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1.
Theranostics ; 12(12): 5522-5536, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35910791

RESUMO

Objective: Nobody knows when the COVID-19 pandemic will end or when and where the next coronavirus will outbreak. Therefore, it is still necessary to develop SARS-CoV-2 inhibitors for different variants or even the new coronavirus. Since SARS-CoV-2 uses its surface spike-protein to recognize hACE2, mediating its entry into cells, ligands that can specifically recognize the spike-protein have the potential to prevent infection. Methods: We have recently discovered DNA aptamers against the S2-domain of the WT spike-protein by exploiting the selection process called SELEX. After optimization, among all candidates, the aptamer S2A2C1 has the shortest sequence and the best binding affinity toward the S2-protein. More importantly, the S2A2C1 aptamer does not bind to the RBD of the spike-protein, but it efficiently blocks the spike-protein/hACE2 interaction, suggesting an RBD-independent inhibition approach. To further improve its performance, we conjugated the S2A2C1 aptamer with a reported anti-RBD aptamer, S1B6C3, using various linkers and constructed hetero-bivalent fusion aptamers. Binding affinities of mono and fusion aptamers against the spike-proteins were measured. The inhibition efficacies of mono and fusion aptamers to prevent the hACE2/spike-protein interaction were determined using ELISA. Results: Anti-spike-protein aptamers, including S2A2C1 and S1B6C3-A5-S2A2C1, maintained high binding affinity toward the WT, Delta, and Omicron spike-proteins and high inhibition efficacies to prevent them from binding to hACE2, rendering them well-suited as diagnostic and therapeutic molecular tools to target SARS-CoV-2 and its variants. Conclusions: Overall, we discovered the anti-S2 aptamer, S2A2C1, which inhibits the hACE2/spike-protein interaction via an RBD-independent approach. The anti-S2 and anti-RBD aptamers were conjugated to obtain the fusion aptamer, S1B6C3-A5-S2A2C1, which recognizes the spike-protein by an RBD-dependent approach. Our strategies, which discovered aptamer inhibitors targeting the highly conserved S2-protein, as well as the design of fusion aptamers, can be used to target new coronaviruses as they emerge.


Assuntos
Enzima de Conversão de Angiotensina 2 , Aptâmeros de Nucleotídeos , COVID-19 , Glicoproteína da Espícula de Coronavírus , Enzima de Conversão de Angiotensina 2/imunologia , Anticorpos Neutralizantes/imunologia , Aptâmeros de Nucleotídeos/imunologia , Aptâmeros de Nucleotídeos/farmacologia , COVID-19/imunologia , COVID-19/virologia , Humanos , Pandemias , Peptidil Dipeptidase A/metabolismo , Ligação Proteica , SARS-CoV-2/imunologia , Glicoproteína da Espícula de Coronavírus/imunologia
2.
PLoS One ; 17(7): e0271112, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35830431

RESUMO

The outbreak of the coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 triggered a global pandemic where control is needed through therapeutic and preventive interventions. This study aims to identify natural compounds that could affect the fusion between the viral membrane (receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 spike protein) and the human cell receptor angiotensin-converting enzyme 2. Accordingly, we performed the enzyme-linked immunosorbent assay-based screening of 10 phytochemicals that already showed numerous positive effects on human health in several epidemiological studies and clinical trials. Among these phytochemicals, epigallocatechin gallate, a polyphenol and a major component of green tea, could effectively inhibit the interaction between the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 spike protein and the human cell receptor angiotensin-converting enzyme 2. Alternately, in silico molecular docking studies of epigallocatechin gallate and angiotensin-converting enzyme 2 indicated a binding score of -7.8 kcal/mol and identified a hydrogen bond between R393 and angiotensin-converting enzyme 2, which is considered as a key interacting residue involved in binding with the severe acute respiratory syndrome coronavirus 2 spike protein receptor-binding domain, suggesting the possible blocking of interaction between receptor-binding domain and angiotensin-converting enzyme 2. Furthermore, epigallocatechin gallate could attenuate severe acute respiratory syndrome coronavirus 2 infection and replication in Caco-2 cells. These results shed insight into identification and validation of severe acute respiratory syndrome coronavirus 2 entry inhibitors.


Assuntos
Enzima de Conversão de Angiotensina 2 , COVID-19 , Catequina , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Enzima de Conversão de Angiotensina 2/metabolismo , COVID-19/tratamento farmacológico , COVID-19/metabolismo , COVID-19/virologia , Células CACO-2 , Catequina/análogos & derivados , Catequina/farmacologia , Humanos , Simulação de Acoplamento Molecular , Peptidil Dipeptidase A/metabolismo , Ligação Proteica , SARS-CoV-2/metabolismo , Glicoproteína da Espícula de Coronavírus/metabolismo
3.
PLoS One ; 17(7): e0270761, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35793377

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-1), notoriously known as COVID-19, emerged in 2019 and was responsible for causing acute respiratory collapse. Moreover, in September 2020, new variant cases of severe acute respiratory syndrome coronavirus 2 were reported in the United Kingdom, with many patients and deaths. This study aimed to see knowledge, perception, and fear among the global population towards a new variant of severe acute respiratory syndrome coronavirus 2, known as Omicron (B.1.1.529). This online cross-sectional global study was conducted during the emergence of the B.1.1.529 variant, also known as the Omicron variant. The survey was carried out from 2nd December 2021 to 3rd January 2022. The descriptive analysis was presented as frequencies (N), percentages (%), and mean ± standard deviation (m ± SD). The association between dependent and categorical independent variables was determined using the Chi-square test (x2). Statistical analysis was performed by using SPSS version 23. Of 353 respondents, approximately 61% were females. One hundred fifty-four respondents were in the age group of 18-27 years. The average age was 31.53±10.3 (mean± SD). The majority of respondents (43.9%) were from Indonesia. The mean knowledge score about the Omicron variant was 3.18±1.14. Our study suggests that people have some knowledge about the new variant, Omicron (B.1.1.529). Besides, there was a significant association (p = 0.05) for the perception of the fatality rate of Omicron among the respondents from different countries. However, there is still an ample research gap in enlightening people about this infection (B.1.1.529).


Assuntos
COVID-19 , Adolescente , Adulto , COVID-19/epidemiologia , COVID-19/virologia , Estudos Transversais , Medo , Conhecimentos, Atitudes e Prática em Saúde , Humanos , Percepção , SARS-CoV-2 , Adulto Jovem
4.
Int J Mol Sci ; 23(14)2022 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-35886958

RESUMO

Despite the growing list of identified SARS-CoV-2 receptors, the human angiotensin-converting enzyme 2 (ACE2) is still viewed as the main cell entry receptor mediating SARS-CoV-2 internalization. It has been reported that wild-type mice, like other rodent species of the Muridae family, cannot be infected with SARS-CoV-2 due to differences in their ACE2 receptors. On the other hand, the consensus heparin-binding motif of SARS-CoV-2's spike protein, PRRAR, enables the attachment to rodent heparan sulfate proteoglycans (HSPGs), including syndecans, a transmembrane HSPG family with a well-established role in clathrin- and caveolin-independent endocytosis. As mammalian syndecans possess a relatively conserved structure, we analyzed the cellular uptake of inactivated SARS-CoV-2 particles in in vitro and in vivo mice models. Cellular studies revealed efficient uptake into murine cell lines with established syndecan-4 expression. After intravenous administration, inactivated SARS-CoV-2 was taken up by several organs in vivo and could also be detected in the brain. Internalized by various tissues, inactivated SARS-CoV-2 raised tissue TNF-α levels, especially in the heart, reflecting the onset of inflammation. Our studies on in vitro and in vivo mice models thus shed light on unknown details of SARS-CoV-2 internalization and help broaden the understanding of the molecular interactions of SARS-CoV-2.


Assuntos
COVID-19 , SARS-CoV-2 , Distribuição Tecidual , Internalização do Vírus , Enzima de Conversão de Angiotensina 2/metabolismo , Animais , COVID-19/metabolismo , COVID-19/virologia , Proteoglicanas de Heparan Sulfato/metabolismo , Humanos , Mamíferos/metabolismo , Camundongos , SARS-CoV-2/metabolismo , Sindecanas/metabolismo , Distribuição Tecidual/fisiologia
5.
Genes (Basel) ; 13(8)2022 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-35893066

RESUMO

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of the worldwide pandemic due to Coronavirus Disease 2019 (COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full-length SARS-CoV-2 genome on the 10 January 2020, with the hope of turning the table against the worsening pandemic situation. Previous studies in respiratory virus characterization require mapping of raw sequences to the human genome in the downstream bioinformatics pipeline as part of metagenomic principles. Illumina, as the major player in the NGS arena, took action by releasing guidelines for improved enrichment kits called the Respiratory Virus Oligo Panel (RVOP) based on a hybridization capture method capable of capturing targeted respiratory viruses, including SARS-CoV-2; therefore, allowing a direct map of raw sequences data to SARS-CoV-2 genome in downstream bioinformatics pipeline. Consequently, two bioinformatics pipelines emerged with no previous studies benchmarking the pipelines. This study focuses on gaining insight and understanding of target enrichment workflow by Illumina through the utilization of different bioinformatics pipelines named as 'Fast Pipeline' and 'Normal Pipeline' to SARS-CoV-2 strains isolated from Yogyakarta and Central Java, Indonesia. Overall, both pipelines work well in the characterization of SARS-CoV-2 samples, including in the identification of major studied nucleotide substitutions and amino acid mutations. A higher number of reads mapped to the SARS-CoV-2 genome in Fast Pipeline and merely were discovered as a contributing factor in a higher number of coverage depth and identified variations (SNPs, insertion, and deletion). Fast Pipeline ultimately works well in a situation where time is a critical factor. On the other hand, Normal Pipeline would require a longer time as it mapped reads to the human genome. Certain limitations were identified in terms of pipeline algorithm, whereas it is highly recommended in future studies to design a pipeline in an integrated framework, for instance, by using NextFlow, a workflow framework to combine all scripts into one fully integrated pipeline.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/virologia , Biologia Computacional/métodos , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , SARS-CoV-2/genética
6.
Viruses ; 14(8)2022 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-35893668

RESUMO

The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of an Omicron strain with lowered lethality, yet enhanced transmissibility. This direction of evolution might be partly explained by virus adaptation to therapeutic agents and enhanced escape from vaccine-induced and natural immunity formed by other SARS-CoV-2 strains. Omicron's high mutation rate in the Spike protein, as well as its previously described high genome mutation rate (Kandeel et al., 2021), revealed a gap between it and other SARS-CoV-2 strains, indicating the absence of a transitional evolutionary form to the Omicron strain. Therefore, Omicron has emerged as a new serotype divergent from the evolutionary lineage of other SARS-CoV-2 strains. Omicron is a rapidly evolving variant of high concern, whose new subvariants continue to manifest. Its further understanding and the further monitoring of key mutations that provide virus immune escape and/or high affinity towards the receptor could be useful for vaccine and therapeutic development in order to control the evolutionary direction of the COVID-19 pandemic.


Assuntos
COVID-19 , Evolução Molecular , Evasão da Resposta Imune , SARS-CoV-2 , COVID-19/imunologia , COVID-19/virologia , Humanos , Mutação , Pandemias , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética
7.
Viruses ; 14(7)2022 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-35891394

RESUMO

The rapid spread of the coronavirus disease COVID-19 has imposed clinical and financial burdens on hospitals and governments attempting to provide patients with medical care and implement disease-controlling policies. The transmissibility of the disease was shown to be correlated with the patient's viral load, which can be measured during testing using the cycle threshold (Ct). Previous models have utilized Ct to forecast the trajectory of the spread, which can provide valuable information to better allocate resources and change policies. However, these models combined other variables specific to medical institutions or came in the form of compartmental models that rely on epidemiological assumptions, all of which could impose prediction uncertainties. In this study, we overcome these limitations using data-driven modeling that utilizes Ct and previous number of cases, two institution-independent variables. We collected three groups of patients (n = 6296, n = 3228, and n = 12,096) from different time periods to train, validate, and independently validate the models. We used three machine learning algorithms and three deep learning algorithms that can model the temporal dynamic behavior of the number of cases. The endpoint was 7-week forward number of cases, and the prediction was evaluated using mean square error (MSE). The sequence-to-sequence model showed the best prediction during validation (MSE = 0.025), while polynomial regression (OLS) and support vector machine regression (SVR) had better performance during independent validation (MSE = 0.1596, and MSE = 0.16754, respectively), which exhibited better generalizability of the latter. The OLS and SVR models were used on a dataset from an external institution and showed promise in predicting COVID-19 incidences across institutions. These models may support clinical and logistic decision-making after prospective validation.


Assuntos
COVID-19 , Modelos Epidemiológicos , Algoritmos , COVID-19/epidemiologia , COVID-19/virologia , Aprendizado Profundo , Humanos , Aprendizado de Máquina , Máquina de Vetores de Suporte , Carga Viral
8.
Proc Natl Acad Sci U S A ; 119(30): e2123065119, 2022 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-35858407

RESUMO

SARS-CoV-2, the causative agent of the COVID-19 pandemic, undergoes continuous evolution, highlighting an urgent need for development of novel antiviral therapies. Here we show a quantitative mass spectrometry-based succinylproteomics analysis of SARS-CoV-2 infection in Caco-2 cells, revealing dramatic reshape of succinylation on host and viral proteins. SARS-CoV-2 infection promotes succinylation of several key enzymes in the TCA, leading to inhibition of cellular metabolic pathways. We demonstrated that host protein succinylation is regulated by viral nonstructural protein (NSP14) through interaction with sirtuin 5 (SIRT5); overexpressed SIRT5 can effectively inhibit virus replication. We found succinylation inhibitors possess significant antiviral effects. We also found that SARS-CoV-2 nucleocapsid and membrane proteins underwent succinylation modification, which was conserved in SARS-CoV-2 and its variants. Collectively, our results uncover a regulatory mechanism of host protein posttranslational modification and cellular pathways mediated by SARS-CoV-2, which may become antiviral drug targets against COVID-19.


Assuntos
Antivirais , COVID-19 , Interações Hospedeiro-Patógeno , Terapia de Alvo Molecular , Processamento de Proteína Pós-Traducional , SARS-CoV-2 , Antivirais/farmacologia , Antivirais/uso terapêutico , COVID-19/tratamento farmacológico , COVID-19/metabolismo , COVID-19/virologia , Células CACO-2 , Exorribonucleases/metabolismo , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Humanos , Processamento de Proteína Pós-Traducional/efeitos dos fármacos , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/fisiologia , Sirtuínas/metabolismo , Succinatos/metabolismo , Proteínas não Estruturais Virais/metabolismo , Replicação Viral/efeitos dos fármacos
12.
Proc Natl Acad Sci U S A ; 119(31): e2204336119, 2022 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-35858382

RESUMO

The durability of vaccine-mediated immunity to SARS-CoV-2, the durations to breakthrough infection, and the optimal timings of booster vaccination are crucial knowledge for pandemic response. Here, we applied comparative evolutionary analyses to estimate the durability of immunity and the likelihood of breakthrough infections over time following vaccination by BNT162b2 (Pfizer-BioNTech), mRNA-1273 (Moderna), ChAdOx1 (Oxford-AstraZeneca), and Ad26.COV2.S (Johnson & Johnson/Janssen). We evaluated anti-Spike (S) immunoglobulin G (IgG) antibody levels elicited by each vaccine relative to natural infection. We estimated typical trajectories of waning and corresponding infection probabilities, providing the distribution of times to breakthrough infection for each vaccine under endemic conditions. Peak antibody levels elicited by messenger RNA (mRNA) vaccines mRNA-1273 and BNT1262b2 exceeded that of natural infection and are expected to typically yield more durable protection against breakthrough infections (median 29.6 mo; 5 to 95% quantiles 10.9 mo to 7.9 y) than natural infection (median 21.5 mo; 5 to 95% quantiles 3.5 mo to 7.1 y). Relative to mRNA-1273 and BNT1262b2, viral vector vaccines ChAdOx1 and Ad26.COV2.S exhibit similar peak anti-S IgG antibody responses to that from natural infection and are projected to yield lower, shorter-term protection against breakthrough infection (median 22.4 mo and 5 to 95% quantiles 4.3 mo to 7.2 y; and median 20.5 mo and 5 to 95% quantiles 2.6 mo to 7.0 y; respectively). These results leverage the tools from evolutionary biology to provide a quantitative basis for otherwise unknown parameters that are fundamental to public health policy decision-making.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Imunogenicidade da Vacina , SARS-CoV-2 , Anticorpos Antivirais/sangue , Anticorpos Antivirais/imunologia , Formação de Anticorpos , COVID-19/imunologia , COVID-19/prevenção & controle , COVID-19/virologia , Vacinas contra COVID-19/imunologia , Vacinas contra COVID-19/uso terapêutico , Humanos , Imunoglobulina G/sangue , Imunoglobulina G/imunologia , SARS-CoV-2/imunologia , Glicoproteína da Espícula de Coronavírus/imunologia , Fatores de Tempo
14.
Proc Natl Acad Sci U S A ; 119(32): e2205690119, 2022 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-35881779

RESUMO

The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif (ΔQTQTN). Here, we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated, and disruption of its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site-the FCS, loop length, and glycosylation-are required for efficient SARS-CoV-2 replication and pathogenesis.


Assuntos
COVID-19 , Furina , Proteólise , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Motivos de Aminoácidos/genética , Animais , COVID-19/virologia , Chlorocebus aethiops , Furina/química , Humanos , SARS-CoV-2/genética , SARS-CoV-2/fisiologia , Deleção de Sequência , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Células Vero , Replicação Viral/genética
15.
Artigo em Inglês | MEDLINE | ID: mdl-35886225

RESUMO

The COVID-19 pandemic caused by SARS-CoV-2 is still raging. Similar to other RNA viruses, SARS-COV-2 is constantly mutating, which leads to the production of many infectious and lethal strains. For instance, the omicron variant detected in November 2021 became the leading strain of infection in many countries around the world and sparked an intense public debate on social media. The aim of this study is to explore the Chinese public's perception of the omicron variants on social media. A total of 121,632 points of data relating to omicron on Sina Weibo from 0:00 27 November 2021 to 23:59:59 30 March 2022 (Beijing time) were collected and analyzed with LDA-based topic modeling and DLUT-Emotion ontology-based sentiment analysis. The results indicate that (1) the public discussion of omicron is based on five topics, including omicron's impact on the economy, the omicron infection situation in other countries/regions, the omicron infection situation in China, omicron and vaccines and pandemic prevention and control for omicron. (2) From the 3 sentiment orientations of 121,632 valid Weibo posts, 49,402 posts were judged as positive emotions, accounting for approximately 40.6%; 47,667 were negative emotions, accounting for nearly 39.2%; and 24,563 were neutral emotions, accounting for about 20.2%. (3) The result of the analysis of the temporal trend of the seven categories of emotion attribution showed that fear kept decreasing, whereas good kept increasing. This study provides more insights into public perceptions of and attitudes toward emerging SARS-CoV-2 variants. The results of this study may provide further recommendations for the Chinese government, public health authorities, and the media to promote knowledge about SARS-CoV-2 variant pandemic-resistant messages.


Assuntos
COVID-19 , Emoções , Análise de Classes Latentes , Opinião Pública , SARS-CoV-2 , Análise de Sentimentos , Mídias Sociais , Atitude , COVID-19/economia , COVID-19/epidemiologia , COVID-19/prevenção & controle , COVID-19/virologia , Vacinas contra COVID-19 , China/epidemiologia , Governo Federal , Educação em Saúde , Humanos , Internacionalidade , Pandemias/prevenção & controle , Pandemias/estatística & dados numéricos , Saúde Pública
16.
Proc Natl Acad Sci U S A ; 119(31): e2200592119, 2022 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-35858386

RESUMO

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant contains extensive sequence changes relative to the earlier-arising B.1, B.1.1, and Delta SARS-CoV-2 variants that have unknown effects on viral infectivity and response to existing vaccines. Using SARS-CoV-2 virus-like particles (VLPs), we examined mutations in all four structural proteins and found that Omicron and Delta showed 4.6-fold higher luciferase delivery overall relative to the ancestral B.1 lineage, a property conferred mostly by enhancements in the S and N proteins, while mutations in M and E were mostly detrimental to assembly. Thirty-eight antisera samples from individuals vaccinated with Pfizer/BioNTech, Moderna, or Johnson & Johnson vaccines and convalescent sera from unvaccinated COVID-19 survivors had 15-fold lower efficacy to prevent cell transduction by VLPs containing the Omicron mutations relative to the ancestral B.1 spike protein. A third dose of Pfizer vaccine elicited substantially higher neutralization titers against Omicron, resulting in detectable neutralizing antibodies in eight out of eight subjects compared to one out of eight preboosting. Furthermore, the monoclonal antibody therapeutics casirivimab and imdevimab had robust neutralization activity against B.1 and Delta VLPs but no detectable neutralization of Omicron VLPs, while newly authorized bebtelovimab maintained robust neutralization across variants. Our results suggest that Omicron has similar assembly efficiency and cell entry compared to Delta and that its rapid spread is due mostly to reduced neutralization in sera from previously vaccinated subjects. In addition, most currently available monoclonal antibodies will not be useful in treating Omicron-infected patients with the exception of bebtelovimab.


Assuntos
Anticorpos Monoclonais Humanizados , Anticorpos Neutralizantes , Anticorpos Antivirais , COVID-19 , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Anticorpos Monoclonais Humanizados/uso terapêutico , Anticorpos Neutralizantes/imunologia , Anticorpos Neutralizantes/uso terapêutico , Anticorpos Antivirais/uso terapêutico , COVID-19/terapia , COVID-19/virologia , Humanos , Mutação , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade , Glicoproteína da Espícula de Coronavírus/genética
17.
PLoS One ; 17(7): e0270276, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35895734

RESUMO

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs. Differences in nucleotide and protein sequence composition within related ß-coronaviruses are often used to better understand CoV evolution, host adaptation, and their emergence as human pathogens. Here we report the comprehensive analysis of amino acid residue changes that have occurred in lineage B ß-coronaviruses that show covariance with each other. This analysis revealed patterns of covariance within conserved viral proteins that potentially define conserved interactions within and between core proteins encoded by SARS-CoV-2 related ß-coronaviruses. We identified not only individual pairs but also networks of amino acid residues that exhibited statistically high frequencies of covariance with each other using an independent pair model followed by a tandem model approach. Using 149 different CoV genomes that vary in their relatedness, we identified networks of unique combinations of alleles that can be incrementally traced genome by genome within different phylogenic lineages. Remarkably, covariant residues and their respective regions most abundantly represented are implicated in the emergence of SARS-CoV-2 and are also enriched in dominant SARS-CoV-2 variants.


Assuntos
COVID-19 , Evolução Molecular , SARS-CoV-2 , Aminoácidos/genética , Animais , COVID-19/virologia , Genoma Viral , Humanos , SARS-CoV-2/genética
18.
Commun Biol ; 5(1): 651, 2022 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-35778545

RESUMO

Angiotensin-converting enzyme 2 (ACE2) has been identified as a primary receptor for severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2). Here, we investigated the expression regulation of ACE2 in enterocytes under amino acid deprivation conditions. In this study, we found that ACE2 expression was upregulated upon all or single essential amino acid deprivation in human colonic epithelial CCD841 cells. Furthermore, we found that knockdown of general control nonderepressible 2 (GCN2) reduced intestinal ACE2 mRNA and protein levels in vitro and in vivo. Consistently, we revealed two GCN2 inhibitors, GCN2iB and GCN2-IN-1, downregulated ACE2 protein expression in CCD841 cells. Moreover, we found that increased ACE2 expression in response to leucine deprivation was GCN2 dependent. Through RNA-sequencing analysis, we identified two transcription factors, MAFB and MAFF, positively regulated ACE2 expression under leucine deprivation in CCD841 cells. These findings demonstrate that amino acid deficiency increases ACE2 expression and thereby likely aggravates intestinal SARS-CoV-2 infection.


Assuntos
Aminoácidos , Enzima de Conversão de Angiotensina 2 , COVID-19 , Enterócitos , Proteínas Serina-Treonina Quinases , Aminoácidos/deficiência , Aminoácidos/metabolismo , Enzima de Conversão de Angiotensina 2/biossíntese , Enzima de Conversão de Angiotensina 2/genética , Enzima de Conversão de Angiotensina 2/metabolismo , COVID-19/enzimologia , COVID-19/genética , COVID-19/virologia , Enterócitos/enzimologia , Enterócitos/metabolismo , Humanos , Leucina/farmacologia , Peptidil Dipeptidase A/fisiologia , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , SARS-CoV-2/metabolismo
19.
Nat Commun ; 13(1): 3921, 2022 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-35798721

RESUMO

Due to differences in human and murine angiotensin converting enzyme 2 (ACE-2) receptor, initially available SARS-CoV-2 isolates could not infect mice. Here we show that serial passaging of USA-WA1/2020 strain in mouse lungs results in "mouse-adapted" SARS-CoV-2 (MA-SARS-CoV-2) with mutations in S, M, and N genes, and a twelve-nucleotide insertion in the S gene. MA-SARS-CoV-2 infection causes mild disease, with more pronounced morbidity depending on genetic background and in aged and obese mice. Two mutations in the S gene associated with mouse adaptation (N501Y, H655Y) are present in SARS-CoV-2 variants of concern (VoCs). N501Y in the receptor binding domain of viruses of the B.1.1.7, B.1.351, P.1 and B.1.1.529 lineages (Alpha, Beta, Gamma and Omicron variants) is associated with high transmissibility and allows VoCs to infect wild type mice. We further show that S protein mutations of MA-SARS-CoV-2 do not affect neutralization efficiency by human convalescent and post vaccination sera.


Assuntos
COVID-19 , Evasão da Resposta Imune , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Idoso , Animais , COVID-19/virologia , Humanos , Soros Imunes , Camundongos , Mutação , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética
20.
World J Microbiol Biotechnol ; 38(9): 161, 2022 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-35834025

RESUMO

A violacein-producing bacterium was isolated from a mud sample collected near a hot spring on Kümbet Plateau in Giresun Province and named the GK strain. According to the phylogenetic tree constructed using 16S rRNA gene sequence analysis, the GK strain was identified and named Janthinobacterium sp. GK. The crude violacein pigments were separated into three different bands on a TLC sheet. Then violacein and deoxyviolacein were purified by vacuum liquid column chromatography and identified by NMR spectroscopy. According to the inhibition studies, the HIV-1 RT inhibition rate of 1 mM violacein from the GK strain was 94.28% and the CoV-2 spike RBD:ACE2 inhibition rate of 2 mM violacein was 53%. In silico studies were conducted to investigate the possible interactions between violacein and deoxyviolacein and three reference molecules with the target proteins: angiotensin-converting enzyme 2 (ACE2), HIV-1 reverse transcriptase, and SARS-CoV-2 spike receptor binding domain. Ligand violacein binds strongly to the receptor ACE2, HIV-1 reverse transcriptase, and SARS-CoV-2 spike receptor binding domain with a binding energy of -9.94 kcal/mol, -9.32 kcal/mol, and -8.27 kcal/mol, respectively. Deoxyviolacein strongly binds to the ACE2, HIV-1 reverse transcriptase, and SARS-CoV-2 spike receptor binding domain with a binding energy of -10.38 kcal/mol, -9.50 kcal/mol, and -8.06 kcal/mol, respectively. According to these data, violacein and deoxyviolacein bind to all the receptors quite effectively. SARS-CoV-2 spike protein and HIV-1-RT inhibition studies with violacein and deoxyviolacein were performed for the first time in the literature.


Assuntos
Enzima de Conversão de Angiotensina 2 , COVID-19 , HIV-1 , Indóis , Glicoproteína da Espícula de Coronavírus , COVID-19/metabolismo , COVID-19/virologia , HIV-1/metabolismo , Indóis/metabolismo , Indóis/farmacologia , Peptidil Dipeptidase A/química , Peptidil Dipeptidase A/metabolismo , Filogenia , Ligação Proteica , RNA Ribossômico 16S , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus/metabolismo
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