HPV68 E6, E7 were analyzed by PSIPRED server and SWISS-MODEL respectively. T-cell and B-cell antigen epitopes of HPV68 E6, E7 were predicted by immune epitope Database Analysis (IEDB) resource and ABCpred server respectivelyResults:a total of 10650 cell samples were collected for detecting and typing, and 2939 (27.60%, 2939/10650) positive samples were detected, 174 (5.92%, 174/2939) were HPV68; 150 HPV68 E6-E7 were successful amplified and analyzed, 32 nucleotide mutations were observed in this study, 50% (16/32) were non-synonymous mutations; among them, 4 non-synonymous mutations were detected in E6 gene (one in the Coil and three in the Strand), 12 were in E7 gene (four in the alpha helix, two in the Coil and six in the Strand). Phylogenetic analysis of HPV68 E6-E7 suggested that C was the most frequent HPV68 lineage in Sichuan China. 82-90SESVYATTL, 85-93VYATTLETI, 13-21KLPDLCRTL and 67-81-SCIKFYAKIRELRYY, 68-82CIKFYAKIRELRYYS, 66-80QSCIKFYAKIRELRY were the most potential HPV68 E6 HLA-Ⅰ, HLA-Ⅱepitopes respectively; and B-cell epitopes were 138-153CRHCWTSKREDRRRTR, 82-97SESVYATTLETITNTK. 92-101LLFMDSLNFV, 45-53AVNHHQHQL and 20-35EIEPVDLVCHEQLGDS were the most potential HPV68 E7 HLA-Ⅰand B-cell epitopes. 3 HPV68 E6 positive selection sites and 5 HPV68 E7 were detected, and they all had a certain influence on the proteins structure and epitopes affinity.Conclusion:Non-synonymous mutations of HPV 68 located in positive selection sites resulted in differences in protein structure and epitopes affinity, that may affect the pathogenicity and adaptability of HPV68 to the environment. HPV68 data enrichment is of great significance for understanding the inherent geographical and biological differences of HPV68 in china; and targeting potential epitopes for therapeutic vaccines may improve the effective of vaccines design for specific populations.


mBio ◽  
2021 ◽  
Author(s):  
Jiong Wang ◽  
Dongmei Li ◽  
Sheldon Perry ◽  
Shannon P. Hilchey ◽  
Alexander Wiltse ◽  
...  

The antigenic shift and draft of hemagglutinin (HA) in influenza viruses is accepted as one of the major reasons for immune evasion. The analysis of B cell immune responses to influenza infection and vaccination is complicated by the impact of exposure history and antibody cross-reactions between antigenically similar influenza strains.


2003 ◽  
Vol 43 (12) ◽  
pp. 1399 ◽  
Author(s):  
N. R. Adams ◽  
S. M. Liu

The capacity of sheep to withstand and repel intestinal parasites is a neglected component of effective parasite control. The immune response is strongly influenced by the nutritional status of the sheep. However, we are unable take advantage of this to develop effective control programs because we have neither an adequate understanding nor appropriate quantitative data on the impacts of protein and energy on sheep nutrition. This paper reviews some aspects of current knowledge about the impact on immune responsiveness of nutrient flows within the animal as well as hormonal partitioning mechanisms, and assesses research needs in this area. The availability of nutrients to the immune response in the gut is determined by the supply of nutrients to the sheep from both feed intake and body reserves, and the demands of other physiological processes such as growth, wool growth, pregnancy or lactation. Hormones coordinate nutrient flow among these processes. Breakdowns in immunity appear most severe when animals are faced with a demand for growth or lactation, but no single partitioning mechanism can explain all the observations in the field. Therefore, it is unrealistic to seek to establish a hierarchy of partitioning priorities. Protein appears to have a greater impact on immune responsiveness to parasites than energy. However, energy affects the availability of amino acids through a number of mechanisms including protein deposition and mobilisation, so protein supply cannot be considered in isolation. It is appealing to believe that specific limiting nutrients such as sulfur amino acids might explain the relationship between susceptibility to parasites and wool growth, but the experimental evidence for this view is still inconclusive. Rather, it appears that the total flow of nutrients from feed intake and body reserves is more important than specific partitioning mechanisms, or specific limiting nutrients. The potential conflict between role of the gut as a source of mobilisable protein reserves, and the need for protein in the gut to develop local immune responses, need to be explored experimentally. Practical applications of nutritional knowledge are likely to come through improved timing of management procedures rather than better supplements, which are rarely economic. The conclusions outline a number of research questions that must be answered before we can develop programs that integrate immune competence with drenching and other procedures in a holistic way.


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