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1.
American Journal of Reproductive Immunology ; 89(Supplement 1):40, 2023.
Article in English | EMBASE | ID: covidwho-20241541

ABSTRACT

Problem: COVID-19 placentitis is a rare complication of maternal SARS-CoV-2 respiratory infection associated with serious adverse obstetric outcomes, including intra-uterine death. The precise role of SARS-CoV-2 in COVID-19 placentitis is uncertain, as trophoblast infection is only observed in around one-half of the affected placenta. Method of Study: Through multi-omic spatial profiling, including Nanostring GeoMX digital spatial profiling and Lunaphore COMET multiplex IHC, we provide a deep characterization of the immunopathology of placentitis from obstetrically complicated maternal COVID-19 infection. Result(s):We show that SARS-CoV-2 infection of placental trophoblasts is associated with a distinct innate and adaptive immune cell infiltrate, florid cytokine expression and upregulation of viral restriction factors. Quantitative spatial analyses reveal a unique microenvironment surrounding virus-infected trophoblasts characterizedd by multiple immune evasion mechanisms, including immune checkpoint expression, cytotoxic T-cell exclusion, and interferon blunting. Placental viral loads inversely correlated with the duration of maternal infection consistent with progressive virus clearance, potentially explaining the absence of virus in some cases. Conclusion(s): Our results demonstrate a central role for placental SARS-CoV-2 infection in driving the unique immunopathology of COVID-19 placentitis.

2.
mBio ; : e0067923, 2023 Jun 05.
Article in English | MEDLINE | ID: covidwho-20244869

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving, bringing great challenges to the control of the virus. In the present study, we investigated the characteristics of SARS-CoV-2 within-host diversity of human hosts and its implications for immune evasion using about 2,00,000 high-depth next-generation genome sequencing data of SARS-CoV-2. A total of 44% of the samples showed within-host variations (iSNVs), and the average number of iSNVs in the samples with iSNV was 1.90. C-to-U is the dominant substitution pattern for iSNVs. C-to-U/G-to-A and A-to-G/U-to-C preferentially occur in 5'-CG-3' and 5'-AU-3' motifs, respectively. In addition, we found that SARS-CoV-2 within-host variations are under negative selection. About 15.6% iSNVs had an impact on the content of the CpG dinucleotide (CpG) in SARS-CoV-2 genomes. We detected signatures of faster loss of CpG-gaining iSNVs, possibly resulting from zinc-finger antiviral protein-mediated antiviral activities targeting CpG, which could be the major reason for CpG depletion in SARS-CoV-2 consensus genomes. The non-synonymous iSNVs in the S gene can largely alter the S protein's antigenic features, and many of these iSNVs are distributed in the amino-terminal domain (NTD) and receptor-binding domain (RBD). These results suggest that SARS-CoV-2 interacts actively with human hosts and attempts to take different evolutionary strategies to escape human innate and adaptive immunity. These new findings further deepen and widen our understanding of the within-host evolutionary features of SARS-CoV-2.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of the coronavirus disease 2019, has evolved rapidly since it was discovered. Recent studies have pointed out that some mutations in the SARS-CoV-2 S protein could confer SARS-CoV-2 the ability to evade the human adaptive immune system. In addition, it is observed that the content of the CpG dinucleotide in SARS-CoV-2 genome sequences has decreased over time, reflecting the adaptation to the human host. The significance of our research is revealing the characteristics of SARS-CoV-2 within-host diversity of human hosts, identifying the causes of CpG depletion in SARS-CoV-2 consensus genomes, and exploring the potential impacts of non-synonymous within-host variations in the S gene on immune escape, which could further deepen and widen our understanding of the evolutionary features of SARS-CoV-2.

3.
Influenza Other Respir Viruses ; 17(6): e13144, 2023 06.
Article in English | MEDLINE | ID: covidwho-20244279

ABSTRACT

New immune evasive variants of SARS-CoV-2 continue to emerge, potentially causing new waves of covid-19 disease. Here, we evaluate levels of neutralizing antibodies against isolates of Omicron variants, including BQ.1.1 and XBB, in sera harvested 3-4 weeks after vaccination or breakthrough infections. In addition, we evaluate neutralizing antibodies in 32 sera from October 2022, to evaluate immunity in Norwegian donors prior to the winter season. Most serum samples harvested in October 2022 had low levels of neutralizing antibodies against BQ.1.1 and especially XBB, explaining why these variants and their descendants have dominated in Norway during the 2022 and 2023 winter season.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , Norway/epidemiology , Antibodies, Neutralizing , Antibodies, Viral
4.
Front Immunol ; 14: 1172000, 2023.
Article in English | MEDLINE | ID: covidwho-20243355

ABSTRACT

Type I interferons (IFNs-α/ß) are antiviral cytokines that constitute the innate immunity of hosts to fight against viral infections. Recent studies, however, have revealed the pleiotropic functions of IFNs, in addition to their antiviral activities, for the priming of activation and maturation of adaptive immunity. In turn, many viruses have developed various strategies to counteract the IFN response and to evade the host immune system for their benefits. The inefficient innate immunity and delayed adaptive response fail to clear of invading viruses and negatively affect the efficacy of vaccines. A better understanding of evasion strategies will provide opportunities to revert the viral IFN antagonism. Furthermore, IFN antagonism-deficient viruses can be generated by reverse genetics technology. Such viruses can potentially serve as next-generation vaccines that can induce effective and broad-spectrum responses for both innate and adaptive immunities for various pathogens. This review describes the recent advances in developing IFN antagonism-deficient viruses, their immune evasion and attenuated phenotypes in natural host animal species, and future potential as veterinary vaccines.


Subject(s)
Interferon Type I , RNA Viruses , Vaccines , Animals , Immune Evasion , Antiviral Agents/pharmacology
5.
Front Immunol ; 14: 1159326, 2023.
Article in English | MEDLINE | ID: covidwho-20242832

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), has affected all countries worldwide. Although some symptoms are relatively mild, others are still associated with severe and even fatal clinical outcomes. Innate and adaptive immunity are important for the control of SARS-CoV-2 infections, whereas a comprehensive characterization of the innate and adaptive immune response to COVID-19 is still lacking and the mechanisms underlying immune pathogenesis and host predisposing factors are still a matter of scientific debate. Here, the specific functions and kinetics of innate and adaptive immunity involved in SARS-CoV-2 recognition and resultant pathogenesis are discussed, as well as their immune memory for vaccinations, viral-mediated immune evasion, and the current and future immunotherapeutic agents. We also highlight host factors that contribute to infection, which may deepen the understanding of viral pathogenesis and help identify targeted therapies that attenuate severe disease and infection.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Immunity, Innate , Adaptive Immunity , Causality
6.
J Med Virol ; 95(6): e28881, 2023 06.
Article in English | MEDLINE | ID: covidwho-20235484

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an unprecedented threat to human health since late 2019. Notably, the progression of the disease is associated with impaired antiviral interferon (IFN) responses. Although multiple viral proteins were identified as potential IFN antagonists, the underlying molecular mechanisms remain to be fully elucidated. In this study, we firstly demonstrate that SARS-CoV-2 NSP13 protein robustly antagonizes IFN response induced by the constitutively active form of transcription factor IRF3 (IRF3/5D). This induction of IFN response by IRF3/5D is independent of the upstream kinase, TBK1, a previously reported NSP13 target, thus indicating that NSP13 can act at the level of IRF3 to antagonize IFN production. Consistently, NSP13 exhibits a specific, TBK1-independent interaction with IRF3, which, moreover, is much stronger than that of NSP13 with TBK1. Furthermore, the NSP13-IRF3 interaction was shown to occur between the NSP13 1B domain and IRF3 IRF association domain (IAD). In agreement with the strong targeting of IRF3 by NSP13, we then found that NSP13 blocks IRF3-directed signal transduction and antiviral gene expression, counteracting IRF3-driven anti-SARS-CoV-2 activity. These data suggest that IRF3 is likely to be a major target of NSP13 in antagonizing antiviral IFN responses and provide new insights into the SARS-CoV-2-host interactions that lead to viral immune evasion.


Subject(s)
COVID-19 , Interferon Regulatory Factor-3 , Viral Nonstructural Proteins , Humans , COVID-19/immunology , Immune Evasion , Interferon Regulatory Factor-3/genetics , Interferons , SARS-CoV-2 , Viral Nonstructural Proteins/genetics
7.
Front Immunol ; 14: 1162211, 2023.
Article in English | MEDLINE | ID: covidwho-20231099

ABSTRACT

Spatiotemporal separation of cellular components is vital to ensure biochemical processes. Membrane-bound organelles such as mitochondria and nuclei play a major role in isolating intracellular components, while membraneless organelles (MLOs) are accumulatively uncovered via liquid-liquid phase separation (LLPS) to mediate cellular spatiotemporal organization. MLOs orchestrate various key cellular processes, including protein localization, supramolecular assembly, gene expression, and signal transduction. During viral infection, LLPS not only participates in viral replication but also contributes to host antiviral immune responses. Therefore, a more comprehensive understanding of the roles of LLPS in virus infection may open up new avenues for treating viral infectious diseases. In this review, we focus on the antiviral defense mechanisms of LLPS in innate immunity and discuss the involvement of LLPS during viral replication and immune evasion escape, as well as the strategy of targeting LLPS to treat viral infectious diseases.


Subject(s)
Antiviral Agents , Cell Nucleus , Immunity
8.
International Journal of Pharmaceutical Sciences and Research ; 14(5):2104-2116, 2023.
Article in English | EMBASE | ID: covidwho-2323559

ABSTRACT

In mid-November 2021, the new OMICRON variety was first discovered in South Africa. As of today, the OMICRON version already appeared on December 15, 2021. Around 77 countries are affected, with the bulk of cases originating in the United States, India, the United Kingdom, and South Africa. OMICRON-positive instances were also reported. The first mortality associated with the novel COVID-19 mutation was reported in the United Kingdom. Recently, a sister variant of OMICRON, 21L or BA.2, has also been discovered. Due to its enormously high number of mutations, viewed enhancement in immune evasion and transmissibility, OMICRON was developed as a new variant of concern (VOC) by the WHO on 26 November 2021. On a global pandemic scale, positive selection of SARSCoV-2 mutations appears to have begun in late 2020. Since then, the virus has been evolving on two fronts: immune evasion and enhanced transmissibility, as expressed by Delta. This review elaborates the effects of drugs in the management of OMICRON.Copyright © 2023 Society of Pharmaceutical Sciences and Research. All rights reserved.

9.
J Infect Dis ; 2023 May 17.
Article in English | MEDLINE | ID: covidwho-2326360

ABSTRACT

BACKGROUND: The association between SARS-CoV-2 genomic variation and breakthrough infection is not well-defined among persons with Delta variant SARS-CoV-2 infection. METHODS: In a retrospective cohort we assessed whether individual non-lineage defining mutations and overall genomic variation (including low frequency alleles) were associated with breakthrough infection defined as SARS-CoV-2 infection after COVID-19 primary vaccine series. We identified all non-synonymous single nucleotide polymorphisms, insertions and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. Using Poisson regression, we assessed the association with breakthrough infection for each individual mutation and a viral genomic risk score. RESULTS: Thirty-six mutations met our inclusion criteria. Among 12,744 persons infected with Delta variant SARS-CoV-2, 5,949 (47%) were vaccinated and 6,795 (53%) were unvaccinated. Viruses with a viral genomic risk score in the highest quintile were 9% more likely to be associated with breakthrough infection than viruses in the lowest quintile, but including the risk score improved overall predictive model performance (measured by c-statistic) by only +0.0006. CONCLUSIONS: Genomic variation within SARS-CoV-2 Delta variant was weakly associated with breakthrough infection, however several potential non-lineage defining mutations were identified that might contribute to immune evasion by SARS-CoV-2.

10.
Medical Journal of Malaysia ; 77(Supplement 5):3, 2022.
Article in English | EMBASE | ID: covidwho-2315511

ABSTRACT

Real-world effectiveness studies are important for monitoring the performance of COVID-19 vaccination strategies and informing COVID-19 prevention and control policies. The Real-World Effectiveness of COVID-19 Vaccine under the Malaysian National COVID-19 Immunisation Program (RECoVaM) analysed effectiveness of a range of homologous primary, as well as heterologous and homologous booster COVID-19 vaccines, which comprised of BNT162b2 (mRNA), CoronaVac (inactivated) and AZD1222 (viral vectored), against SARS-CoV-2 infection and severe COVID-19. Nationally comprehensive administrative data at both individual- and aggregate-levels were consolidated for each analysis. These were the Malaysia national COVID-19 vaccinations register (MyVAS), COVID-19 cases line listing, intensive care unit (ICU) admissions register, deaths line listing, supervised test registry (SIMKA), and the MySejahtera check-ins-based automated contact tracing registry (AutoTrace). RECoVaM adopted several observational study designs. Exposure periods were carefully calibrated to account for the structure of Malaysia's COVID-19 data, and epidemiological context, to estimate vaccine effectiveness. Importantly, RECoVaM also compared effectiveness measures during both the Delta-dominant, and Omicron-dominant periods. Effectiveness estimates for primary vaccinations showed a reduction in risk of SARS-CoV-2 infections by 87 - 91%, and symptomatic infections by 85 - 89%, as well as ICU admission by 82 - 84% among COVID-19 cases, and death by 86 - 88% among COVID-19 cases. All vaccine platforms were effective in reducing risk against ICU admission and death. Subsequently, significant waning of protection was demonstrated against COVID-19 infection among BNT162b2 (90.8 to 79.3%) and CoronaVac (74.5 to 30.4%) recipients 3 to 5 months post-primary vaccinations. Protection against ICU admission for CoronaVac waned (56.0 to 28.7%) and was more substantial among the elderly (aged 60 years and above). The estimates of marginal Vaccine Effectiveness (mVE) for boosters showed that recipients of booster doses were at least 90% less likely to be infected with COVID-19 relative to primary BNT162b2 vaccination during the Delta-dominant period. In both Delta and Omicron-dominant periods, homologous BNT162b2 boosting offered the highest protection against infection relative to primary BNT162b2 vaccination. This is followed by heterologous boosting with either AZD1222 or BNT162b2 for recipients primed with CoronaVac or AZD1222, and finally homologous boosting with AZD1222 and CoronaVac. The mVE estimates for all booster combinations in the Omicrondominant period was about half that of Delta. Vaccination with a primary COVID-19 vaccines were effective in reducing COVID-19 infection but wanes after 3-5 months. Additional booster doses were more effective than primary series alone in preventing COVID-19 infection but demonstrated an interplay of immune evasion during the Omicron-dominant period. Homologous BNT162b2 boosting aside, and heterologous boosting appeared to be more protective than homologous boosting. Although vaccination is still protective against severe infection, ongoing community transmission could facilitate viral mutation. Next generation, multivalent vaccines aimed at stemming transmission, are warranted.

11.
Cell Rep ; 42(5): 112443, 2023 05 30.
Article in English | MEDLINE | ID: covidwho-2306918

ABSTRACT

Omicron subvariants continuingly challenge current vaccination strategies. Here, we demonstrate nearly complete escape of the XBB.1.5, CH.1.1, and CA.3.1 variants from neutralizing antibodies stimulated by three doses of mRNA vaccine or by BA.4/5 wave infection, but neutralization is rescued by a BA.5-containing bivalent booster. CH.1.1 and CA.3.1 show strong immune escape from monoclonal antibody S309. Additionally, XBB.1.5, CH.1.1, and CA.3.1 spike proteins exhibit increased fusogenicity and enhanced processing compared with BA.2. Homology modeling reveals the key roles of G252V and F486P in the neutralization resistance of XBB.1.5, with F486P also enhancing receptor binding. Further, K444T/M and L452R in CH.1.1 and CA.3.1 likely drive escape from class II neutralizing antibodies, whereas R346T and G339H mutations could confer the strong neutralization resistance of these two subvariants to S309-like antibodies. Overall, our results support the need for administration of the bivalent mRNA vaccine and continued surveillance of Omicron subvariants.


Subject(s)
Antibodies, Monoclonal , Antibodies, Neutralizing , Antibody Formation , Mutation/genetics , RNA, Messenger/genetics , Vaccines, Combined , Antibodies, Viral
12.
Vaccines (Basel) ; 11(4)2023 Apr 16.
Article in English | MEDLINE | ID: covidwho-2305133

ABSTRACT

The rapid emergence of immune-evading viral variants of SARS-CoV-2 calls into question the practicality of a vaccine-only public-health strategy for managing the ongoing COVID-19 pandemic. It has been suggested that widespread vaccination is necessary to prevent the emergence of future immune-evading mutants. Here, we examined that proposition using stochastic computational models of viral transmission and mutation. Specifically, we looked at the likelihood of emergence of immune escape variants requiring multiple mutations and the impact of vaccination on this process. Our results suggest that the transmission rate of intermediate SARS-CoV-2 mutants will impact the rate at which novel immune-evading variants appear. While vaccination can lower the rate at which new variants appear, other interventions that reduce transmission can also have the same effect. Crucially, relying solely on widespread and repeated vaccination (vaccinating the entire population multiple times a year) is not sufficient to prevent the emergence of novel immune-evading strains, if transmission rates remain high within the population. Thus, vaccines alone are incapable of slowing the pace of evolution of immune evasion, and vaccinal protection against severe and fatal outcomes for COVID-19 patients is therefore not assured.

13.
Curr Top Med Chem ; 2023 Apr 11.
Article in English | MEDLINE | ID: covidwho-2304070

ABSTRACT

The Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and threatens public health and safety. Nowadays, modern society has faced a new challenging problem, the emergence of novel SARS-CoV-2 variants of concern (VOCs). In this context, the Omicron (B.1.1.529) variant, having more than 60 mutations when compared to its ancestral wild-type virus, has infected many individuals around the world. It is rapidly spread person-to-person due to its increased transmissibility. Additionally, it was demonstrated that this newest variant and its subvariants have the capability of evading the host immune system, being resistant to neutralizing antibodies. Moreover, it has been proven to be resistant to monoclonal antibodies and several different vaccines. This ability is associated with a huge number of mutations associated with its spike (S) glycoprotein, which presents at least 15 mutations. These mutations are able to modify the way how this virus interacts with the host angiotensin-converting enzyme 2 (ACE2), increasing its infectivity and making the therapeutic alternatives more ineffective. Concerning its chymotrypsin-like picornavirus 3C-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp), it has been seen that some compounds can be active against different SARS-CoV-2 variants, in a similar mode than its wild-type precursor. This broad spectrum of action for some drugs could be attributed to the fact that the currently identified mutations found in 3CLpro and RNA proteins being localized near the catalytic binding site, conserving their activities. Herein this review, we provide a great and unprecedented compilation of all identified and/or repurposed compounds/drugs against this threatening variant, Omicron. The main targets for those compounds are the protein-protein interface (PPI) of S protein with ACE2, 3CLpro, RdRp, and Nucleocapsid (N) protein. Some of these studies have presented only in silico data, having a lack of experimental results to prove their findings. However, these should be considered here since other research teams can use their observations to design and investigate new potential agents. Finally, we believe that our review will contribute to several studies that are in progress worldwide, compiling several interesting aspects about VOCs associated with SARS-CoV2, as well as describing the results for different chemical classes of compounds that could be promising as prototypes for designing new and more effective antiviral agents.

14.
Viruses ; 15(4)2023 03 29.
Article in English | MEDLINE | ID: covidwho-2291466

ABSTRACT

The COVID-19 pandemic has resulted in upwards of 6.8 million deaths over the past three years, and the frequent emergence of variants continues to strain global health. Although vaccines have greatly helped mitigate disease severity, SARS-CoV-2 is likely to remain endemic, making it critical to understand its viral mechanisms contributing to pathogenesis and discover new antiviral therapeutics. To efficiently infect, this virus uses a diverse set of strategies to evade host immunity, accounting for its high pathogenicity and rapid spread throughout the COVID-19 pandemic. Behind some of these critical host evasion strategies is the accessory protein Open Reading Frame 8 (ORF8), which has gained recognition in SARS-CoV-2 pathogenesis due to its hypervariability, secretory property, and unique structure. This review discusses the current knowledge on SARS-CoV-2 ORF8 and proposes actualized functional models describing its pivotal roles in both viral replication and immune evasion. A better understanding of ORF8's interactions with host and viral factors is expected to reveal essential pathogenic strategies utilized by SARS-CoV-2 and inspire the development of novel therapeutics to improve COVID-19 disease outcomes.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Open Reading Frames , Pandemics , Antiviral Agents
15.
Med Microbiol Immunol ; 2022 Apr 02.
Article in English | MEDLINE | ID: covidwho-2298572

ABSTRACT

The innate immune system is a powerful barrier against invading pathogens. Interferons (IFNs) are a major part of the cytokine-mediated anti-viral innate immune response. After recognition of a pathogen by immune sensors, signaling cascades are activated that culminate in the release of IFNs. These activate cells in an autocrine or paracrine fashion eventually setting cells in an anti-viral state via upregulation of hundreds of interferon-stimulated genes (ISGs). To evade the anti-viral effect of the IFN system, successful viruses like the pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolved strategies to counteract both IFN induction and signaling. In fact, more than half of the about 30 proteins encoded by SARS-CoV-2 target the IFN system at multiple levels to escape IFN-mediated restriction. Here, we review recent insights into the molecular mechanisms used by SARS-CoV-2 proteins to suppress IFN production and the establishment of an anti-viral state.

16.
Advancements in Life Sciences ; 9(4):429-436, 2022.
Article in English | Scopus | ID: covidwho-2266153

ABSTRACT

Since the first coronavirus disease-19 (COVID-19) outbreak, variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have continued to dominate the global population. The repeated waves of emerging variants, each replacing the previous one with a greater rate of transmissibility and mutations, are the primary cause of the global pandemic. Public health concerns dramatically rose when a highly mutated variant, omicron (B.1.1.529) emerged in late 2021. Omicron has more than 50 mutations, and over 30 mutations are in their spike protein that contributes to the virologic characteristics of the variant. Omicron is more contagious than previously reported SARS-CoV-2 strains and can re-infect people who have already contracted other SARS-CoV-2 infections. The variant has acquired a unique immune escape mechanism against monoclonal antibodies and vaccines. Currently, there are no specific therapeutic drugs or vaccines available to prevent omicron infection and sub lineages emergence. The review was designed to search the recent research or literature papers and compile the most pertinent data on the virologic characteristics of the variant of concern. The study reviewed and discussed the present prevalence, infectivity, dominance, immune evasion, therapeutic options, vaccine efficacy, and the future prospect of the omicron variant. Omicron variant has become a global public health concern due to the emergence of highly mutated sub lineages. Developing variant-specific therapeutic drugs or vaccines is desirable to prevent the spread of these contagious variants globally. © 2022, The Running Line. All rights reserved.

17.
Coronaviruses ; 2(2):159-171, 2021.
Article in English | EMBASE | ID: covidwho-2265577

ABSTRACT

An urgent vaccine development is required against the recent pandemic of a novel coronavi-rus. Currently, there is no approved vaccine against COVID-19. Vaccination is proved to be the most beneficial way to protect humans from infections. Several vaccine candidates have been conducted to different phases of clinical trials, and more vaccine candidates are on the way to enter the trials. Different vaccine types have developed, including inactivated virus vaccines, subunit-based vaccines, adenovi-rus-vector vaccines, DNA-based vaccines, DC-based vaccines, and mRNA-based vaccines. The mRNA-1273 was the first vaccine candidate that started evaluating in the clinical trial. Also, AZD1222 is the first vaccine candidate that started phase II/III of clinical trials. Both of these vaccine candidates were considered as promising vaccine candidates against SARS-CoV-2. This review aims to overview and share various strategies to develop efficient therapeutic and preventive vaccines based on the origin, bi-ology, structure, and immune-evasion of SARS-CoV-2.Copyright © 2021 Bentham Science Publishers.

18.
Acta Virologica ; 66(4):332-338, 2022.
Article in English | EMBASE | ID: covidwho-2265386

ABSTRACT

This study aims to fill a knowledge gap in our understanding of Omicron variant receptor-binding domain (RBD) interactions with host cell receptor, angiotensin-converting enzyme 2 (ACE2). Protein-protein docking, scoring, and filtration were all performed using the HDOCK server. A coarse-grained prediction of the changes in binding free energy caused by point mutations in Omicron RBD was requested from the Binding Affinity Changes upon Mutation (BeAtMuSiC) tools. GROMACS was utilized to perform molecular dynamics simulations (MD). Within the 15 mutations in Omicron RBD, several mutations have been linked to increased receptor affinity, immunological evasion, and inadequate antibody response. Wild-type (wt) SARS-CoV-2 and its Omicron variant have 92.27% identity. Nonetheless, Omicron RBD mutations resulted in a slight increase in the route mean square deviations (RMSD) of the Omicron structural model during protein-protein docking, as evidenced by RMSDs of 0.47 and 0.85 A for the wt SARS-CoV-2 and Omicron RBD-ACE2 complexes, respectively. About five-point mutations had essentially an influence on binding free energy, namely G6D, S38L, N107K, E151A, and N158Y. The rest of the mutations were expected to reduce the binding affinity of Omicron RBD and ACE2. The MD simulation supports the hypothesis that Omicron RBD is more stably bound to ACE2 than wt SARS-CoV-2 RBD. Lower RMSD and greater radius of gyration (Rg) imply appropriate Omicron structure 3D folding and stability. However, the increased solvent accessible surface area (SASA) with a greater Omicron shape may have a different interaction with receptor binding and regulate virus entrance. Omicron RBD's mutations help it maintain its structural stability, compactness, ACE2 binding, and immune evasion.Copyright © 2022 AEPress, s.r.o.. All rights reserved.

19.
Chinese Journal of Clinical Infectious Diseases ; 14(2):97-101, 2021.
Article in Chinese | EMBASE | ID: covidwho-2261426

ABSTRACT

COVID-19 has swept across the world, causing widespread epidemics and millions of life lost worldwide. After infected with 2019-nCoV, the body quickly mobilizes the innate immune response and produces type interferon (IFN-). IFN- plays an important role in virus clearance in the early stage of disease. This article reviews the innate immune recognition after virus infection and the interaction between 2019-nCoV and IFN-, which would be conductive to understanding the pathogenesis and antiviral treatment of COVID-19.Copyright © 2021 Chinese Medical Association

20.
Chinese Journal of Clinical Infectious Diseases ; 14(2):97-101, 2021.
Article in Chinese | EMBASE | ID: covidwho-2261425

ABSTRACT

COVID-19 has swept across the world, causing widespread epidemics and millions of life lost worldwide. After infected with 2019-nCoV, the body quickly mobilizes the innate immune response and produces type interferon (IFN-). IFN- plays an important role in virus clearance in the early stage of disease. This article reviews the innate immune recognition after virus infection and the interaction between 2019-nCoV and IFN-, which would be conductive to understanding the pathogenesis and antiviral treatment of COVID-19.Copyright © 2021 Chinese Medical Association

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