scholarly journals Emergence of a putative novel SARS-CoV-2 P.X lineage harboring N234P and E471Q spike protein mutations in Southern Brazil

2021 ◽  
Author(s):  
Mariana Soares da Silva ◽  
Juliana Schons Gularte ◽  
Meriane Demoliner ◽  
Alana Witt Hansen ◽  
Fágner Henrique Heldt ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune Escape ◽  
Variant Calling ◽  
Phylogenetic Inference ◽  
Spike Protein ◽  
Southern Brazil ◽  
S Protein ◽  
Synonymous Substitutions ◽  
Synonymous Mutations ◽  
Protein Mutations

Abstract Novel SARS-CoV-2 lineages are constantly reported worldwide, raising concerns about transmissibility, virulence, immune response and vaccine/antigenic escape. Variants of concern (VOCs), as B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta), caused epidemic outbreaks due their higher potential of transmissibility when compared with earlier waves of SARS-CoV-2 in 2019. B.1.1.28 lineage has been evolving in Brazil since February 2020 and originated P.1 (VOC), P.2 (VOI) and other P.Xs proposed as new variants. This lineage harbors specific defining mutations including two non-synonymous substitutions in the Spike (S) protein (D614G and V1176F). In this study, employing variant calling analysis on FASTQ reads and phylogenetic inference, we report a potentially new SARS-CoV-2 P.X variant. Variant calling mutational profile was investigated and presented additionally non-synonymous mutations when compared to B.1.1.28, including N234P and E471Q in S protein. Further studies are required to understand the spread of P.X variant and its potential effects on transmissibility and immune escape.

scholarly journals Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies

2021 ◽  
Vol 12 ◽  
Author(s):  
Chengchao Ding ◽  
Jun He ◽  
Xiangyu Zhang ◽  
Chengcheng Jiang ◽  
Yong Sun ◽  
...  
Keyword(s):  
Immune Response ◽  
Monoclonal Antibodies ◽  
Humoral Immune Response ◽  
Immune Escape ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Humoral Immune ◽  
Cross Neutralization ◽  
Altered Sensitivity ◽  
Single Amino Acid Mutation

Small number of SARS-CoV-2 epidemic lineages did not efficiently exhibit a neutralization profile, while single amino acid mutation in the spike protein has not been confirmed in altering viral antigenicity resulting in immune escape. To identify crucial mutations in spike protein that escape humoral immune response, we evaluated the cross-neutralization of convalescent plasmas and RBD-specific monoclonal antibodies (mAbs) against various spike protein-based pseudoviruses. Three of 24 SARS-CoV-2 pseudoviruses containing different mutations in spike protein, including D614G, A475V, and E484Q, consistently showed an altered sensitivity to neutralization by convalescent plasmas. A475V and E484Q mutants are highly resistant to neutralization by mAb B38 and 2-4, suggesting that some crucial mutations in spike protein might evolve SARS-CoV-2 variants capable of escaping humoral immune response.

scholarly journals SARS-CoV-2 Infection, COVID-19, and long covid: Saga of erratic immune response, waning immunity, and immune system failure

2021 ◽  
Vol 5 (1) ◽  
pp. 077-086
Author(s):  
Nikhra Vinod
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Disease Transmission ◽  
Neutralizing Antibodies ◽  
Evolutionary Dynamics ◽  
Immune Escape ◽  
Clinical Manifestations ◽  
System Failure ◽  
S Protein ◽  
Adaptive Mutations

Introduction - evolution of SARS-CoV-2 variants: With the unrestrained pandemic for over last one-and-half year, SARS-CoV-2 seems to have adapted to its habitat, the human host, through mutations that facilitate its replication and transmission. The G variant incorporating D614G mutation, potently more transmissible than the ancestral virus arose during January 2020 and spread widely. Since then, various SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs) with higher infectivity or virulence or both, have evolved on the background of G variant, and spread widely. SARS-CoV-2 infection and the immunodynamics: As the virus becomes more transmissible, its lethality may drop. Apart from the humoral immunity, T-cell recognition from a previous SARS-CoV-2 infection or vaccination may modify the disease transmission correlates and its clinical manifestations. On the other hand, the immunity generated may reduce probability of re-infection as well as limit evolution of adaptive mutations, and emergence of highly infectious and immune-escape variants. There are complex issues related to the SARS-CoV-2 evolutionary dynamics and host’s immunodynamics. Trending etiopathoimmunological correlates: The evolution potential of SARS-CoV-2 is limited because of proofreading function of nsp14. The S protein mutations affect transmissibility, virulence, and vaccine efficacy. The D614G mutation in G variant with higher infectivity has turned the Chinese epidemic into a pandemic. Other SARS-CoV-2 variants, such as Alpha, Beta, Gamma, and Delta seem to have evolved as result of adaptation to selective pressures during periods of prolonged infections and subsequent transmission. Further, there is issue of convergent association of mutations. Basics of immunity and immune system failure: The nature of the immune response after natural SARS-CoV-2 infection is variable and diverse. There are pre-existing neutralizing antibodies and sensitized T cells elicited during previous infection with seasonal CoVs influencing the disease susceptibility and course. The virus has evolved adaptive mechanisms to reduce its exposure to IFN-I and there are issues related to erratic and overactive immune response. The altered neutralizing epitopes in the S protein in SARS-CoV-2 variants modify the immune landscapes and clinical manifestations. Conclusion: current scenarios and prospects: Presently, the SARS-CoV-2 infection is widespread with multiple evolving infectious variants. There is probability of its transition from epidemic to endemic phase in due course manifesting as a mild disease especially in the younger population. Conversely, the pandemic may continue with enhanced disease severity due to evolving variants, expanded infection pool, and changing immunity landscape. There is need to plan for the transition and continued circulation of the virus during the endemic phase or continuing pandemic for indefinite period.

scholarly journals Sensitivity of two SARS-CoV-2 variants with spike protein mutations to neutralising antibodies

Virus Genes ◽  
2021 ◽  
Author(s):  
Katharina Müller ◽  
Philipp Girl ◽  
Andreas Giebl ◽  
Stefanie Gruetzner ◽  
Markus Antwerpen ◽  
...  
Keyword(s):  
Immune Response ◽  
Humoral Immune Response ◽  
Point Of View ◽  
Spike Protein ◽  
Wild Type ◽  
Serum Samples ◽  
Antibody Treatment ◽  
Neutralising Antibodies ◽  
Humoral Immune ◽  
Protein Mutations

AbstractSARS-CoV-2 infections elicit a humoral immune response capable of neutralising the virus. However, multiple variants have emerged with mutations in the spike protein amongst others, the key target of neutralising antibodies. We evaluated the neutralising efficacy of 89 serum samples from patients, infected with SARS-CoV-2 in the beginning of 2020, against two virus variants isolated from acutely infected patients and harbouring spike protein mutations. One isolate was assigned to lineage B.1.351 (MUC-IMB-B.1.351) whilst the other (MUC-484) was isolated from an immunocompromised patient, sharing some but not all mutations with B.1.351 and representing a transitional variant. Both variants showed a significant reduction in neutralisation sensitivity compared to wild-type SARS-CoV-2 with MUC-IMB-B.1.351 being almost completely resistant to neutralisation. The observed reduction in neutralising activity of wild-type-specific antibodies against both variants suggests that individual mutations in the spike protein are sufficient to confer a potent escape from the humoral immune response. In addition, the effect of escape mutations seems to accumulate, so that more heavily mutated variants show a greater loss of sensitivity to neutralisation up to complete insensitivity as observed for MUC-IMB-B.1.351. From a clinical point of view, this might affect the efficacy of (monoclonal) antibody treatment of patients with prolonged infections as well as patients infected with variants other than the donor. At the same, this could also negatively influence the efficacy of current vaccines (as they are based on wild-type spike protein) emphasising the need to thoroughly surveil the emergence and distribution of variants and adapt vaccines and therapeutics accordingly.

scholarly journals Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients

2020 ◽  
Author(s):  
Yang Li ◽  
Dan-yun Lai ◽  
Hai-nan Zhang ◽  
He-wei Jiang ◽  
Xiao-long Tian ◽  
...  
Keyword(s):  
Immune Response ◽  
Neutralizing Antibodies ◽  
World Wide ◽  
Cell Entry ◽  
Spike Protein ◽  
Peptide Microarray ◽  
S Protein ◽  
Linear Epitopes

AbstractSARS-CoV-2 outbreak is a world-wide pandemic. The Spike protein plays central role in cell entry of the virus, and triggers significant immuno-response. Our understanding of the immune-response against S protein is still very limited. Herein, we constructed a peptide microarray and analyzed 55 convalescent sera, three areas with rich linear epitopes were identified. Potent neutralizing antibodies enriched from sera by 3 peptides, which do not belong to RBD were revealed.

scholarly journals Delta infection following vaccination elicits potent neutralizing immunity against the SARS-CoV-2 Omicron

2022 ◽  
Author(s):  
Mai-Juan Ma ◽  
Lin Yao ◽  
Hui-Xia Gao ◽  
Ka-Li Zhu ◽  
Jun Rong ◽  
...  
Keyword(s):  
South Africa ◽  
Immune Response ◽  
Immune Escape ◽  
Spike Protein ◽  
Amino Acid Substitutions ◽  
High Potency ◽  
Breakthrough Infection ◽  
Neutralizing Activity ◽  
Humoral Immune ◽  
Delta Infection

Abstract Since the initial detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) in November 2021 in South Africa, it has caused a rapid increase in infections globally. The Omicron variant encodes 37 amino acid substitutions in its spike protein, and early reports have provided evidence for extensive immune escape and reduced vaccine effectiveness. We assessed serum neutralizing activity in sera from Delta infection following vaccination of CoronaVac or ZF2001 and Delta infection only against SARS-CoV-2 Wuhan-Hu-1 (WA1), Beta, Delta, and Omicron. We found that sera from Delta infection only could neutralize WA1 and Delta pseudoviruses but nearly completely lost capacity to neutralize Beta and Omicron pseudoviruses. However, Delta infection following vaccination resulted in a significant increase of serum neutralizing activity against WA1, Beta, and Omicron. This study demonstrates that breakthrough infection of Delta in previously vaccinated individuals substantially induced high potency humoral immune response against the Omicron variant and other emerged variants.

scholarly journals Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development

2004 ◽  
Vol 50 (6) ◽  
pp. 1036-1042 ◽  
Author(s):  
Wai-Yan Choy ◽  
Shu-Guang Lin ◽  
Paul Kay-Sheung Chan ◽  
John Siu-Lun Tam ◽  
Y M Dennis Lo ◽  
...  
Keyword(s):  
Immune Response ◽  
Severe Acute Respiratory Syndrome ◽  
Synthetic Peptide ◽  
Synthetic Peptides ◽  
Vaccine Development ◽  
Biologically Active ◽  
Spike Protein ◽  
Antibody Specificity ◽  
S Protein ◽  
Specific Antibodies

Abstract Background: The S (spike) protein of the etiologic coronavirus (CoV) agent of severe acute respiratory syndrome (SARS) plays a central role in mediating viral infection via receptor binding and membrane fusion between the virion and the host cell. We focused on using synthetic peptides for developing antibodies against SARS-CoV, which aimed to block viral invasion by eliciting an immune response specific to the native SARS-CoV S protein. Methods: Six peptide sequences corresponding to the surface regions of SARS-CoV S protein were designed and investigated by use of combined bioinformatics and structural analysis. These synthetic peptides were used to immunize both rabbits and monkeys. Antisera collected 1 week after the second immunization were analyzed by ELISA and tested for antibody specificity against SARS-CoV by immunofluorescent confocal microscopy. Results: Four of our six synthetic peptides (S2, S3, S5, and S6) elicited SARS-CoV-specific antibodies, of which S5 (residues 788–820) and S6 (residues 1002–1030) exhibited immunogenic responses similar to those found in a parallel investigation using truncated recombinant protein analogs of the SARS-CoV S protein. This suggested that our S5 and S6 peptides may represent two minimum biologically active sequences of the immunogenic regions of the SARS-CoV S protein. Conclusions: Synthetic peptides can elicit specific antibodies to SARS-CoV. The study provides insights for the future development of SARS vaccine via the synthetic-peptide-based approach.

scholarly journals Exploring COVID-19: Relating the spike protein to infectivity, pathogenicity and Immunogenicity

2021 ◽  
Vol 5 (1) ◽  
pp. 001-010
Author(s):  
Nikhra Vinod
Keyword(s):  
Immune Response ◽  
Life Cycle ◽  
Host Cell ◽  
Disease Transmission ◽  
Vaccine Development ◽  
Spike Protein ◽  
Structural Proteins ◽  
Causative Organism ◽  
S Protein ◽  
New Variant

Introduction: SARS-CoV-2 life cycle: The disease which reportedly began in Chinese city Wuhan in November-December 2019 manifesting as severe respiratory illness, soon spread to various parts of the world, and was named COVID-19, and declared a pandemic by WHO. The life cycle of SARS-CoV-2 begins with membrane fusion mediated by Spike (S) protein binding to the ACE2 receptors. Following viral entry and release of genome into the host cell cytoplasm there occurs replication and transcription to generate viral structural and non-structural proteins. Finally, VLPs are produced and the mature virions are released from the host cell. Immunogenicity of the spike protein: The S protein is considered the main antigenic component among structural proteins of SARS-CoV-2 and responsible for inducing the host immune response. The neutralising antibodies (nAbs) targeting the S protein are produced and may confer a protective immunity against the viral infection. Further, the role of the S protein in infectivity also makes it an important tool for diagnostic antigen-based testing and vaccine development. The S-specific antibodies, memory B and circulating TFH cells are consistently elicited following SARS-CoV-2 infection, and COVID-19 vaccine shots in clinical trials. The emerging SARS-CoV-2 variants: The early genomic variations in SARS-CoV-2 have gone almost unnoticed having lacked an impact on disease transmission or its clinical course. Some of the recently discovered mutations, however, have impact on transmissibility, infectivity, or immune response. One such mutation is the D614G variant, which has increased in prevalence to currently become the dominant variant world-over. Another, relatively new variant, named VUI-202012/01 or B.1.1.7 has acquired 17 genomic alterations and carries the risk of enhanced infectivity. Further, its potential impact on vaccine efficacy is a worrisome issue. Conclusion: THE UNMET CHALLENGES: COVID-19 as a disease and SARS-CoV-2 as its causative organism, continue to remain an enigma. While we continue to explore the agent factors, disease transmission dynamics, pathogenesis and clinical spectrum of the disease, and therapeutic modalities, the grievous nature of the disease has led to emergency authorizations for COVID-19 vaccines in various countries. Further, the virus may continue to persist and afflict for years to come, as future course of the disease is linked to certain unknown factors like effects of seasonality on virus transmission and unpredictable nature of immune response to the disease.

Sanger sequencing of SARS-CoV-2 Spike protein v1

2021 ◽  
Author(s):  
Tiago S. Salles* ◽  
Andrea Cony Cavalcanti* ◽  
Fabio Burack da Costa ◽  
Renata Campos Azevedo
Keyword(s):  
Sanger Sequencing ◽  
Evolutionary Dynamics ◽  
Spike Protein ◽  
Nucleotide Sequencing ◽  
S Protein ◽  
New Generation Sequencing ◽  
Protein Mutations ◽  
Controlling Measures ◽  
New Generation ◽  
Generation Sequencing

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike protein. Monitoring the S protein mutations is crucial for successful controlling measures and detect variants that can evade vaccine immunity. Even after the costs reduction imposed by the pandemic, the new generation sequencing methodologies remain unavailable to many scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S protein, this work describes a protocol for complete nucleotide sequencing of the S protein using the Sanger technique. Thus, any laboratory with experience in sequencing can adopt this protocol.

scholarly journals A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Niklas Vesper ◽  
Yaneth Ortiz ◽  
Frauke Bartels-Burgahn ◽  
Jianying Yang ◽  
Kathrin de la Rosa ◽  
...  
Keyword(s):  
Immune Response ◽  
Humoral Immune Response ◽  
Immune Escape ◽  
Flow Cytometric Assay ◽  
Health Crisis ◽  
S Protein ◽  
Humoral Immune ◽  
Flow Cytometric ◽  
Specific Igg ◽  
S Proteins

The SARS-CoV-2 pandemic has spread to all parts of the world and can cause life-threatening pneumonia and other severe disease manifestations known as COVID-19. This health crisis has resulted in a significant effort to stop the spread of this new coronavirus. However, while propagating itself in the human population, the virus accumulates mutations and generates new variants with increased fitness and the ability to escape the human immune response. Here we describe a color-based barcoded spike flow cytometric assay (BSFA) that is particularly useful to evaluate and directly compare the humoral immune response directed against either wild type (WT) or mutant spike (S) proteins or the receptor-binding domains (RBD) of SARS-CoV-2. This assay employs the human B lymphoma cell line Ramos, transfected for stable expression of WT or mutant S proteins or a chimeric RBD-CD8 fusion protein. We find that the alpha and beta mutants are more stably expressed than the WT S protein on the Ramos B cell surface and/or bind with higher affinity to the viral entry receptor ACE2. However, we find a reduce expression of the chimeric RBD-CD8 carrying the point mutation N501Y and E484K characteristic for the alpha and beta variant, respectively. The comparison of the humoral immune response of 12 vaccinated probands with 12 COVID-19 patients shows that after the boost, the S-specific IgG class immune response in the vaccinated group is similar to that of the patient group. However, in comparison to WT the specific IgG serum antibodies bind less well to the alpha variant and only poorly to the beta variant S protein. This is in line with the notion that the beta variant is an immune escape variant of SARS-CoV-2. The IgA class immune response was more variable than the IgG response and higher in the COVID-19 patients than in the vaccinated group. In summary, we think that our BSFA represents a useful tool to evaluate the humoral immunity against emerging variants of SARS-CoV-2 and to analyze new vaccination protocols against these variants.

Computational analysis of the effect of SARS-CoV-2 variant Omicron Spike protein mutations on dynamics, ACE2 binding and propensity for immune escape

2021 ◽  
Author(s):  
Natalia Teruel ◽  
Matthew Crown ◽  
Matthew Bashton ◽  
Rafael Najmanovich
Keyword(s):  
Binding Affinity ◽  
Immune Escape ◽  
Pearson Correlation ◽  
Potential Effect ◽  
Spike Protein ◽  
Vibrational Entropy ◽  
Contributing Factors ◽  
S Protein ◽  
The One ◽  
Opposing Effects

The recently reported Omicron (B.1.1.529) SARS-CoV-2 variant has a large number of mutations in the Spike (S) protein compared to previous variants. Here we evaluate the potential effect of Omicron S mutations on S protein dynamics and ACE2 binding as contributing factors to infectivity as well as propensity for immune escape. We define a consensus set of mutations from 77 sequences assigned as Omicron in GISAID as of November 25. We create structural models of the Omicron S protein in the open and closed states, as part of a complex with ACE2 and for each of 77 complexes of S bound to different antibodies with known structures. We have previously utilized Dynamical Signatures (DS) and the Vibrational Entropy Score (VDS) to evaluate the propensity of S variants to favour the open state. Here, we introduce the Binding Influence Score (BIS) to evaluate the influence of mutations on binding affinity based on the net gain or loss of interactions within the protein-protein interface. BIS shows excellent correlation with experimental data (Pearson correlation coefficient of 0.87) on individual mutations in the ACE2 interface for the Alpha, Beta, Gamma, Delta and Omicron variants combined. On the one hand, the DS of Omicron highly favours a more rigid open state and a more flexible closed state with the largest VDS of all variants to date, suggesting a large increase in the chances to interact with ACE2. On the other hand, the BIS shows that apart from N501Y, all other mutations in the interface reduce ACE2 binding affinity. VDS and BIS show opposing effects on the overall effectiveness of Omicron mutations to promote binding to ACE2 and therefore initiate infection. To evaluate the propensity for immune escape we calculated the net change of favourable and unfavourable interactions within each S-antibody interface. The net change of interactions shows a positive score (a net increase of favourable interactions and decrease of unfavourable ones) for 41 out of 77 antibodies, a nil score for 15 and a negative score for 21 antibodies. Therefore, in only 28% of S-antibody complexes (21/77) we predict some level of immune escape due to a weakening of the interactions with Omicron S. Considering that most antibody epitopes and the mutations are within the S-ACE2 interface our results suggest that mutations within the RBD of Omicron may give rise to only partial immune escape, which comes at the expense of reduced ACE2 binding affinity. However, this reduced ACE2 affinity appears to have been offset by increasing the occupancy of the open state of the Spike protein.

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