scholarly journals B.1.617.3 SARS CoV-2 spike E156G/Δ157-158 mutations contribute to reduced neutralization sensitivity and increased infectivity

2021 ◽  
Author(s):  
Tarun Mishra ◽  
Garima Joshi ◽  
Atul Kumar ◽  
Rishikesh Dalavi ◽  
Pankaj Pandey ◽  
...  
Keyword(s):  
Immune Evasion ◽  
Neutralizing Antibodies ◽  
Immune Escape ◽  
Coding Region ◽  
Rt Pcr ◽  
Breakthrough Infection ◽  
Neutralization Sensitivity ◽  
Spike Gene ◽  
Spike Coding ◽  
The Usa

SARS CoV-2 variants raise significant concerns due to their ability to cause vaccine breakthrough infections. Here, we sequence-characterized the spike gene, isolated from a breakthrough infection, that corresponded to B.1.617.3 lineage. Delineating the functional impact of spike mutations using reporter pseudoviruses (PV) revealed that N-terminal domain (NTD)-specific E156G/Δ157-158 contributed to increased infectivity and reduced sensitivity to ChAdOx1 nCoV-19 vaccine (CovishieldTM)-elicited neutralizing antibodies. A six-nucleotide deletion (467-472) in the spike coding region introduced this change in the NTD. We confirmed the presence of E156G/Δ157-158 in the RT-PCR-positive cases concurrently screened, in addition to other circulating spike (S1) mutations like T19R, T95I, L452R, E484Q, and D614G. Notably, E156G/Δ157-158 was present in more than 85% of the sequences reported from the USA, UK, and India in August 2021. The spike PV bearing combination of E156G/Δ157-158 and L452R further promoted infectivity and conferred immune evasion. Additionally, increased cell-to-cell fusion was observed when spike harbored E156G/Δ157-158, L452R, and E484Q, suggesting a combinatorial effect of these mutations. Notwithstanding, the plasma from a recovered individual robustly inhibited mutant spike PV, indicating the increased breadth of neutralization post-recovery. Our data highlights the importance of spike NTD-specific changes in determining infectivity and immune escape of variants.

scholarly journals A Rapid and Consistent Method To Identify SARS-CoV-2 Variants By RT-PCR

2021 ◽  
Author(s):  
Marco Fabiani ◽  
Katia Margiotti ◽  
Manuela Sabatino ◽  
Antonella Viola ◽  
Alvaro Mesoraca ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Immune Escape ◽  
Low Cost ◽  
Gene Mutations ◽  
Nucleotide Polymorphisms ◽  
Rt Pcr ◽  
Spike Gene ◽  
Natural Defense ◽  
The Uk ◽  
Next Generation Sequencing Ngs

Abstract Background Since 2020, the COVID-19 pandemic spread worldwide causing health, economic, and social distresses. Containment strategy relay on rapid and consistent methodology for molecular detection and characterization. The emerging variants of concern (VOCs) are currently associated with increased infectivity, and immune escape (natural defense mechanisms as well as a vaccine). Several VOCs has been detected and include lineage B.1.1.7 first identified in the UK, linage B.1.351 in South Africa, and lineage P.1 (B.1.1.28.1) in Brazil. Here we validated a rapid and low-cost technique to distinguish B.1.1.7, B.1.351 and P.1 SARS-CoV-2 variants by detecting Spike gene mutations using RT-PCR methodology. Results We recruited 77 positive patients affected by Coronavirus Disease-19 (COVID-19). Specific Real-time reverse transcription-polymerase chain reaction (RT-PCR) was employed targeting single nucleotide polymorphisms (SNPs) to screen Spike protein mutations. All data were validated by next generation sequencing (NGS) methodology and using sequence from a public database.Among 77 COVID-19 positive samples we could discriminate with 100% of concordance all the investigated SARS-CoV-2 variants when comparing with NGS method. Conclusions PCR-based assays for identification of circulating VOCs of SARS-CoV-2 resulted in a rapid method to identify the specific SARS-CoV-2 variants allowing a better survey of the spread of the virus and its transmissibility in the pandemic phase.

scholarly journals SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants

PLoS Medicine ◽  
2021 ◽  
Vol 18 (7) ◽  
pp. e1003656
Author(s):  
Fiona Tea ◽  
Alberto Ospina Stella ◽  
Anupriya Aggarwal ◽  
David Ross Darley ◽  
Deepti Pilli ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Rt Pcr ◽  
Breakthrough Infection ◽  
Nucleocapsid Proteins ◽  
Viral Neutralization ◽  
Polymerase Chain ◽  
Serial Samples ◽  
High Responders ◽  
Neutralization Response ◽  
Selection Of

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antibody neutralization response and its evasion by emerging viral variants and variant of concern (VOC) are unknown, but critical to understand reinfection risk and breakthrough infection following vaccination. Antibody immunoreactivity against SARS-CoV-2 antigens and Spike variants, inhibition of Spike-driven virus–cell fusion, and infectious SARS-CoV-2 neutralization were characterized in 807 serial samples from 233 reverse transcription polymerase chain reaction (RT-PCR)–confirmed Coronavirus Disease 2019 (COVID-19) individuals with detailed demographics and followed up to 7 months. A broad and sustained polyantigenic immunoreactivity against SARS-CoV-2 Spike, Membrane, and Nucleocapsid proteins, along with high viral neutralization, was associated with COVID-19 severity. A subgroup of “high responders” maintained high neutralizing responses over time, representing ideal convalescent plasma donors. Antibodies generated against SARS-CoV-2 during the first COVID-19 wave had reduced immunoreactivity and neutralization potency to emerging Spike variants and VOC. Accurate monitoring of SARS-CoV-2 antibody responses would be essential for selection of optimal responders and vaccine monitoring and design.

scholarly journals Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies

2021 ◽  
Vol 17 (8) ◽  
pp. e1009772
Author(s):  
Marta Alenquer ◽  
Filipe Ferreira ◽  
Diana Lousa ◽  
Mariana Valério ◽  
Mónica Medina-Lopes ◽  
...  
Keyword(s):  
Amino Acid ◽  
Immune Evasion ◽  
Neutralizing Antibodies ◽  
Immune Escape ◽  
Host Immunity ◽  
Arms Race ◽  
Spike Protein ◽  
Antibody Neutralization ◽  
Angiotensin Converting Enzyme 2 ◽  
The Core

Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics.

scholarly journals Human neutralizing antibodies for SARS-CoV-2 prevention and immunotherapy

2021 ◽  
Author(s):  
Dongyan Zhou ◽  
Runhong Zhou ◽  
Zhiwei Chen
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Neutralizing Antibodies ◽  
Immune Escape ◽  
Passive Immunization ◽  
Clinical Development ◽  
Vaccine Research ◽  
Breakthrough Infection ◽  
Clinical Benefits

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). SARS-CoV-2 has been spreading worldwide since December 2019, resulting in the ongoing COVID-19 pandemic with 237 million infections and 4.8 million deaths by 11 October 2021. While there are great efforts of global vaccination, ending this pandemic has been challenged by issues of exceptionally high viral transmissibility, re-infection, vaccine-breakthrough infection, and immune escape variants of concerns. Besides the record-breaking speed of vaccine research and development, antiviral drugs including SARS-CoV-2-specific human neutralizing antibodies (HuNAbs) have been actively explored for passive immunization. In support of HuNAb-based immunotherapy, passive immunization using convalescent patients’ plasma have generated promising evidence on clinical benefits for both mild and severe COVID-19 patients. Since the source of convalescent plasma is limited, the discovery of broadly reactive HuNAbs may have significant impacts on the fight against the COVID-19 pandemic. In this review, therefore, we discuss the current technologies of gene cloning, modes of action, in vitro and in vivo potency and breadth, and clinical development for potent SARS-CoV-2-specific HuNAbs.

scholarly journals Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity

2021 ◽  
Vol 22 (17) ◽  
pp. 9131 ◽  
Author(s):  
Vipul Kumar ◽  
Jasdeep Singh ◽  
Seyed E. Hasnain ◽  
Durai Sundar
Keyword(s):  
Binding Energy ◽  
Neutralizing Antibodies ◽  
Immune Escape ◽  
Spike Protein ◽  
Rt Pcr ◽  
Dynamic Simulations ◽  
Global Pandemic ◽  
Hydrogen Interaction ◽  
Alpha Variant ◽  
The Stability

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has created alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests. It has also increased the chances of reinfection and immune escape. Recently various lineages namely, B.1.1.7 (Alpha), B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3 have caused rapid infection around the globe. To understand the biophysical perspective, we have performed molecular dynamic simulations of four different spikes (receptor binding domain)-hACE2 complexes, namely wildtype (WT), Alpha variant (N501Y spike mutant), Kappa (L452R, E484Q) and Delta (L452R, T478K), and compared their dynamics, binding energy and molecular interactions. Our results show that mutation has caused significant increase in the binding energy between the spike and hACE2 in Alpha and Kappa variants. In the case of Kappa and Delta variants, the mutations at L452R, T478K and E484Q increased the stability and intra-chain interactions in the spike protein, which may change the interaction ability of neutralizing antibodies to these spike variants. Further, we found that the Alpha variant had increased hydrogen interaction with Lys353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2.

scholarly journals Neutralization of ancestral SARS-CoV-2 and variants Alpha, Beta, Gamma, Delta, Zeta and Omicron by mRNA vaccination and infection-derived immunity through homologous and heterologous variants

2021 ◽  
Author(s):  
Meriem Bekliz ◽  
Kenneth Adea ◽  
Pauline Vetter ◽  
Christiane S Eberhardt ◽  
Krisztina Hosszu-Fellous ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Immune Escape ◽  
Neutralization Assay ◽  
Significant Loss ◽  
Antigenic Relationship ◽  
Double Dose ◽  
Gamma Delta ◽  
Breakthrough Infection ◽  
Neutralizing Capacity ◽  
Alpha Beta

Emerging SARS-CoV-2 variants of concern/interest (VOC/VOI) raise questions about effectiveness of neutralizing antibodies derived from infection or vaccination. As the population immunity to SARS-CoV-2 has become more complex due to prior infection and/or vaccination, understanding the antigenic relationship between variants is needed. Here, we have assessed in total 104 blood specimens from convalescent individuals after infection with early-pandemic SARS-CoV-2 (pre-VOC) or with Alpha, Beta, Gamma or Delta, post-vaccination after double-dose mRNA-vaccination and break through infections due to Delta or Omicron. Neutralization against seven authentic SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta, Omicron) was assessed by plaque-reduction neutralization assay. We found highest neutralization titers against the homologous (previously infecting) variant, with lower neutralization efficiency against heterologous variants. Significant loss of neutralization for Omicron was observed but to a varying degree depending on previously infecting variant (23.0-fold in Beta-convalescence up to 56.1-fold in Alpha-convalescence), suggesting that infection-derived immunity varies, but independent of the infecting variant is only poorly protective against Omicron. Of note, Zeta VOI showed also pronounced escape from neutralization of up to 28.2-fold in Alpha convalescent samples. Antigenic mapping reveals both Zeta and Omicron as separate antigenic clusters. Double dose vaccination showed robust neutralization for Alpha, Beta, Gamma, Delta and Zeta, with fold-change reduction of only 2.8 (for Alpha) up to 6.9 (for Beta). Escape from neutralization for Zeta was largely restored in vaccinated individuals, while Omicron still showed a loss of neutralization of 85.7-fold compared to pre-VOC SARS-CoV-2. Combined immunity from infection followed by vaccination or vaccine breakthrough infection showed highest titers and most robust neutralization for heterologous variants. Breakthrough infection with Delta showed only 12.5-fold reduced neutralization for Omicron, while breakthrough infection with Omicron showed only a 1.5-fold loss for Delta, suggests that infection with antigenically different variants can boost immunity for antigens closer to the vaccine strain. Antigenic cartography showed also a tendency towards broader neutralizing capacity for heterologous variants. We conclude that the complexity of background immunity needs to be taken into account when assessing new VOCs. Development towards separate serotypes such as Zeta was already observed before Omicron emergence, thus other factors than just immune escape must contribute to Omicrons rapid dominance. However, combined infection/vaccination immunity could ultimately lead to broad neutralizing capacity also against non-homologous variants.

scholarly journals A Rapid and Consistent Method to Identify SARS-CoV-2 Variants by RT-PCR

2021 ◽  
Author(s):  
Marco Fabiani ◽  
Katia Margiotti ◽  
Manuela Sabatino ◽  
Antonella Viola ◽  
Alvaro Mesoraca ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Immune Escape ◽  
Low Cost ◽  
Gene Mutations ◽  
Nucleotide Polymorphisms ◽  
Rt Pcr ◽  
Spike Gene ◽  
Natural Defense ◽  
The Uk ◽  
Next Generation Sequencing Ngs

Abstract Background: Since 2020, the COVID-19 pandemic spread worldwide causing health, economic, and social distresses. Containment strategy relay on rapid and consistent methodology for molecular detection and characterization. The emerging variants of concern (VOCs) are currently associated with increased infectivity, and immune escape (natural defense mechanisms as well as a vaccine). Several VOCs has been detected and include lineage B.1.1.7 first identified in the UK, linage B.1.351 in South Africa, and lineage P.1 (B.1.1.28.1) in Brazil. Here we validated a rapid and low-cost technique to distinguish B.1.1.7, B.1.351 and P.1 SARS-CoV-2 variants by detecting Spike gene mutations using RT-PCR methodology. Results: We recruited 77 positive patients affected by Coronavirus Disease-19 (COVID-19). Specific Real-time reverse transcription-polymerase chain reaction (RT-PCR) was employed targeting single nucleotide polymorphisms (SNPs) to screen Spike protein mutations. All data were validated by next generation sequencing (NGS) methodology and using sequence from a public database.Among 77 COVID-19 positive samples we could discriminate with 100% of concordance all the investigated SARS-CoV-2 variants when comparing with NGS method.Conclusions: PCR-based assays for identification of circulating VOCs of SARS-CoV-2 resulted in a rapid method to identify the specific SARS-CoV-2 variants allowing a better survey of the spread of the virus and its transmissibility in the pandemic phase.

scholarly journals Evaluation of a Pseudovirus Neutralization Assay for SARS-CoV-2 and Correlation with Live Virus-Based Micro Neutralization Assay

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 994
Author(s):  
Ahmed Majdi K. Tolah ◽  
Sayed S. Sohrab ◽  
Khaled Majdi K. Tolah ◽  
Ahmed M. Hassan ◽  
Sherif A. El-Kafrawy ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Epidemiological Studies ◽  
Neutralization Assay ◽  
Serum Samples ◽  
Live Virus ◽  
Spike Gene ◽  
Microneutralization Assay ◽  
Viral Particles ◽  
Reliable Performance ◽  
Prior Infection

The unusual cases of pneumonia outbreak were reported from Wuhan city in late December 2019. Serological testing provides a powerful tool for the identification of prior infection and for epidemiological studies. Pseudotype virus neutralization assays are widely used for many viruses and applications in the fields of serology. The accuracy of pseudotype neutralizing assay allows for its use in low biosafety lab and provides a safe and effective alternative to the use of wild-type viruses. In this study, we evaluated the performance of this assay compared to the standard microneutralization assay as a reference. The lentiviral pseudotype particles were generated harboring the Spike gene of SARS-CoV-2. The generated pseudotype particles assay was used to evaluate the activity of neutralizing antibodies in 300 human serum samples from a COVID-19 sero-epidemiological study. Testing of these samples resulted in 55 positive samples and 245 negative samples by pseudotype viral particles assay while microneutralization assay resulted in 64 positive and 236 negative by MN assay. Compared to the MN, the pseudotyped viral particles assay showed a sensitivity of 85.94% and a specificity of 100%. Based on the data generated from this study, the pseudotype-based neutralization assay showed a reliable performance for the detection of neutralizing antibodies against SARS-CoV-2 and can be used safely and efficiently as a diagnostic tool in a biosafety level 2 laboratory.

scholarly journals Elicitation of Broadly Neutralizing Antibodies against B.1.1.7, B.1.351, and B.1.617.1 SARS-CoV-2 Variants by Three Prototype Strain-Derived Recombinant Protein Vaccines

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1421
Author(s):  
Yong Yang ◽  
Jinkai Zang ◽  
Shiqi Xu ◽  
Xueyang Zhang ◽  
Sule Yuan ◽  
...  
Keyword(s):  
Recombinant Protein ◽  
Neutralizing Antibodies ◽  
Wild Type Strain ◽  
Immune Escape ◽  
High Titer ◽  
Prototype Strain ◽  
Vaccine Antigen ◽  
Broadly Neutralizing Antibodies ◽  
Continued Use ◽  
Further Development

The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Most of the currently approved SARS-CoV-2 vaccines use the prototype strain-derived spike (S) protein or its receptor-binding domain (RBD) as the vaccine antigen. The emergence of several novel SARS-CoV-2 variants has raised concerns about potential immune escape. In this study, we performed an immunogenicity comparison of prototype strain-derived RBD, S1, and S ectodomain trimer (S-trimer) antigens and evaluated their induction of neutralizing antibodies against three circulating SARS-CoV-2 variants, including B.1.1.7, B.1.351, and B.1.617.1. We found that, at the same antigen dose, the RBD and S-trimer vaccines were more potent than the S1 vaccine in eliciting long-lasting, high-titer broadly neutralizing antibodies in mice. The RBD immune sera remained highly effective against the B.1.1.7, B.1.351, and B.1.617.1 variants despite the corresponding neutralizing titers decreasing by 1.2-, 2.8-, and 3.5-fold relative to that against the wild-type strain. Significantly, the S-trimer immune sera exhibited comparable neutralization potency (less than twofold variation in neutralizing GMTs) towards the prototype strain and all three variants tested. These findings provide valuable information for further development of recombinant protein-based SARS-CoV-2 vaccines and support the continued use of currently approved SARS-CoV-2 vaccines in the regions/countries where variant viruses circulate.

Immune Evasion of SARS-CoV-2 Variants of Concern is Driven by Low Affinity to Neutralizing Antibodies

2021 ◽  
Author(s):  
Matheus Ferraz ◽  
Emerson Moreira ◽  
Danilo F. Coêlho ◽  
Gabriel Wallau ◽  
Roberto Lins
Keyword(s):  
Immune Evasion ◽  
Neutralizing Antibodies ◽  
Cross Reactivity ◽  
Class I ◽  
Minor Role ◽  
A Minor

SARS-CoV-2 VOCs immune evasion is mainly due to lower cross-reactivity from previously elicited class I/II neutralizaing antibodies, while increased affinity to hACE2 plays a minor role. Affinity between antibodies and...

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