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Introduction: Covid-19 epidemic results from an infection caused by SARS-CoV2. Evolution-based analyses on the nucleotide sequences show that SARS-CoV2 is a member of the genus Beta-coronaviruses and its genome consists of a single-stranded RNA, encoding 16 proteins. Among the structural proteins, the nucleocapsid is the most abundant protein in virus structure, highly immunogenic, with sequence conservatory. Due to a large number of mutations in the spike protein, the aim of this study was to investigate bioinformatics, expression of nucleocapsid protein and evaluate its immunogenicity as an immunogenic candidate. Materials and Methods: B and T cell epitopes of nucleocapsid protein were examined in the IEDB database. The PET28a-N plasmid was transferred to E. coli BL21(DE3) expression host, and IPTG induced recombinant protein expression. The protein was purified using Ni-NTA column affinity chromatography, and the Western blotting method was utilized to confirm it. Finally, mice were immunized with three routes of purified protein. Statistical analysis of the control group injection and test results was carried out by t-test from SPSS software. Results: The optimized gene had a Codon adaptation index (CAI) of 0/97 Percentage of codons having high- frequency distribution was improved to 85%. Expression of recombinant protein in E. coli led to the production of BoNT/B-HCC with a molecular weight of 45 kDa. The total yield of purified protein was 43 mg/L. Immunization of mice induced serum antibody response. Statistical analysis showed that the antibody titer ratio was significantly different compared to the control sample and the antibody titer was acceptable up to a dilution of 1.256000. Conclusion: According to the present study results, the protein can be used as an immunogenic candidate for developing vaccines against SARS-CoV2 in future research.
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Of various SARS-CoV-2 variants, some have drawn special concern or interest because of their heightened disease threat. The mutability of individual SARS-CoV-2 genes/proteins presumably varies. The present study quantified gene/protein mutations in 13 major SARS-CoV-2 variants of concern/interest, and analyzed viral protein antigenicity using bioinformatics. The results from 187 carefully perused genome clones showed significantly higher mean percent mutations in the spike, ORF8, nucleocapsid, and NSP6 than in other viral proteins. The ORF8 and spike proteins also tolerated higher maximal percent mutations. The omicron variant presented more percent mutations in the NSP6 and structural proteins, whereas the delta featured more in the ORF7a. Omicron subvariant BA.2 exhibited more mutations in ORF6, and omicron BA.4 had more in NSP1, ORF6, and ORF7b, relative to omicron BA.1. Delta subvariants AY.4 and AY.5 bore more mutations in ORF7b and ORF8 than delta B.1.617.2. Predicted antigen ratios of SARS-CoV-2 proteins significantly vary (range: 38-88%). To overcome SARS-CoV-2 immune evasion, the relatively conserved, potentially immunogenic NSP4, NSP13, NSP14, membrane, and ORF3a viral proteins may serve as more suitable targets for molecular vaccines or therapeutics than the mutation-prone NSP6, spike, ORF8, or nucleocapsid protein. Further investigation into distinct mutations of the variants/subvariants may help understand SARS-CoV-2 pathogenesis.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Antigens, Viral , Mutation , Spike Glycoprotein, Coronavirus/geneticsABSTRACT
The aim of this study was to clone, express and identify the truncated S1 gene of nephrotropic infectious bronchitis virus (IBV) and granulocyte-monocyte colony stimulating factor (GM-CSF) of chicken. Firstly, two genes were amplified by polymerase chain reaction (PCR) and cloned into pMD18-T vector. The truncated S1 gene designated as Sf200 containing five antigenic sites of S1 glycoprotein on amino acid residues (aa) 24-61, (aa) 291-398 and (aa) 497-543 and GM-CSF were then amplified from the respective recombinant pMD18-T plasmids and cloned into pET-32a (+) vector resulting pET-Sf200, pET-GM which were identified by restriction enzyme digestion and sequencing analysis. The in vitro expression of truncated Sf200 and GM-CSF constructs were later expressed in E. coli BL21 with a molecular mass of approximately 38 kDa and 29 kDa respectively as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. Polyclonal antibodies were developed by injecting E. coli expressed Sf200 and GM-CSF into the SPF mice and were used to identify the recombinant proteins by Western blot analysis. These findings indicated that the polyclonal antibodies produced in mice could be used to detect the recombinant truncated Sf200 and GM-CSF and vice versa.
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Intro: The COVID-19 pandemic is caused by the SARS-CoV-2 virus, an enveloped RNA of the coronavirus family. The advancement in molecular technology and biochemistry has accelerated the development of diagnostic reagents and assays. Much attention has been focused on the S protein, but the high mutation rate in this region could lead to false negative results. Thus, a better target protein for diagnostic application is needed for accurate detection. Method(s): Nucleotide sequences encoded for membrane (M) glycoprotein gene region of SARS-CoV-2 from Malaysian isolates were extracted from GISAID, aligned, and selected accordingly. The DNA plasmid was commercially synthesized with codon optimization for Escherichia coli (E. coli), and the presence of the M gene was confirmed by PCR. The plasmid was then transformed into E. coli. Later, the expression of M glycoprotein was induced, separated on an SDS-PAGE gel, and transferred onto a nitrocellulose membrane, followed by immunostaining. Finding(s): The analysis of the M glycoprotein against the Omicron strains demonstrated that the amino acid is conserved (99.5%). The M glycoprotein was successfully expressed and detected with antibodies from SARS-CoV-2 infected patients at ~26 kDa. The protein is currently upscale for the generation of monoclonal Ab (Mab). Discussion(s): The M protein of SARS-CoV-2 is more conserved among the virus and also has been reported to confer antigenic properties. Selection of M protein perhaps a better option compared to current detection assays that use spike (S) protein, which could lead to false negative results, as this gene region particularly the ribosome-binding domain (RBD) rapidly undergoes mutations. The utilization of M protein potentially improves negative predictive value (NPV) of the diagnostic test. Conclusion(s): Further development of diagnostic reagents is needed to improve the assay's specificity. The newly developed M protein and the MAb can be used to generate a more accurate viral detection assay.Copyright © 2023
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Backgrounds: Although conventional therapies have played an essential role in the treatment of many diseases, emerging diseases require new treatment methods with less complications. Therefore, it is important to develop an effective vaccine for infections caused by the coronavirus to prevent mortality and create immunity the community. Material(s) and Method(s): In this research bioinformatics tools were used to design a vaccine against the M membrane protein of SARS-CoV-2. A total of 27 epitopes confined to B cells and MHC I and II alleles were structurally constructed in M protein for immune stimulation and antibody recognition which were used in the construction of a chimeric peptide vaccine. Finding(s): The vaccine was predicted to be a stable, antigenic, and non-allergenic compound. TRL5/vaccine complex analysis and docking simulation indicated a sufficiently stable binding with appropriated receptor activation. The immune response simulation following hypothetical immunization indicated the potential of this vaccine to stimulate the production of active and memory B cells, CD8 + T and, CD4 + T cells, and effective immunological responses induced by Th2 and Th1. Conclusion(s): The analysis of in-silico processes showed that the vaccine structure induced high antigenicity and good cellular immunity in the host body and stimulates various immune receptors such as TLR5, MHC I, and MHC II. Vaccine function was also associated with an increase in IgM and IgG antibodies and a set of Th1 and Th2 cytokines. But the final confirmation of the effectiveness of the designed vaccine requires clinical processes.Copyright © 2022, TMU Press.
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Case Report: Cryptococcosis is an opportunistic infection caused by the encapsulated yeast Cryptococcus, with C. neoformans and C. gattii being the most common species to cause human disease. Immunocompromised individuals are predisposed to infections with C. neoformans, which has known predilection to CNS and pulmonary lymph nodes. We present a unique case of disseminated cryptococcosis in the setting of end-stage renal disease (ESRD), cirrhosis, tumor necrosis factor inhibitor use and steroid use for COVID19. Method(s): A single-patient case report was conducted after IRB approval. Case Presentation: A 55-year-old woman with uncontrolled diabetes, lupus, rheumatoid arthritis on adalimumab, hepatitis C status post boceprevir, cirrhosis, former IV drug use, and ESRD on hemodialysis via bovine arterial-venous fistula graft presented with worsening dyspnea, cough, and altered mental status. Three months prior, patient was admitted to an outside hospital for COVID19, complicated by pulmonary embolism status post anticoagulation therapy. Patient was treated with an unknown steroid regimen, which was continued by a second outside facility when symptoms failed to improve. Patient then presented to our facility 24 hours after discharge due to continued symptoms. On admission, patient was noted to have altered mentation and hypoxia with pulmonary edema on chest x-ray and was urgently hemodialyzed. Further work-up was obtained due to non-resolving symptoms, including blood and sputum cultures, cocci serology and QuantiFERON gold. CT chest revealed bilateral consolidations. Patient was started on antibiotics for presumed hospital-acquired pneumonia. During the hospital stay, preliminarily blood cultures grew yeast and patient was started on Micafungin. However, Micafungin was changed to Liposomal Amphotericin B as ovoid structures seen on gram stain could not confirm nor rule out cryptococcus. Subsequent bronchial wash and bronchoalveolar lavage cultures, as well as final blood cultures resulted Cryptococcus neoformans. Serum cryptococcus antigen returned reactive, titer 1:512. Antibiotics were discontinued and Isavuconazonium was started with Liposomal Amphotericin B. Due to recurrent headaches, lumbar puncture was obtained and revealed lymphocytic pleocytosis without cryptococcal antigenicity. Patient completed 14 days of Liposomal Amphotericin B and Isavuconazole with continuation of Isavuconazole upon discharge. Conclusion(s): Disseminated cryptococcosis in non-HIV patients is rare in the modern HIV era. Clinicians should be aware and include it in their differential of any patient with multiple risk factors for opportunistic infection. In patients with cirrhosis and ESRD, treatment is limited given altered pharmacokinetics. Studies have shown improved survival with the addition of Isavuconazole in patients with disseminated cryptococcosis with CNS involvement in the setting of chronic liver disease and ESRD.
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BACKGROUND: SARS-CoV-2 infection was an unprecedented pandemic with unprecedented global health and socio-economic impact. More than 13 million cases had been confirmed in Spain by August 2022, and diagnostic testing to detect cases of infection in the country has helped to partially mitigate the spread of the virus. In 2021, the first self-testing antigen tests were marketed for dispensing in community pharmacies, and over-the-counter dispensing was allowed from July of that year. The network of community pharmacies played a key role, not only in the informed dispensing of these tests, but also in actively participating in the performance, supervision and reporting of results to the health authorities, and even in the issuing of digital certificates. A compilation has been made of all the available data on the subject, with a deadline of 13 February 2022, which is considered to be the end of the sixth wave of the epidemic in Spain. The results of the action taken by community pharmacies in twelve Autonomous Communities, which somehow participated in these initiatives by carrying out or supervising a total of 1,043,800 tests, from which 109,570 positive cases (10.5% of the total) were detected and reported to the National Health System, are presented in this article. Although the results are provisional, because many of the programmes are still ongoing, they are a clear demonstration of the potential that community pharmacies can play in Public Health work.
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Infectious bronchitis virus (IBV) has evolved through various mutation mechanisms, including antigenic drift and recombination. Four genotypic lineages of IBVs including GI-15, GI-16, GI-19, and GVI-1 have been reported in Korea. In this study, we isolated two IBVs from chicken farms, designated IBV/Korea/289/2019 (K289/19) and IBV/Korea/163/2021 (K163/21), which are two distinct natural recombinant viruses most likely produced by genetic reassortment between the S1 gene of K40/09 strain (GI-19 lineage) and IBV/Korea/48/2020 (GI-15 lineage) in co-infected commercial chickens. Comparative sequence analysis of hypervariable regions (HVRs) revealed that the K289/19 virus had similar HVR I and II with the K40/09 virus (100% and 99.2% nucleotide sequence identity, respectively), and HVR III with the IBV/Korea/48/2020 virus (100% nucleotide sequence identity). In contrast, the K163/21 virus had HVR I and II similar to the IBV/Korea/48/2020 virus (99.1% and 99.3% nucleotide sequence identity, respectively), and HVR III to the K40/09 virus (96.6% nucleotide sequence identity). The K289/19 virus exhibited similar histopathologic lesions, tissue tropism in trachea and kidney, and antigenicity with the parental K40/09 virus. The K163/21 exhibited similar pathogenicity and tissue tropism with the K40/09 virus, which were similar results with the isolate K289/19. However, it showed a lower antigenic relatedness with both parental strains, exhibiting R-value of 25 and 42, respectively. The continued emergence of the novel reassortant IBVs suggests that multiple recombination events have occurred between different genotypes within Korea. These results suggest that antigenic profiles could be altered through natural recombination in the field, complicating the antigenic match of vaccine strains to field strains. Enhanced surveillance and research into the characteristics of newly emerging IBVs should be carried out to establish effective countermeasures.
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The most significant single nucleotide human leukocyte antigen genes polymorphisms and innate immunity genes associated with varying degrees of acute respiratory infection severity are considered-COVID-19 caused by the SARS-CoV-2 coronavirus. As data accumulated, it became clear that the SARS-CoV-2 virus exhibits significant regional, ethnic, and individual specificity. This is due to the population groups' genetic characteristics. This is necessary to reliably know the human genotype relationship with the COVID-19 course severity (asymptomatic, mild, moderate, severe, and extremely severe up to fatal outcomes) for more successful therapy and vaccination. At the same time, it was also known that the innate immunity system is on the first line of defense against the pathogenic penetration into the body, and the human leukocyte antigen system encodes molecules of the same name on the surface of cells that present various antigens, including viral infection pathogens, and determine the severity of the course of many diseases;therefore, these systems' genes. This approach makes it possible to assess the likelihood of a severe and extremely severe disease course in healthy and infected people, which in turn contributes to the correct therapy strategy, pharmacotherapy, and vaccination, as well as to create new antiviral therapeutic and preventive medicines. The genetically determined immune response heterogeneity to SARS-CoV-2 infection requires further study, since there is no unambiguous opinion about the leading mechanism that determines disease severity.
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Porcine epidemic diarrhea virus (PEDV) is a porcine enteric coronavirus globally, causing serious economic losses to the global pig industry since 2010. Here, a PEDV CH/Yinchuan/2021 strain was isolated in a CV777-vaccinated sow farm which experienced a large-scale PEDV invasion in Yinchuan, China, in 2021. Our results demonstrated that the CH/Yinchuan/2021 isolate could efficiently propagate in Vero cells, and its proliferation ability was weaker than that of CV777 at 10 passages (P10). Phylogenetic analysis of the S gene revealed that CH/Yinchuan/2021 was clustered into subgroup GIIa, forming an independent branch with 2020-2021 isolates in China. Moreover, GII was obviously allocated into four clades, showing regional and temporal differences in PEDV global isolates. Notably, CH/Yinchuan/2021 was analyzed as a recombinant originated from an American isolate and a Chinese isolate, with a big recombinant region spanning ORF1a and S1. Importantly, we found that CH/Yinchuan/2021 harbored multiple mutations relative to CV777 in neutralizing epitopes (S10, S1A, COE, and SS6). Homology modelling showed that these amino acid differences in S protein occur on the surface of its structure, especially the insertion and deletion of multiple consecutive residues at the S10 epitope. In addition, cross-neutralization analysis confirmed that the differences in the S protein of CH/Yinchuan/2021 changed its antigenicity compared with the CV777 strain, resulting in a different neutralization profile. Animal pathogenicity test showed that CH/Yinchuan/2021 caused PEDV-typified symptoms and 100% mortality in 3-day-old piglets. These data will provide valuable information to understand the epidemiology, molecular characteristics, evolution, and antigenicity of PEDV circulating in China.
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This study aimed to evaluate the performance of the PanbioTM Covid-19 Ag Rapid Test (Abbott) in a medical center in Ouagadougou. The PanbioTM COVID-19 Ag test was evaluated from January 26 to March 31, 2021 in symptomatic and asymptomatic patients in the medical Centre of Kossodo. A total of 268 individuals were tested by both SARS-CoV-2 RT-PCR, and antigen RDT. Of these 268 individuals, 52 were positive and 216 were negative for COVID-19 RT-PCR. The performance parameters of the test and its Kappa agreement with the RT-PCR were calculated according to the presence or absence of symptoms in the patients on one hand, and according to the time onset of symptoms on the other hand. The sensitivity of the PanbioTM COVID-19 Ag Rapid Test ranged from 29.63% (95% CI: 13.75 to 50.18) among COVID-19 asymptomatic patients, to 87.5% (95% CI: 52.91 to97.76) among symptomatic patients with symptom onset time of 1-5 days. Similarly, the PanbioTM COVID-19 Ag Rapid Test specificity was 97.3% (95% CI: 90.58 to 99.67) and 96.4% (95% CI: 91.81 to 98.82) in symptomatic and asymptomatic RT PCR negative patients. The PanbioTM COVID-19 Ag Rapid Test shows good performance in detecting COVID-19 cases in patients with a symptom onset time of less than seven (7) days. This performance is even better when the symptom onset is reduced to five (5) days. The results show that the antigen RDT is not suitable for COVID-19 detection among asymptomatic patients.
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Introduction: COVID-19 presents a global emergency in recent days and as a consequence, the whole world is in a state of war. Continuous efforts by researchers are being made to establish a sound scientific understanding regarding the behavior of the virus and its pathogenesis. Background(s): In recent days, a lot of scientific data are published describing viral transfusion into host cells, compared with SARS-CoV-1, viability of SARS-CoV-2, fatality and diagnosis of infection among infected patients, thereby, motivating to make right decisions in order to treat and mitigate COVID-19. Review Results: Coronaviruses usually affect the respiratory tract and produce symptoms similar to pneumonia with varied complications. The spike protein on the surface of the virus makes the SARS-CoV-2 phylogenetically different from other viruses of the corona family. SARS-CoV-2 has an affinity to angiotensin converting enzyme-2 receptors present on human cells. The fatality of the disease is found to be low, but the severity of the disease might vary from person to person. The incubation period is 14 days but the symptoms like dry cough and high fever are evident around 3-7 days. Already known anti-inflammatory immunomodulators and antiviral drugs are being tested and still under clinical trials. Conclusion(s): In this review, we are providing an insight into emergence of COVID-19, its correlation with SARS-CoV-1 and the interpretation of global data representing the severity of unexpected dangers for humanity. Certain structural aspects and studies determining the viability of novel coronavirus have also been described. Moreover, case studies of recovered infected patients from COVID-19 explain the progression and patients' pathophysiological conditions while suffering from the infection. Clinical Significance: There are many current strategies which are being tried and practiced to over-come this pandemic disease apart from precautionary measures. Although now, some decline has been seen, but the question still remains the same of whether the scientists are approaching towards the clinical solution, or are still in the midstream. This requires more study and intensive research to finally come to a concrete conclusion.Copyright © 2021 Bentham Science Publishers.
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This paper describes the clinical signs and use of differential laboratory diagnostic techniques (computed tomography, cytology, histopathology, antigen/antibody detection and polymerase chain reaction) for infectious (viral, bacterial, fungal and parasitic) and non-infectious (inflammatory/immune mediated, neoplastic, cardiac, malformation, foreign body, smoke inhalation, aspiration of caustic material, non-cardiogenic, pulmonary oedema, traumativ, pneumothorax, pulmonary contusions and idiopathic) causes of respiratory diseases in cats and dogs in Ontario, Canada.
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Melioidosis is a particularly dangerous infection with endemic distribution caused by the Gram-negative microorganism from the pathogenicity group II Burkholderia pseudomallei. In endemic countries, melioidosis holds one of the leading places in mortality rate after HIV, tuberculosis and, in recent years, COVID-19. The natural ecological pathogen niches are located in tropical and subtropical climate zones, primarily in Southeast Asia and Australia, where its existence as a species is maintained in moist soil and water in a certain temperature environmental range. However, at present, more and more often cases of melioidosis are registered outside endemic territories, which emphasizes the relevance of improving the means and methods of laboratory diagnostics of this disease both for countries located in the zone of natural foci as well as for local healthcare of the countries after importation of this poorly known infection into their territory. In such countries, including the Russian Federation, the population has no natural immunity to the pathogen, and therefore this infection acquires even greater clinical and epidemiological significance. In the Volgograd Plague Control Research Institute, an erythrocyte antigenic melioidosis diagnostic agent for IHA was designed allowing to detect the presence of serum melioidosis antibodies. The diagnostic agent was obtained on the basis of a biological carrier - ram erythrocytes sensitized with isolated protein antigenic complexes of B. pseudomallei. The high analytical characteristics of the diagnostic agent were confirmed on sera models of immunized and recovering experimental animals. Using the obtained set of reagents, the level of serum antibodies against the causative agent of melioidosis was studied in residents from the 3 provinces of Vietnam (Ha Giang, Lang Son and Quang Ninh), as well as in control group composed of residents of the Volgograd region. In samples obtained from a non-endemic region, not more than 25% of cases contained IHA titers at lower than 1:10 dilution, which is apparently due to cross-reactivity of serum immunoglobulins. Positive serum samples from clinically healthy residents of Ha Giang, Lang Son and Quang Ninh provinces were at a titer of 1:10 detected in 71.5%, in dilutions of 1:20-1:80 - in 28.5% of cases. Thus, we believe that serum antibody titer of 1:80 established in the IHA results, has a diagnostic significance, reflecting the intensity of the anti-melioidosis populational immunity.Copyright © 2022 Saint Petersburg Pasteur Institute. All rights reserved.
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The lumpy skin disease (LSD) virus of the Poxviridae family is a serious threat that mostly affects cattle and causes significant economic loss. LSD has the potential to spread widely and its rapidly across borders. Despite the availability of information, there is still no competitive vaccine available for LSD. Therefore, the current study was conducted to develop an epitope-based LSD vaccine that is efficient, secure, and biocompatible and stimulates both innate and adaptive immune responses using immunoinformatics techniques. Initially, putative virion core proteins were manipulated;B-cell and T-cell epitopes have been predicted and connected with the help of adjuvants and linkers. Numerous bioinformatics methods, including antigenicity testing, transmembrane topology screening, allergenicity assessment, conservancy analysis, and toxicity evaluation, were employed to find superior epitopes. Based on promising vaccine candidates and immunogenic potential, the vaccine design was selected. Strong interactions between TLR4 and TLR9 and the anticipated vaccine design were revealed by molecular docking. Finally, based on the high docking score, computer simulations were performed in order to assess the stability, efficacy, and compactness of the constructed vaccine. The simulation outcomes showed that the polypeptide vaccine design was remarkably stable, with high expression, stability, immunogenic qualities, and considerable solubility. Additionally, computer-based research shows that the constructed vaccine provides adequate population coverage, making it a promising candidate for use in the design of vaccines against other viruses within the Poxviridae family and potentially other virus families as well. These outcomes suggest that the epitope-based vaccine developed in this study will be a significant candidate against LSD to control and prevent LSDV-related disorders if further investigated experimentally.
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Background & Objective: Biological markers for the prediction of acquiring Covid-19 risk are deficient and there is a dire need of immediate research data. The objective of the study was to predict the link of ABO blood group types along with Rh factor distribution with the severity of Covid-19. Methods: This was an observational cross-sectional survey conducted in medicine department of Pakistan Ordnance Factory Hospital, Wah Cantt Pakistan, from August 2020 to December 2020 after approval of IRB. Participants tested positive for presence of Covid-19 infection by polymerase chain reaction (PCR) were included in the study. Covid-19 infection severity was measured through mild, moderate and severe disease categories and analyzed. ABO blood group and Rh subgroups data for all the Covid-19 infected patients were obtained from the laboratory section of the hospital and analyzed. Data was entered in SPSS v 26 and analyzed. Cox regression model was used to find out the severity of Covid-19. Results: Total 248 patients were included;75% patients were male and 25% were females. The mean age of the patients was 52.77+or-15.58 years. A very significant association was found between ABO blood group types, Rh factor antigen and severity of Covid-19 (p=0.001). When stratified ABO, Rh antigen blood group with health status of all patients there was a very significant association between them (p=0.013). An insignificant association between male and female odds ratio of ABO blood group types but blood group B, Rh positive antigen was more susceptible in Covid-19 positive patients. Conclusion: There is a link between ABO blood group types along with Rh factor antigen (B+ and O+) with the severity of Covid-19 positive patients. ABO blood group types and Rh factor can be used as a potential marker/tool to predict the susceptibility of acquiring Covid-19 infection as well as for severity of the infection.
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ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS"CoV"2) has rapidly evolved in the last couple of years. This has created major havoc and concern because it has affected millions of people around the world. The new variants of covid"19 are classified into two types, VOI (variant of interest) and VOC (variant of concern). The major variants of concern (VOCs) have shared mutations in severe acute respiratory syndrome coronavirus 2 (SARS"CoV"2). The spike proteins of the novel coronavirus located mostly on the S1 unit result in a higher transmissibility rate and affect the viral virulence and clinical outcome. The spike protein and other non"structural protein mutations in VOCs may lead to escape the approved vaccinations. Here the VOC mutations i.e., OMICRON VARIANT have been discussed in detail, and the therapeutic strategies to enhance the host immune responses have been proposed. Additionally, a computational approach is proposed to design the drug and vaccine for the variant. The protein structure for the OMICRON variant has been predicted through bioinformatics tools and several databases have been used to identify suitable natural inhibitors. The OMICRON variant was analyzed to identify suitable vaccine candidates by identifying B"Cell epitopes. To design a drug, REPAGLINIDE and ENT"NATEGLINIDE were identified as natural inhibitors based on docking score. To design a vaccine the B"cell epitope i.e., CLIGAEYVNNSYECD was found to the highest antigenicity score. The present study identifies natural inhibitors and potential antigenic Epitopes which may be used as effective drug and vaccine candidates to suppress the novel coronavirus.
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Melioidosis is a particularly dangerous infection with endemic distribution caused by the Gram-negative microorganism from the pathogenicity group II Burkholderia pseudomallei. In endemic countries, melioidosis holds one of the leading places in mortality rate after HIV, tuberculosis and, in recent years, COVID-19. The natural ecological pathogen niches are located in tropical and subtropical climate zones, primarily in Southeast Asia and Australia, where its existence as a species is maintained in moist soil and water in a certain temperature environmental range. However, at present, more and more often cases of melioidosis are registered outside endemic territories, which emphasizes the relevance of improving the means and methods of laboratory diagnostics of this disease both for countries located in the zone of natural foci as well as for local healthcare of the countries after importation of this poorly known infection into their territory. In such countries, including the Russian Federation, the population has no natural immunity to the pathogen, and therefore this infection acquires even greater clinical and epidemiological significance. In the Volgograd Plague Control Research Institute, an erythrocyte antigenic melioidosis diagnostic agent for IHA was designed allowing to detect the presence of serum melioidosis antibodies. The diagnostic agent was obtained on the basis of a biological carrier - ram erythrocytes sensitized with isolated protein antigenic complexes of B. pseudomallei. The high analytical characteristics of the diagnostic agent were confirmed on sera models of immunized and recovering experimental animals. Using the obtained set of reagents, the level of serum antibodies against the causative agent of melioidosis was studied in residents from the 3 provinces of Vietnam (Ha Giang, Lang Son and Quang Ninh), as well as in control group composed of residents of the Volgograd region. In samples obtained from a non-endemic region, not more than 25% of cases contained IHA titers at lower than 1:10 dilution, which is apparently due to cross-reactivity of serum immunoglobulins. Positive serum samples from clinically healthy residents of Ha Giang, Lang Son and Quang Ninh provinces were at a titer of 1:10 detected in 71.5%, in dilutions of 1:20-1:80 - in 28.5% of cases. Thus, we believe that serum antibody titer of 1:80 established in the IHA results, has a diagnostic significance, reflecting the intensity of the anti-melioidosis populational immunity.
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The rapid evolution of SARS-CoV-2 Omicron sublineages mandates a better understanding of viral replication and cross-neutralization among these sublineages. Here we used K18-hACE2 mice and primary human airway cultures to examine the viral fitness and antigenic relationship among Omicron sublineages. In both K18-hACE2 mice and human airway cultures, Omicron sublineages exhibited a replication order of BA.5 ≥ BA.2 ≥ BA.2.12.1 > BA.1; no difference in body weight loss was observed among different sublineage-infected mice. The BA.1-, BA.2-, BA.2.12.1-, and BA.5-infected mice developed distinguishable cross-neutralizations against Omicron sublineages, but exhibited little neutralization against the index virus (i.e. USA-WA1/2020) or the Delta variant. Surprisingly, the BA.5-infected mice developed higher neutralization activity against heterologous BA.2 and BA.2.12.1 than that against homologous BA.5; serum neutralizing titres did not always correlate with viral replication levels in infected animals. Our results revealed a distinct antigenic cartography of Omicron sublineages and support the bivalent vaccine approach.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Animals , Mice , SARS-CoV-2/genetics , Melphalan , Antibodies, Viral , Antibodies, NeutralizingABSTRACT
The SARS-CoV-2 Omicron variant evades most neutralizing vaccine-induced antibodies and is associated with lower antibody titers upon breakthrough infections than previous variants. However, the mechanism remains unclear. Here, we find using a geometric deep-learning model that Omicron's extensively mutated receptor binding site (RBS) features reduced antigenicity compared with previous variants. Mice immunization experiments with different recombinant receptor binding domain (RBD) variants confirm that the serological response to Omicron is drastically attenuated and less potent. Analyses of serum cross-reactivity and competitive ELISA reveal a reduction in antibody response across both variable and conserved RBD epitopes. Computational modeling confirms that the RBS has a potential for further antigenicity reduction while retaining efficient receptor binding. Finally, we find a similar trend of antigenicity reduction over decades for hCoV229E, a common cold coronavirus. Thus, our study explains the reduced antibody titers associated with Omicron infection and reveals a possible trajectory of future viral evolution.