scholarly journals Structural and Biochemical Rationale for Enhanced Spike Protein Fitness in Delta and Kappa SARS-CoV-2 Variants

2021 ◽  
Author(s):  
James W. Saville ◽  
Dhiraj Mannar ◽  
Xing Zhu ◽  
Shanti S. Srivastava ◽  
Alison M. Berezuk ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Viral Fitness ◽  
Spike Protein ◽  
Wild Type ◽  
Antibody Neutralization ◽  
Vaccination Rates ◽  
Modest Increase ◽  
Terminal Domain ◽  
Cryo Electron Microscopy ◽  
Neutralizing Epitopes

The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a novel head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant.

Identification of a novel neutralizing epitope on the N-terminal domain of the HCoV-229E spike protein

2021 ◽  
Author(s):  
Jiale Shi ◽  
Yuejun Shi ◽  
Ruixue Xiu ◽  
Gang Wang ◽  
Rui Liang ◽  
...  
Keyword(s):  
Epitope Mapping ◽  
Vaccine Development ◽  
Selective Pressure ◽  
Spike Protein ◽  
Neutralizing Epitope ◽  
Change Over Time ◽  
S Protein ◽  
Terminal Domain ◽  
Neutralizing Epitopes ◽  
Over Time

The receptor binding domain (RBD) of the coronavirus spike protein (S) has been verified to be the main target for potent neutralizing antibodies (nAbs) in most coronaviruses, and the N-terminal domain (NTD) of some betacoronaviruses has also been indicated to induce nAbs. For alphacoronavirus HCoV-229E, its RBD has been shown to have neutralizing epitopes, and these epitopes could change over time. However, whether neutralizing epitopes exist on the NTD and whether these epitopes change like those of the RBD are still unknown. Here, we verified that neutralizing epitopes exist on the NTD of HCoV-229E. Furthermore, we characterized an NTD targeting nAb 5H10, which could neutralize both pseudotyped and authentic HCoV-229E VR740 in vitro. Epitope mapping indicated that 5H10 targeted motif E1 (147-167 aa) and identified F159 as critical for 5H10 binding. More importantly, our results revealed that motif E1 was highly conserved among clinical isolates except for F159. Further data proved that mutations at position 159 gradually appeared over time and could completely abolish the neutralizing ability of 5H10, supporting the notion that position 159 may be under selective pressure during the human epidemic. In addition, we also found that contemporary clinical serum has a stronger binding capacity for the NTD of contemporary strains than historic strains, proving that the epitope on the NTD could change over time. In summary, these findings define a novel neutralizing epitope on the NTD of HCoV-229E S and provide a theoretical basis for the design of vaccines against HCoV-229E or related coronaviruses. Importance Characterization of the neutralizing epitope of the spike (S) protein, the major invasion protein of coronaviruses, can help us better understand the evolutionary characteristics of these viruses and promote vaccine development. To date, the neutralizing epitope distribution of alphacoronaviruses is not well known. Here, we identified a neutralizing antibody that targeted the N-terminal domain (NTD) of the alphacoronavirus HCoV-229E S protein. Epitope mapping revealed a novel epitope that was not previously discovered in HCoV-229E. Further studies identified an important residue, F159. Mutations that gradually appeared over time at this site abolished the neutralizing ability of 5H10, indicating that selective pressure occurred at this position in the spread of HCoV-229E. Furthermore, we found that the epitopes within the NTD also changed over time. Taken together, our findings defined a novel neutralizing epitope and highlighted the role of the NTD in the future prevention and control of HCoV-229E or related coronaviruses.

scholarly journals Cryo-electron Microscopy Reconstruction and Stability Studies of the Wild Type and the R432A Variant of Adeno-associated Virus Type 2 Reveal that Capsid Structural Stability Is a Major Factor in Genome Packaging

2016 ◽  
Vol 90 (19) ◽  
pp. 8542-8551 ◽  
Author(s):  
Lauren M. Drouin ◽  
Bridget Lins ◽  
Maria Janssen ◽  
Antonette Bennett ◽  
Paul Chipman ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Intramolecular Interactions ◽  
Single Amino Acid ◽  
Fold Axis ◽  
Wild Type ◽  
Scanning Calorimetry ◽  
Genome Packaging ◽  
Cryo Electron Microscopy ◽  
Empty Capsid ◽  
Packaging Efficiency

ABSTRACTThe adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at an ∼5.0-Å resolution (medium) and also at 3.8- and 3.7-Å resolutions (high), respectively. The high resolution structures showed that removal of the arginine side chain in AAV2-R432A eliminated hydrogen bonding interactions, resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis toward the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an ∼10°C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. In addition, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the βA strand region under the icosahedral 2-fold axis rather than antiparallel to the βB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency.IMPORTANCEThe mechanism of AAV genome packaging is still poorly understood, particularly with respect to the capsid determinants of the required capsid-Rep interaction. Understanding this mechanism may aid in the improvement of AAV packaging efficiency, which is currently ∼1:10 (10%) genome packaged to empty capsid in vector preparations. This report identifies regions of the AAV capsid that play roles in genome packaging and that may be important for Rep recognition. It also demonstrates the need to maintain capsid stability for the success of this process. This information is important for efforts to improve AAV genome packaging and will also inform the engineering of AAV capsid variants for improved tropism, specific tissue targeting, and host antibody escape by defining amino acids that cannot be altered without detriment to infectious vector production.

scholarly journals Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

2016 ◽  
Vol 23 (10) ◽  
pp. 899-905 ◽  
Author(s):  
Alexandra C Walls ◽  
M Alejandra Tortorici ◽  
Brandon Frenz ◽  
Joost Snijder ◽  
Wentao Li ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Spike Protein ◽  
Cryo Electron Microscopy

scholarly journals Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation

2021 ◽  
Author(s):  
Xianding Deng ◽  
Miguel A Garcia-Knight ◽  
Mir M. Khalid ◽  
Venice Servellita ◽  
Candace Wang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Cell Cultures ◽  
Spike Protein ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Wild Type ◽  
Antibody Neutralization ◽  
Protein Mutation ◽  
Viral Shedding

AbstractWe identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.

scholarly journals Distinct evolution of infection-enhancing and neutralizing epitopes in the spike protein of SARS-CoV-2 variants (from alpha to omicron) : a structural and molecular epidemiology study

2021 ◽  
Author(s):  
Patrick GUERIN ◽  
Nouara YAHI ◽  
Fodil AZZAZ ◽  
Henri CHAHINIAN ◽  
Jean-Marc SABATIER ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Structural Dynamics ◽  
Neutralizing Antibodies ◽  
Mass Vaccination ◽  
Spike Protein ◽  
Epidemiology Study ◽  
Gamma Delta ◽  
Los Alamos ◽  
Terminal Domain ◽  
Neutralizing Epitopes

Abstract Infection-enhancing antibodies may limit the efficiency of Covid-19 vaccines. We analyzed the evolution ofneutralizing and facilitating epitopes in 1,860,489 SARS-CoV-2 genomes stored in the Los Alamos databasefrom June to November 2021. The structural dynamics of these epitopes was determined by molecular modelingof the spike protein on a representative panel of SARS-CoV-2 variants. D614, which belongs to an antibody-dependent-enhancement (ADE) epitope common to SARS-CoV-1 and SARS-CoV-2, has mutated to D614G in2020, which could explain why ADE has not been detected following mass vaccination. A second epitopelocated in the N-terminal domain (NTD), specific of SARS-CoV-2, is highly conserved among most variants. Incontrast, the neutralizing epitope of the NTD showed extensive variations in SARS-CoV-2 variants. The balancebetween facilitating and neutralizing antibodies is in favor of neutralization for the Wuhan strain, alpha and betavariants, but not for gamma, delta, lambda, and mu. The recently emerging omicron variant is atypic as itsmutational profiles affects both neutralization and ADE epitopes. Overall, our data reveal that the evolution ofSARS-CoV-2 has dramatically affected the ADE/neutralization balance. Future vaccines should consider thesefindings to design new formulations adapted to SARS-CoV-2 variants and lacking ADE epitopes in the spikeprotein.

scholarly journals Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants

2021 ◽  
Author(s):  
Shuo Du ◽  
Pulan Liu ◽  
Zhiying Zhang ◽  
Tianhe Xiao ◽  
Ayijiang Yasimayi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Monoclonal Antibodies ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Antibody Responses ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Humoral Antibody ◽  
Cryo Electron Microscopy ◽  
Antibody Cocktail

The spread of the SARS-CoV-2 variants could seriously dampen the global effort to tackle the COVID-19 pandemic. Recently, we investigated the humoral antibody responses of SARS-CoV-2 convalescent patients and vaccinees towards circulating variants, and identified a panel of monoclonal antibodies (mAbs) that could efficiently neutralize the B.1.351 (Beta) variant. Here we investigate how these mAbs target the B.1.351 spike protein using cryo-electron microscopy. In particular, we show that two superpotent mAbs, BD-812 and BD-836, have non-overlapping epitopes on the receptor-binding domain (RBD) of spike. Both block the interaction between RBD and the ACE2 receptor; and importantly, both remain fully efficacious towards the B.1.617.1 (Kappa) and B.1.617.2 (Delta) variants. The BD-812/BD-836 pair could thus serve as an ideal antibody cocktail against the SARS-CoV-2 VOCs.

scholarly journals Asumsi masyarakat mengenai keselamatan pasien pada masa covid 19 di rumah sakit

2020 ◽  
Author(s):  
Raudatun Hasanah
Keyword(s):  
Electron Microscopy ◽  
Membrane Protein ◽  
World Health Organization ◽  
Envelope Protein ◽  
Protein S ◽  
Spike Protein ◽  
World Health ◽  
Cryo Electron Microscopy ◽  
Health Organization

Rumah sakit sebagai sarana pelayanan kesehatan pada dasarnya adalah untuk menyelamatkan pasien, keselamatan pasien merupakan prioritas bagi pelaksanaan lima isu penting tentang keselamatan di rumah sakit, karena masalah keselamatan pasien berkaitan erat dengan kualitas dan citra rumah sakit itu sendiri. Perkembangan ilmu pengetahuan dan tekhnologi yang sedemikian pesat menyebabkan pelayanan kesehatan di rumah sakit menjadi sangat kompleks sehingga jika tidak dilakukan dengan benar dan hati-hati akan berpotensi untuk terjadinya Insiden Keselamatan Pasien (IKP) yang terdiri dari Kejadian Tidak Diharapkan (KTD), Kejadian Nyaris Cedera (KNC), Kejadian Tidak Cedera (KTC) dan Kondisi Potensial Cedera (KPC) (Depkes,2006).Setiap rumah sakit sudah diwajibkan untuk melakukan gerakan keselamatan pasien, apalagi PERSI sudah menerbitkan buku tentang pelaksanan keselamatan pasien di rumah sakit dan dalam waktu mendatang keselamatan pasien termasuk dalam penilaian akreditasi rumah sakit. Pada prinsipnya pelaksaan keselamatan pasien sesuai dengan standar departemen kesehatan, namun didalam pelaksanaan keselamatan pasien hampir sama pada setiap rumah sakit.Diawal tahun ini keselamatan pasien harus semakin ditingkatkan disebabkan munculnya virus covid 19 yang awalnya terjadi di Wuhan, provinsi Hubei, China dan dikaitkan dengan pasar binatang. Dalam rentang waktu satu bulan terjadi peningkatan kasus yang signifikan dan meluas ke beberapa provinsi di China, bahkan ke Jepang, Thailand dan Korea Selatan.satu Penyebaran penyakit yang begitu cepat serta meluas ke beberapa negara menyebabkan World Health Organization (WHO) akhirnya mengumumkan COVID-19 sebagai pandemi pada 12 Maret 2020. Virus corona berbentuk bulat dengan diameter sekitar 125 nm seperti yang digambarkan dalam penelitian menggunakan cryo-electron microscopy. Partikel virus corona mengandung empat protein struktural utama, yaitu protein S (spike protein) yang berbentuk seperti paku, protein M (membrane protein), protein E (envelope protein), dan protein N (nucleocapside protein). Protein S (~150 kda), protein M (~25– 30 kda), protein E (~8–12 kda) sedangkan protein N terdapat di dalam nukleokapsid.Virus corona merupakan zoonosis, sehingga terdapat kemungkinkan virus berasal dari hewan dan ditularkan ke manusia. Pada COVID-19 belum diketahui dengan pasti proses penularan dari Perkembangan data selanjutnya menunjukkan penularan antar manusia (human to human), yaitu diprediksi melalui droplet dan kontak dengan virus yang dikeluarkan dalam droplet. Penularan ini terjadi umumnya melalui droplet dan kontak dengan virus kemudian virus dapat masuk ke dalam mukosa yang terbuka. Suatu analisis mencoba mengukur laju penularan berdasarkan masa inkubasi, gejala dan durasi antara gejala dengan pasien yang diisolasi. Analisis tersebut mendapatkan hasil penularan dari 1 pasien ke sekitar 3 orang di sekitarnya, tetapi kemungkinan penularan di masa inkubasi menyebabkan masa kontak pasien ke orang sekitar lebih lama sehingga risiko jumlah kontak tertular dari 1 pasien mungkin dapat lebih besar.

Considerable escape of SARS-CoV-2 variant Omicron to antibody neutralization

2021 ◽  
Author(s):  
Delphine Planas ◽  
Nell Saunders ◽  
Piet Maes ◽  
Florence Guivel Benhassine ◽  
Cyril Planchais ◽  
...  
Keyword(s):  
South Africa ◽  
Monoclonal Antibodies ◽  
Receptor Binding ◽  
Binding Domain ◽  
Viral Fitness ◽  
Receptor Binding Domain ◽  
Antibody Neutralization ◽  
Neutralizing Activity ◽  
Terminal Domain ◽  
Therapeutic Monoclonal Antibodies

The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa. It has in the meantime spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of about 32 mutations in the Spike, located mostly in the N-terminal domain (NTD) and the receptor binding domain (RBD), which may enhance viral fitness and allow antibody evasion. Here, we isolated an infectious Omicron virus in Belgium, from a traveller returning from Egypt. We examined its sensitivity to 9 monoclonal antibodies (mAbs) clinically approved or in development, and to antibodies present in 90 sera from COVID-19 vaccine recipients or convalescent individuals. Omicron was totally or partially resistant to neutralization by all mAbs tested. Sera from Pfizer or AstraZeneca vaccine recipients, sampled 5 months after complete vaccination, barely inhibited Omicron. Sera from COVID-19 convalescent patients collected 6 or 12 months post symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titers 5 to 31 fold lower against Omicron than against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and to a large extent vaccine-elicited antibodies.

Cryo-Electron Microscopy of Aura Viruses

1998 ◽  
Vol 4 (S2) ◽  
pp. 946-947
Author(s):  
W. Zhang ◽  
N. H. Olson ◽  
B. R. McKinney ◽  
R. J. Kuhn ◽  
T. S. Baker
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Single Copy ◽  
Wild Type Virus ◽  
Genomic Rna ◽  
Wild Type ◽  
Subgenomic Rna ◽  
Enveloped Viruses ◽  
Virus Particles ◽  
Cryo Electron Microscopy

Alphaviruses are a group of enveloped viruses in the Togaviridae family. Studies of several alphaviruses, including Ross River, Sindbis and Semliki Forest viruses, by cryo-electron microscopy (cryo-EM), three-dimensional (3D) image resconstruction and other techniques have illustrated that these spherical viruses have a T=4, multi-layered structure.Aura virus, which is closely related to Sindbis, was first isolated in South America. Unlike the other alphaviruses, both genomic RNA (12kb, 49S) and subgenomic RNA(4.2kb, 26S) are encapsidated efficiently and form mature virions. Studies on negatively-stained virus particles demonstrated that there are two major size classes. The first contains particles of ∼72nm diameter, which are most similar to wild type virus, whereas the second class includes particles of ∼62nm in diameter. The 72nm particles are believed to have one copy of genomic RNA or one to three copies of subgenomic RNA, and a T=4 structure. The 62nm particles probably only have a single copy of subgenomic RNA and are presumed to be T=3 structures.

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