scholarly journals COVID-19 in Russia: Clinical and Immunological Features of the First-Wave Patients

Acta Naturae ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 102-115
Author(s):  
Tatiana V. Bobik ◽  
N. N. Kostin ◽  
G. A. Scriabin ◽  
P. N. Tsabai ◽  
M. A. Simonova ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Correlation Analysis ◽  
Occurrence Rate ◽  
Immunoglobulin Level ◽  
Specific Class ◽  
S Protein ◽  
Specific Antibodies ◽  
N Protein ◽  
Elisa Kit ◽  
Conformational Epitopes

The coronavirus disease outbreak in 2019 (COVID-19) has now achieved the level of a global pandemic and affected more than 100 million people on all five continents and caused over 2 million deaths. Russia is, needless to say, among the countries affected by SARS-CoV-2, and its health authorities have mobilized significant efforts and resources to fight the disease. The paper presents the result of a functional analysis of 155 patients in the Moscow Region who were examined at the Central Clinical Hospital of the Russian Academy of Sciences during the first wave of the pandemic (FebruaryJuly, 2020). The inclusion criteria were a positive PCR test and typical, computed tomographic findings of viral pneumonia in the form of ground-glass opacities. A clinical correlation analysis was performed in four groups of patients: (1) those who were not on mechanical ventilation, (2) those who were on mechanical ventilation, and (3) those who subsequently recovered or (4) died. The correlation analysis also considered confounding comorbidities (diabetes, metabolic syndrome, hypertension, etc.). The immunological status of the patients was examined (levels of immunoglobulins of the M, A, G classes and their subclasses, as well as the total immunoglobulin level) using an original SARS-CoV-2 antibody ELISA kit. The ELISA kit was developed using linear S-protein RBD-SD1 and NTD fragments, as well as the N-protein, as antigens. These antigens were produced in the prokaryotic E. coli system. Recombinant RBD produced in the eukaryotic CHO system (RBD CHO) was used as an antigen representing conformational RBD epitopes. The immunoglobulin A level was found to be the earliest serological criterion for the development of a SARS-CoV-2 infection and it yielded the best sensitivity and diagnostic significance of ELISA compared to that of class M immunoglobulin. We demonstrated that the seroconversion rate of early N-protein-specific IgM and IgA antibodies is comparable to that of antibodies specific to RBD conformational epitopes. At the same time, seroconversion of SARS-CoV-2 N-protein-specific class G immunoglobulins was significantly faster compared to that of other specific antibodies. Our findings suggest that the strong immunogenicity of the RBD fragment is for the most part associated with its conformational epitopes, while the linear RBD and NTD epitopes have the least immunogenicity. An analysis of the occurrence rate of SARS-CoV-2-specific immunoglobulins of different classes revealed that RBD- and N-specific antibodies should be evaluated in parallel to improve the sensitivity of ELISA. An analysis of the immunoglobulin subclass distribution in sera of seropositive patients revealed uniform induction of N-protein-specific IgG subclasses G1G4 and IgA subclasses A1A2 in groups of patients with varying severity of COVID-19. In the case of the S-protein, G1, G3, and A1 were the main subclasses of antibodies involved in the immune response.

scholarly journals An Optimized High-Throughput Neutralization Assay for Hepatitis E Virus (HEV) Involving Detection of Secreted Porf2

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 64 ◽  
Author(s):  
Chang Liu ◽  
Wei Cai ◽  
Xin Yin ◽  
Zimin Tang ◽  
Guiping Wen ◽  
...  
Keyword(s):  
High Throughput ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Neutralization Assay ◽  
The Novel ◽  
Specific Antibodies ◽  
Neutralizing Activity ◽  
Elisa Kit ◽  
Neutralizing Capacity ◽  
Potential Threshold

Hepatitis E virus (HEV) is a common cause of acute hepatitis worldwide. Current methods for evaluating the neutralizing activity of HEV-specific antibodies include immunofluorescence focus assays (IFAs) and real-time PCR, which are insensitive and operationally complicated. Here, we developed a high-throughput neutralization assay by measuring secreted pORF2 levels using an HEV antigen enzyme-linked immunosorbent assay (ELISA) kit based on the highly replicating HEV genotype (gt) 3 strain Kernow. We evaluated the neutralizing activity of HEV-specific antibodies and the sera of vaccinated individuals (n = 15) by traditional IFA and the novel assay simultaneously. A linear regression analysis shows that there is a high degree of correlation between the two assays. Furthermore, the anti-HEV IgG levels exhibited moderate correlation with the neutralizing titers of the sera of vaccinated individuals, indicating that immunization with gt 1 can protect against gt 3 Kernow infection. We then determined specificity of the novel assay and the potential threshold of neutralizing capacity using anti-HEV IgG positive sera (n = 27) and anti-HEV IgG negative sera (n = 23). The neutralizing capacity of anti-HEV IgG positive sera was significantly stronger than that of anti-HEV IgG negative. In addition, ROC curve analysis shows that the potential threshold of neutralizing capacity of sera was 8.07, and the sensitivity and specificity of the novel assay was 88.6% and 100%, respectively. Our results suggest that the neutralization assay using the antigen ELISA kit could be a useful tool for HEV clinical research.

scholarly journals Humoral Immunity and Adverse Events after Vaccination Against COVID-19 By a Vector Based Vaccine Sputnik V in Patients with Chronic Myeloid Leukemia

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4599-4599
Author(s):  
Ekaterina Yu. Chelysheva ◽  
Anna Petrova ◽  
Oleg A. Shukhov ◽  
Margarita Gurianova ◽  
Anastasiya Bykova ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Adverse Events ◽  
Myeloid Leukemia ◽  
Reverse Correlation ◽  
Molecular Response ◽  
Elderly Persons ◽  
S Protein ◽  
Specific Antibodies ◽  
Test Systems ◽  
Antibody Levels

Abstract Introduction Data on the effectiveness and safety of new vaccines against COVID-19 in patients (pts) with hematological diseases are just beginning to accumulate. We planned to obtain such information for pts with chronic myeloid leukemia (CML) during vaccination. Objective. To evaluate the antibodies formation and adverse events (AEs) after vaccination against COVID-19 in pts with CML Materials and methods. All pts with CML diagnosis who applied to the National Research Center for Hematology (NRCH, Moscow, Russia) for outpatient or remote consultations were suggested to prospectively report the AEs after getting a vaccination against COVID-19 by the most frequently used vector-based vaccine GamCovidVac (Sputnik V). Two vaccine components with the interval of 21 days were given at the vaccination facilities, as prescribed. At least after 3 weeks after the 2 nd injection, pts were advised to perform a blood test for the specific antibodies against spike (S) protein of SARS-CoV-2. A semi-quantitative test detecting the SARS-CoV-2 S1 subunit (RBD) IgG antibodies by enzyme-linked immunoassay (ELISA) kit was used in the clinic. The results were considered positive with the cutoff index >1,1. The use of any other lab tests detecting antibodies to S protein of SARS-CoV-2 was acceptable as well. Results. In total, 66 pts with chronic phase of CML received a vaccination by Sputnik V in the 7 months period (from 18.12.2020 to 20.07.2021). Me age was 54 years (range 29 - 89 years), 34 (52%) were males. Median (Me) CML duration was 8 years (from the moment of diagnostics up to 20 years). Fifty one (77%) pt received TKI therapy and 15 (23%) were off-therapy at the time of vaccination, including 12 (18%) in a treatment-free remission and 3 (4,5%) pts in the process of diagnosis. Deep and major molecular response (MMR) was in 46 (70%) and 7 (11%) pts, respectively. Two (3%) pts had a molecular response MR2, 11 (17%) had no MR2. Eight (12%) pts had a history of COVID-19 manifestation prior to vaccination. Me time for testing for the antibodies was 27 days (range 5-77) after the 2 nd vaccine injection. The tests were done in 44 (67%) of pts and revealed positive by any of the test systems in 42 (95%) pts. ELISA test was used in 30 (45%) pts and was positive in 25 (83%) of 30 pts. Me cutoff index in the positive samples was 7,7 (range 1,1 - 12) and corresponded to the value observed in healthy people after vaccination (medical stuff, data not shown). In all 3 pts with the history COVID 19, the index of positivity was above the Me value (Fig. 1, 2). Other test systems were used in 14 (21%) pts, in all 14 (100%) the antibodies were found. In 3 of 5 patients with the cutoff index<1 the antibodies were detected by using other test systems, but all with a level slightly above the detection threshold. Me age of these 5 pts was 63 years (range 59- 70), Me time of analysis was 49 days (range 23-59) after 2 nd vaccine shot. All these pts were on treatment by tyrosine kinase inhibitors, 3 pts with MMR and deeper, 1 pt with MR2 and 1 pt without MR2. A weak reverse correlation of the antibody levels with the time after vaccination was noted ( r = - 0,39, p = 0,033). A very weak reverse correlation with age was observed ( r = - 0,28, p = 0,127) (Fig. 1, 2). No AEs after the vaccination were observed in 25 (38%) pts while 41 (62%) pts reported the AEs and 7 (10%) pts did not report their reactions. The AEs were as follows: local pain/discomfort in the injection site in 19 (29%) pts, weakness and/or drowsiness in 20 (30%), fever and/or chills in 16 (24%), other reactions in 8 (12%) including headache, heartbeat, lower back pain, pain in limbs, activation of herpes infection. Conclusion: The single center study revealed no unusual or unexpected AEs in CML pts after the vaccination against COVID-19 by Sputnik V vaccine. The proportion of CML pts with specific antibodies after was 95% which is close to the published results of the 3rd phase study. No significant correlation was found with age (r = -0,28, p = 0,127), however, the absence or very low antibody levels were detected in individual patients aged about 60-70 years. This data raise a question of a necessity for a non-specific protection (masks, respirators, distance etc) and probably considering additional vaccination in some elderly persons. The duration of a humoral response against COVID-19, protective antibody titer and connection with clinical outcomes in CML pts need further evaluation in parallel with a common population. Figure 1 Figure 1. Disclosures Chelysheva: Pfizer: Speakers Bureau; Pharmstandart: Speakers Bureau; Bristol Myers Squibb: Speakers Bureau; Novartis Pharma: Speakers Bureau. Petrova: Pfizer: Speakers Bureau; Novartis Pharma: Speakers Bureau. Gurianova: Pfizer: Speakers Bureau. Turkina: Pharmstandart: Speakers Bureau; Pfizer: Speakers Bureau; Novartis Pharma: Speakers Bureau; Bristol Myers Squibb: Speakers Bureau.

scholarly journals Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

2021 ◽  
Author(s):  
Jasdeep Singh ◽  
Nasreen Z. Ehtesham ◽  
Syed Asad Rahman ◽  
Seyed E. Hasnain
Keyword(s):  
Central China ◽  
Structural Proteins ◽  
Structural Function ◽  
Upper Respiratory Tract ◽  
E Proteins ◽  
Gene Target ◽  
S Protein ◽  
N Protein ◽  
Synonymous Mutations ◽  
South East England

AbstractThe SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 and nucleocapsid (N) protein of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2.SummarySince initial outbreak of COVID-19 in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N), membrane (M), and envelope (E) proteins. The S protein mediates initial contacts with human hosts while the E and M proteins function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein (Clade G), G251V in ORF3a (Clade V) and L84S in ORF 8 (Clade S) were observed [2–4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness [5, 6]. As per latest WHO reports on COVID-19, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise in COVID-19 detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.

scholarly journals Potential immune epitope map for structural proteins of SARS-CoV-2

2020 ◽  
Author(s):  
Yengkhom Damayanti Devi ◽  
Himanshu Ballav Goswami ◽  
Sushmita Konwar ◽  
Chandrima Doley ◽  
Anutee Dolley ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
Cell Epitope ◽  
Class I ◽  
Structural Proteins ◽  
S Protein ◽  
N Protein ◽  
B Cell Epitope

Abstract Researchers around the world are developing more than 145 vaccines (DNA/mRNA/whole-virus/viral-vector/protein-based/repurposed vaccine) against the SARS-CoV-2 and 21 vaccines are in human trials. However, a limited information is available about which SARS-CoV-2 proteins are recognized by human B- and T-cell immune responses. Using a comprehensive computational prediction algorithm and stringent selection criteria, we have predicted and identified potent B- and T-cell epitopes in the structural proteins of SARS-CoV and SARS-CoV-2. The amino acid residues spanning the predicted linear B-cell epitope in the RBD of S protein (370-NSASFSTFKCYGVSPTKLNDLCFTNV-395) have recently been identified for interaction with the CR3022, a previously described neutralizing antibody known to neutralize SARS-CoV-2 through binding to the RBD of the S protein. Intriguingly, most of the amino acid residues spanning the predicted B-cell epitope (aa 331-NITNLCPFGEVFNATRFASVYAWNRK-356, 403-RGDEVRQIAPGQTGKIADYNYKLPD-427 and aa 437- NSNNLDSKVGGNYNYLYRLFRKSNL-461) of the S protein have been experimentally verified to interact with the cross-neutralizing mAbs (S309 and CB6) in an ACE2 receptor-S protein interaction independent-manner. In addition, we found that computationally predicted epitope of S protein (370-395) is likely to function as both linear B-cell and MHC class II epitope. Similarly, 403-27 and 437-461 peptides of S protein were predicted as linear B cell and MHC class I epitope while, 177-196 and 1253-1273 peptides of S protein were predicted as linear and conformational B cell epitope. We found MHC class I epitope 316-GMSRIGMEV-324 predicted as high affinity epitope (HLA-A*02:03, HLA-A*02:01, HLA-A*02:06) common to N protein of both SARS-CoV-2 and SARS-CoV (N317-325) was previously shown to induce interferon-gamma (IFN-γ) in PBMCs of SARS-recovered patients. Interestingly, two MHC class I epitopes, 1041-GVVFLHVTY-1049 (HLA-A*11:01, HLA-A*68:01, HLA-A*03:01) and 1202-FIAGLIAIV-1210 (HLA-A*02:06, HLA-A*68:02) derived from SARS-CoV S protein with epitope conservancy between 85 to 100% with S protein of SARS-CoV-2 was experimentally verified using PBMCs derived from SARS-CoV patients. We observed that HLA-A*02:01, HLA-A*02:03, HLA-A*02:06, HLA-A*11:01, HLA-A*30:01, HLA-A*68:01, HLA-A*68:02, HLA-B*15:01 and HLA-B*35:01 have been predicted to bind to the maximum number of MHC class I epitope (based on the criterion of allele predicted to bind more than 30 epitopes) of S protein of SARS-CoV-2. Similarly, we observed that HLA-A*02:06, HLA-A*30:01, HLA-A*30:02, HLA-A*31:01, HLA-A*32:01, HLA-A*68:01, HLA-A*68:02, HLA-B*15:01 and HLA-B*35:01 are predicted to bind to the maximum number of MHC class I epitope of N protein of SARS-CoV-2. We found that HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DRB5*01:01, HLA-DQA1*04:01, DQB1*04:02, HLA-DPA1*02:01, DPB1*01:01, HLA-DPA1*01:03, DPB1*02:01, HLA-DPA1*01:03, DPB1*04:01, HLA-DPA1*03:01, DPB1*04:02, HLA-DPA1*02:01, DPB1*05:01, HLA-DPA1*02:01, and DPB1*14:01 are predicted to bind to the maximum number of MHC class II epitope of S protein of SARS-CoV-2. Alleles such as HLA-DRB1*04:01, HLA-DRB1*07:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DRB1*11:01, HLA-DRB1*13:02, HLA-DRB3*02:02, HLA-DRB5*01:01, HLA-DQA1*01:02, DQB1*06:02, DPB1*05:01 and HLA-DPA1*02:01 are found to interact with the maximum number of MHC class II epitope of N protein of SARS-CoV-2. Using the IEDB tool we found the occurrence of HLA alleles with population coverage of around 99% throughout the world. The findings of computational predictions of mega-pool of B- and T-cell epitopes identified in the four main structural proteins of SARS-CoV-2 provides a platform for future experimental validations and the results of present works support the use of RBD or the full-length S and N proteins in an effort towards designing of recombinant protein-based vaccine and a serological diagnostic assay for SARS-CoV-2.

scholarly journals COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning

2020 ◽  
Author(s):  
Edison Ong ◽  
Mei U Wong ◽  
Anthony Huffman ◽  
Yongqun He
Keyword(s):  
Machine Learning ◽  
Vaccine Development ◽  
Reverse Vaccinology ◽  
T Cell Epitopes ◽  
Mhc I ◽  
S Protein ◽  
N Protein ◽  
Mhc Ii ◽  
Human Coronaviruses ◽  
New Strategies

AbstractTo ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that the whole virus, as well as the spike (S) protein, nucleocapsid (N) protein, and membrane protein, have been tested for vaccine development against SARS and MERS. We further used the Vaxign reverse vaccinology tool and the newly developed Vaxign-ML machine learning tool to predict COVID-19 vaccine candidates. The N protein was found to be conserved in the more pathogenic strains (SARS/MERS/COVID-19), but not in the other human coronaviruses that mostly cause mild symptoms. By investigating the entire proteome of SARS-CoV-2, six proteins, including the S protein and five non-structural proteins (nsp3, 3CL-pro, and nsp8-10) were predicted to be adhesins, which are crucial to the viral adhering and host invasion. The S, nsp3, and nsp8 proteins were also predicted by Vaxign-ML to induce high protective antigenicity. Besides the commonly used S protein, the nsp3 protein has not been tested in any coronavirus vaccine studies and was selected for further investigation. The nsp3 was found to be more conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV than among 15 coronaviruses infecting human and other animals. The protein was also predicted to contain promiscuous MHC-I and MHC-II T-cell epitopes, and linear B-cell epitopes localized in specific locations and functional domains of the protein. Our predicted vaccine targets provide new strategies for effective and safe COVID-19 vaccine development.

Exploring the COVID-19 Potential Targets: Big Challenges to Quest Specific Treatment

2021 ◽  
Vol 21 ◽  
Author(s):  
Harekrishna Roy ◽  
Asha Gummadi ◽  
Bhabani Shankar Nayak ◽  
Sisir Nandi ◽  
Anil Kumar Saxena
Keyword(s):  
Host Cell ◽  
Viral Genome ◽  
Specific Treatment ◽  
Viral Gene Expression ◽  
Protein S ◽  
Complete Recovery ◽  
Viral Gene ◽  
S Protein ◽  
N Protein ◽  
Terminal Domain

Background: The novel strain SARS-CoV-2 of coronavirus diseases (COVID-19) became pandemic in end of 2019 with an unprecedented global crisis by infecting around 11 million people in more than 200 countries. The condition has now been provoked by the demand, supply, and liquidity shocks that COVID-19 has attacked lives of an incredible population. Objective: Therefore, researchers are trying to encode and understand the viral genome sequence along with various potential targets to explore the transmission mechanism and the mode of treatment for COVID-19. The important structural proteins such as nucleocapsid protein (N), membrane protein (M), an envelope protein (E), and spike protein (S) related to covid-19 are discussed in this manuscript. Methods: The topology of these various targets has been explored utilizing structure-based design and crystallographic studies. Results: The literature reported that the N protein process viral genome to the host cell during replication. The “N terminal domain” and “C terminal domain” contribute towards the localization in the endoplasmic region and dimerization respectively. The M protein determines the shape of coronavirus and also assists the S protein to integrate with the Golgi-endoplasmic region complex leading to the stabilization of the virion. The smallest hydrophobic viroporin termed “E” takes part in morphogenesis and pathogenesis during intracellular infection. The viral spike (S) protein attaches the cellular receptors and initiates virus-cell membrane fusions. The main protease in the proteolytic process during viral gene expression and replication has also been discussed. Conclusion: Currently there is no permanent cure and treatment of COVID-19 hence researchers are repurposing the suitable combination of drugs including antiviral, antimalarial, antiparasitic, and antibacterial, hypertensive receptor blockers, immunosuppressant, anti-arthritis drug, including ayurvedic formulations. In brief, it is justified that, for complete recovery, there is a need for deep and elaborate studies on genomic sequences and invading mechanisms in the host cell.

scholarly journals Analyses of Coronavirus Assembly Interactions with Interspecies Membrane and Nucleocapsid Protein Chimeras

2016 ◽  
Vol 90 (9) ◽  
pp. 4357-4368 ◽  
Author(s):  
Lili Kuo ◽  
Kelley R. Hurst-Hess ◽  
Cheri A. Koetzner ◽  
Paul S. Masters
Keyword(s):  
Nucleocapsid Protein ◽  
Hepatitis Virus ◽  
Virus Assembly ◽  
Mouse Hepatitis Virus ◽  
M Protein ◽  
Growth Defect ◽  
S Protein ◽  
N Protein ◽  
Protein Incorporation ◽  
Carboxy Terminal

ABSTRACTThe coronavirus membrane (M) protein is the central actor in virion morphogenesis. M organizes the components of the viral membrane, and interactions of M with itself and with the nucleocapsid (N) protein drive virus assembly and budding. In order to further define M-M and M-N interactions, we constructed mutants of the model coronavirus mouse hepatitis virus (MHV) in which all or part of the M protein was replaced by its phylogenetically divergent counterpart from severe acute respiratory syndrome coronavirus (SARS-CoV). We were able to obtain viable chimeras containing the entire SARS-CoV M protein as well as mutants with intramolecular substitutions that partitioned M protein at the boundaries between the ectodomain, transmembrane domains, or endodomain. Our results show that the carboxy-terminal domain of N protein, N3, is necessary and sufficient for interaction with M protein. However, despite some previous genetic and biochemical evidence that mapped interactions with N to the carboxy terminus of M, it was not possible to define a short linear region of M protein sufficient for assembly with N. Thus, interactions with N protein likely involve multiple linearly discontiguous regions of the M endodomain. The SARS-CoV M chimera exhibited a conditional growth defect that was partially suppressed by mutations in the envelope (E) protein. Moreover, virions of the M chimera were markedly deficient in spike (S) protein incorporation. These findings suggest that the interactions of M protein with both E and S protein are more complex than previously thought.IMPORTANCEThe assembly of coronavirus virions entails concerted interactions among the viral structural proteins and the RNA genome. One strategy to study this process is through construction of interspecies chimeras that preserve or disrupt particular inter- or intramolecular associations. In this work, we replaced the membrane (M) protein of the model coronavirus mouse hepatitis virus with its counterpart from a heterologous coronavirus. The results clarify our understanding of the interaction between the coronavirus M protein and the nucleocapsid protein. At the same time, they reveal unanticipated complexities in the interactions of M with the viral spike and envelope proteins.

scholarly journals Circulating anti-SARS-CoV-2 nucleocapsid (N)-protein antibodies and anti-SARS-CoV-2 spike (S)-protein antibodies in an African setting: herd immunity, not there yet!

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amandine Mveang Nzoghe ◽  
Marielle Leboueny ◽  
Eliane Kuissi Kamgaing ◽  
Anicet Christel Maloupazoa Siawaya ◽  
Eliode Cyrien Bongho ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Total Population ◽  
Herd Immunity ◽  
Humoral Response ◽  
S Protein ◽  
N Protein ◽  
African Context ◽  
African Setting

Abstract Objective Herd immunity is achieved when in a population, immune individuals are in a sufficiently large proportion. Neutralizing antibodies specific to SARS-CoV-2 that are produced following infection or vaccination are critical for controlling the spread of COVID-19. The objective of the present work was to investigate the rate of SARS-CoV-2 natural immunization in Gabonese. Results One thousand, four hundred and ninety two people were enrolled. The overall prevalence of anti-SARS-CoV-2 antibodies was 36.2%. Moreover, 76.4% of people who developed a humoral response to SARS-CoV-2 produced both anti-SARS-CoV-2 N-protein antibodies and anti-SARS-CoV-2 S-protein antibodies, which correspond to 27.7% of the total population. In infants (0–9 month), children (1–17 years) and adults, the prevalence of anti-SARS-CoV-2 antibodies was relatively the same, between 33 and 37% (any antibody types) and between 25 and 28.6% (neutralizing antibodies). In this African context, one-third (1/3) of the screened population was exposed to SARS-CoV-2 and three-quarter (3/4) of those exposed individuals developed neutralizing antibodies against SARS-CoV-2. This data suggest that herd immunity is not yet to be achieved in Gabon.

scholarly journals Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins

2020 ◽  
Author(s):  
Yuejun Shi ◽  
Jiale Shi ◽  
Limeng Sun ◽  
Yubei Tan ◽  
Gang Wang ◽  
...  
Keyword(s):  
Public Health ◽  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Neutralizing Antibody ◽  
Immune Recognition ◽  
Global Public Health ◽  
S Protein ◽  
Specific Antibodies ◽  
Major Target

AbstractCoronaviruses that infect humans belong to the Alpha-coronavirus (including HCoV-229E) and Beta-coronavirus (including SARS-CoV and SARS-CoV-2) genera. In particular, SARS-CoV-2 is currently a major threat to public health worldwide. However, no commercial vaccines against the coronaviruses that can infect humans are available. The spike (S) homotrimers bind to their receptors through the receptor-binding domain (RBD), which is believed to be a major target to block viral entry. In this study, we selected Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) as models. Their RBDs were observed to adopt two different conformational states (lying or standing). Then, structural and immunological analyses were used to explore differences in the immune response with RBDs among these coronaviruses. Our results showed that more RBD-specific antibodies were induced by the S trimer with the RBD in the “standing” state (SARS-CoV and SARS-CoV-2) than the S trimer with the RBD in the “lying” state (HCoV-229E), and the affinity between the RBD-specific antibodies and S trimer was also higher in the SARS-CoV and SARS-CoV-2. In addition, we found that the ability of the HCoV-229E RBD to induce neutralizing antibodies was much lower and the intact and stable S1 subunit was essential for producing efficient neutralizing antibodies against HCoV-229E. Importantly, our results reveal different vaccine strategies for coronaviruses, and S-trimer is better than RBD as a target for vaccine development in Alpha-coronavirus. Our findings will provide important implications for future development of coronavirus vaccines.ImportanceOutbreak of coronaviruses, especially SARS-CoV-2, poses a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority. Coronavirus spike (S) protein is considered as a major target for vaccine development. Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. Here, we tested the ability of S-trimer and RBD to induce neutralizing antibodies among these coronaviruses. Our results showed that Beta-CoVs RBDs are in a standing state, and their S proteins can induce more neutralizing antibodies targeting RBD. However, HCoV-229E RBD is in a lying state, and its S protein induces a low level of neutralizing antibody targeting RBD. Our results indicate that Alpha-coronavirus is more conducive to escape host immune recognition, and also provide novel ideas for the development of vaccines targeting S protein.

scholarly journals Comparative analysis of antigen-specific anti-SARS-CoV-2 antibody isotypes in COVID-19 patients

2020 ◽  
Author(s):  
Hidetsugu Fujigaki ◽  
Masato Inaba ◽  
Michiko Osawa ◽  
Saya Moriyama ◽  
Yoshimasa Takahashi ◽  
...  
Keyword(s):  
Specific Antibody ◽  
Serological Test ◽  
Polymerase Chain Reaction Test ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serological Tests ◽  
S Protein ◽  
Neutralizing Activity ◽  
N Protein ◽  
Specificity And Sensitivity ◽  
Antibody Isotypes

AbstractSerological tests for detection of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in blood are expected to identify individuals who have acquired immunity against SARS-CoV-2 and indication of seroprevalence of SARS-CoV-2 infection. Many serological tests have been developed to detect antibodies against SARS-CoV-2. However, these tests have considerable variations in their specificity and sensitivity, and whether they can predict levels of neutralizing activity is yet to be determined. This study aimed to investigate the kinetics and neutralizing activity of various antigen-specific antibody isotypes against SARS-CoV-2 in serum of coronavirus disease 2019 (COVID-19) patients confirmed via polymerase chain reaction test. We developed IgG, IgM and IgA measurement assays for each antigen, including receptor-binding domain (RBD) of spike (S) protein, S1 domain, full length S protein, S trimer and nucleocapsid (N) domain, based on enzyme-linked immunosorbent assay. The assays of the S protein for all isotypes showed high specificity, while the assays for all isotypes against N protein showed lower specificity. The sensitivity of all antigen-specific antibody isotypes depended on the timing of the serum collection and all of them, except for IgM against N protein, reached more than 90% at 15-21 days post-symptom onset. The best correlation with virus neutralizing activity was found for IgG against RBD (RBD-IgG), and levels of RBD-IgG in sera from four severe COVID-19 patients increased concordantly with neutralizing activity. Our results provide valuable information regarding the selection of serological test for seroprevalence and vaccine evaluation studies.

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