Bioinformatics and Biology Insights最新文献

{"title":"LC-MS Analysis, Computational Investigation, and Antimalarial Studies of <i>Azadirachta indica</i> Fruit.","authors":"Kolade O Faloye,&nbsp;Stephen A Adesida,&nbsp;Samuel A Oguntimehin,&nbsp;Adetola H Adewole,&nbsp;Olajide B Omoyeni,&nbsp;Sunday J Fajobi,&nbsp;Jeremiah P Ugwo,&nbsp;Isaac D Asiyanbola,&nbsp;Victoria O Bamimore,&nbsp;Emmanuel G Fakola,&nbsp;Olayemi J Oladiran,&nbsp;Michael Spiteller","doi":"10.1177/11779322231154966","DOIUrl":"https://doi.org/10.1177/11779322231154966","url":null,"abstract":"<p><p>Malaria is a deadly disease that continues to pose a threat to children and maternal well-being. This study was designed to identify the chemical constituents in the ethanolic fruit extract of <i>Azadirachta indica</i>, elucidate the pharmacological potentials of identified phytochemicals through the density functional theory method and carry out the antimalarial activity of extract using chemosuppression and curative models. The liquid chromatography-mass spectrometry (LC-MS) analysis of the ethanolic extract was carried out, followed by the density functional theory studies of the identified phytochemicals using B3LYP and 6-31G (d, p) basis set. The antimalarial assays were performed using the chemosuppression (4 days) and curative models. The LC-MS fingerprint of the extract led to the identification of desacetylnimbinolide, nimbidiol, O-methylazadironolide, nimbidic acid, and desfurano-6α-hydroxyazadiradione. Also, the frontier molecular orbital properties, molecular electrostatic potential, and dipole moment studies revealed the identified phytochemicals as possible antimalarial agents. The ethanolic extract of <i>A indica</i> fruit gave 83% suppression at 800 mg/kg, while 84% parasitaemia clearance was obtained in the curative study. The study provided information about the phytochemicals and background pharmacological evidences of the antimalarial ethnomedicinal claim of <i>A indica</i> fruit. Thus, isolation and structure elucidation of the identified phytochemicals from the active ethanolic extract and extensive antimalarial studies towards the discovery of new therapeutic agents is recommended for further studies.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b8/cb/10.1177_11779322231154966.PMC9969453.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9385358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Evidence of Multiple Introductions of SARS-CoV-2 in Mauritania.","authors":"Abdelmalick Abdelmalick,&nbsp;Sofia Sehli,&nbsp;Abdellah Idrissi Azami,&nbsp;Nihal Habib,&nbsp;Najib Al Idrissi,&nbsp;Lahcen Belyamani,&nbsp;Ahmed Houmeida,&nbsp;Hassan Ghazal","doi":"10.1177/11779322231167927","DOIUrl":"https://doi.org/10.1177/11779322231167927","url":null,"abstract":"<p><p>The rapid and global spread of the novel coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has raised serious public health concerns, including in Mauritania. We sequenced and analyzed the entire genome of 13 SARS-CoV-2 virus strains isolated from polymerase chain reaction (PCR)-positive symptomatic patients sampled from March 3 to May 31, 2021 to better understand SARS-CoV-2 introduction, propagation, and evolution in Mauritania. A phylogenetic tree using available data from the EpiCoV GISAID database and a variant network with non-Mauritanian sequences were constructed. Variant analysis of the 13 Mauritanian SARS-CoV-2 genome sequences indicated an average mutational percentage of 0.39, which is similar to that in other countries. Phylogenetic analysis revealed multiple spatiotemporal introductions, mainly from Europe (France, Belgium) and Africa (Senegal, Côte d'Ivoire), which also provided evidence of early community transmission. A total of 2 unique mutations, namely, NSP6_Q208K and NSP15_S273T, were detected in the <i>NSP6</i> and <i>NSP15</i> genes, respectively, confirming the aforementioned introduction of SARS-CoV-2 in Mauritania. These findings highlight the relevance of continuous genomic monitoring strategies for understanding virus transmission dynamics and acquiring knowledge to address forthcoming sources of infection in Africa.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/86/1f/10.1177_11779322231167927.PMC10130938.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9386557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into Omicron's Low Fusogenicity through <i>In Silico</i> Molecular Studies on Spike-Furin Interactions.","authors":"Spencer Mark Mondol,&nbsp;Md Hasib,&nbsp;Md Belayet Hasan Limon,&nbsp;A S M Rubayet Ul Alam","doi":"10.1177/11779322231189371","DOIUrl":"https://doi.org/10.1177/11779322231189371","url":null,"abstract":"<p><p>The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we <i>in silico</i> targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we <i>in silico</i> constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/20/b3/10.1177_11779322231189371.PMC10387760.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9928767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural-Based Virtual Screening of FDA-Approved Drugs Repository for NSP16 Inhibitors, Essential for SARS-COV-2 Invasion Into Host Cells: Elucidation From MM/PBSA Calculation.","authors":"Subodh Kumar,&nbsp;Harvinder Singh,&nbsp;Manisha Prajapat,&nbsp;Phulen Sarma,&nbsp;Anusuya Bhattacharyya,&nbsp;Hardeep Kaur,&nbsp;Gurjeet Kaur,&nbsp;Nishant Shekhar,&nbsp;Karanveer Kaushal,&nbsp;Kalpna Kumari,&nbsp;Seema Bansal,&nbsp;Saniya Mahendiratta,&nbsp;Arushi Chauhan,&nbsp;Ashutosh Singh,&nbsp;Rahul Soloman Singh,&nbsp;Saurabh Sharma,&nbsp;Prasad Thota,&nbsp;Pramod Avti,&nbsp;Ajay Prakash,&nbsp;Anurag Kuhad,&nbsp;Bikash Medhi","doi":"10.1177/11779322231171777","DOIUrl":"https://doi.org/10.1177/11779322231171777","url":null,"abstract":"<p><p>NSP16 is one of the structural proteins of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) necessary for its entrance to the host cells. It exhibits 2'O-methyl-transferase (2'O-MTase) activity of NSP16 using methyl group from S-adenosyl methionine (SAM) by methylating the 5-end of virally encoded mRNAs and shields viral RNA, and also controls its replication as well as infection. In the present study, we used in silico approaches of drug repurposing to target and inhibit the SAM binding site in NSP16 using Food and Drug Administration (FDA)-approved small molecules set from Drug Bank database. Among the 2 456 FDA-approved molecules, framycetin, paromomycin, and amikacin were found to be significant binders against the SAM binding cryptic pocket of NSP16 with docking score of -13.708, -14.997 and -15.841 kcal/mol, respectively. Classical molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA)-based binding free energy calculation depicted that all these three framycetin, paromomycin, and amikacin might be promising therapeutic leads towards SARS-CoV-2 infections via host immune escape inhibition pathway.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7e/50/10.1177_11779322231171777.PMC10392196.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9932956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Investigation of a Chimeric IL24-LK6 Fusion Protein as a Potent Candidate Against Breast Cancer.","authors":"Hafiz Muhammad Rehman,&nbsp;Hafiz Muzzammel Rehman,&nbsp;Muhammad Naveed,&nbsp;Muhammad Tahir Khan,&nbsp;Muhammad Aqib Shabbir,&nbsp;Shakira Aslam,&nbsp;Hamid Bashir","doi":"10.1177/11779322231182560","DOIUrl":"https://doi.org/10.1177/11779322231182560","url":null,"abstract":"<p><p>Targeted delivery of therapeutic anticancer chimeric molecules enhances the efficacy of drug by improving cellular uptake and circulation time. Engineering the molecules to facilitate the specific interaction between chimeric protein and its receptor is critical to elucidate biological mechanism as well as accuracy in modeling of complexes. A theoretically designed novel protein-protein interfaces can serve as a bottom-up method for comprehensive understanding of interacting protein residues. This study was aimed for in silico analyses of a chimeric fusion protein against breast cancer. The amino acid sequences of the interleukin 24 (IL-24) and LK-6 peptide were used to design the chimeric fusion protein via a rigid linker. The secondary and tertiary structures along with physicochemical properties by ProtParam and solubility were predicted using online software. The validation and quality of the fusion protein was confirmed by Rampage and ERRAT2. The newly designed fusion construct has a total length of 179 amino acids. The top-ranked structure from alpha fold2 showed 18.1 KD molecular weight by ProtParam, quality factor of 94.152 by ERRAT, and a valid structure by a Ramachandran plot with 88.5% residues in the favored region. Finally, the docking and simulation studies were performed using HADDOCK and Desmond module of Schrodinger. The quality, validity, interaction analysis, and stability of the fusion protein depict a functional molecule. The fusion gene IL24-LK6 after cloning and expression in a suitable prokaryotic cell might be a useful candidate for developing a novel anticancer therapy.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/db/49/10.1177_11779322231182560.PMC10291407.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10352006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking.","authors":"Md Anisur Rahman,&nbsp;Md Al Amin,&nbsp;Most Nilufa Yeasmin,&nbsp;Md Zahidul Islam","doi":"10.1177/11779322231186481","DOIUrl":"https://doi.org/10.1177/11779322231186481","url":null,"abstract":"<p><p>The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to \"Smoking and COVID-19: a scoping review,\" about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis. We have applied all important methods namely protein-protein interaction, hub-protein interaction, drug-protein interaction, tf-gene interaction, and gene-MiRNA interaction of bioinformatics to analyze to understand deeply the connection between both smoking and COVID-19 severity. We have also analyzed Pathways and Gene Ontology where 5 significant signaling pathways were validated with previous literature. Also, we verified 7 hub-proteins, and finally, we validated a total of 7 drugs with the previous study.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d0/0c/10.1177_11779322231186481.PMC10350588.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9831677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Potential of Ameliorating COVID-19 and Sequelae From <i>Andrographis paniculata</i> via Bioinformatics.","authors":"Hien Thi Nguyen,&nbsp;Van Mai Do,&nbsp;Thanh Thuy Phan,&nbsp;Dung Tam Nguyen Huynh","doi":"10.1177/11779322221149622","DOIUrl":"https://doi.org/10.1177/11779322221149622","url":null,"abstract":"<p><p>The current coronavirus disease 2019 (COVID-19) outbreak is alarmingly escalating and raises challenges in finding efficient compounds for treatment. Repurposing phytochemicals in herbs is an ideal and economical approach for screening potential herbal components against COVID-19. <i>Andrographis paniculata</i>, also known as Chuan Xin Lian, has traditionally been used as an anti-inflammatory and antibacterial herb for centuries and has recently been classified as a promising herbal remedy for adjuvant therapy in treating respiratory diseases. This study aimed to screen Chuan Xin Lian's bioactive components and elicit the potential pharmacological mechanisms and plausible pathways for treating COVID-19 using network pharmacology combined with molecular docking. The results found terpenoid (andrographolide) and flavonoid (luteolin, quercetin, kaempferol, and wogonin) derivatives had remarkable potential against COVID-19 and sequelae owing to their high degrees in the component-target-pathway network and strong binding capacities in docking scores. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the PI3K-AKT signaling pathway might be the most vital molecular pathway in the pathophysiology of COVID-19 and long-term sequelae whereby therapeutic strategies can intervene.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/3c/37/10.1177_11779322221149622.PMC9841859.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9114842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Interaction Analysis of Molecular Markers in Pancreatic Ductal Adenocarcinoma by Bioinformatics and Next-Generation Sequencing Data Analysis.","authors":"Muttanagouda Giriyappagoudar,&nbsp;Basavaraj Vastrad,&nbsp;Rajeshwari Horakeri,&nbsp;Chanabasayya Vastrad","doi":"10.1177/11779322231186719","DOIUrl":"https://doi.org/10.1177/11779322231186719","url":null,"abstract":"<p><strong>Background: </strong>Pancreatic ductal adenocarcinoma (PDAC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the molecular pathogenesis, but the molecular mechanisms of PDAC are still not well understood. The purpose of this study is to further explore the molecular mechanism of PDAC through integrated bioinformatics analysis.</p><p><strong>Methods: </strong>To identify the candidate genes in the carcinogenesis and progression of PDAC, next-generation sequencing (NGS) data set GSE133684 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and Gene Ontology (GO) and pathway enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using Integrated Interactions Database (IID) interactome database and Cytoscape. Subsequently, miRNA-DEG regulatory network and TF-DEG regulatory network were constructed using miRNet database, NetworkAnalyst database, and Cytoscape software. The expression levels of hub genes were validated based on Kaplan-Meier analysis, expression analysis, stage analysis, mutation analysis, protein expression analysis, immune infiltration analysis, and receiver operating characteristic (ROC) curve analysis.</p><p><strong>Results: </strong>A total of 463 DEGs were identified, consisting of 232 upregulated genes and 233 downregulated genes. The enriched GO terms and pathways of the DEGs include vesicle organization, secretory vesicle, protein dimerization activity, lymphocyte activation, cell surface, transferase activity, transferring phosphorus-containing groups, hemostasis, and adaptive immune system. Four hub genes (namely, cathepsin B [CCNB1], four-and-a-half LIM domains 2 (FHL2), major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) and tubulin beta 1 class VI (TUBB1)) were obtained via taking interaction of different analysis results.</p><p><strong>Conclusions: </strong>On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of PDAC and provide potential targets for further investigation.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b1/72/10.1177_11779322231186719.PMC10387711.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9926470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomics Reveals the Microbiome Multifunctionalities of Environmental Importance From Termite Mound Soils.","authors":"Ben Jesuorsemwen Enagbonma,&nbsp;Olubukola Oluranti Babalola","doi":"10.1177/11779322231184025","DOIUrl":"https://doi.org/10.1177/11779322231184025","url":null,"abstract":"<p><p>The ecological deterioration caused by the continuous and excessive use of synthetic inputs in agriculture has prompted the search for environmentally favorable resources for crop production. Many have advocated for the use of soils from termite mounds to improve soil and plant health; therefore, the purpose of this study was to characterize the microbiome multifunctionalities that are important for plant health and growth in termite mound soil. The metagenomics of soil from termite mounds revealed taxonomic groups with functional potentials associated with promoting the growth and health of plants in nutrient-poor, virtually dry environments. Analysis of microorganisms revealed that <i>Proteobacteria</i> dominated the soil of termite colonies, while <i>Actinobacteria</i> ranked second. The predominance of <i>Proteobacteria</i> and <i>Actinobacteria</i>, the well-known antibiotic-producing populations, indicates that the termite mound soil microbiome possesses metabolic resistance to biotic stresses. Functions recognized for diverse proteins and genes unveiled that a multi-functional microbiome carry out numerous metabolic functions including virulence, disease, defense, aromatic compound and iron metabolism, secondary metabolite synthesis, and stress response. The abundance of genes in termite mound soils associated with these prominent functions could unquestionably validate the enhancement of plants in abiotic and biotically stressed environments. This study reveals opportunities to revisit the multifunctionalities of termite mound soils in order to establish a connection between taxonomic diversity, targeted functions, and genes that could improve plant yield and health in unfavorable soil conditions.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fd/93/10.1177_11779322231184025.PMC10328015.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10300407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia.","authors":"Gabriella Sgorlon,&nbsp;Tárcio Peixoto Roca,&nbsp;Ana Maisa Passos-Silva,&nbsp;Márlon Grégori Flores Custódio,&nbsp;Jackson Alves da Silva Queiroz,&nbsp;André Luiz Ferreira da Silva,&nbsp;Karolaine Santos Teixeira,&nbsp;Flávia Serrano Batista,&nbsp;Juan Miguel Villalobos Salcedo,&nbsp;Rita de Cassia P Rampazzo,&nbsp;Felipe Gomes Naveca,&nbsp;Deusilene Vieira","doi":"10.1177/11779322231186477","DOIUrl":"https://doi.org/10.1177/11779322231186477","url":null,"abstract":"<p><p>The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced. We analyzed the quality and mutations of the genomes and maximum likelihood phylogenetic inference. However, 3 main clusters were observed, referring to Gamma (52.91%), Delta (24.38%), and Omicron (20.38%) VOCs with wide distribution in all health regions of the Rondônia state. Regarding the vaccination profile, there was a higher percentage of unvaccinated and partially vaccinated individuals, with more representatives by the Gamma variant. A total of 1412 sequences were suitable for mutation analysis in the S gene region. The Omicron VOC showed 38 mutations, with the Delta and Gamma variants with 16 and 17, respectively. The VOC Omicron and Gamma shared 4 mutations E484K, H655Y, N501Y, and N679K with high frequency, and Delta and Omicron 2 mutations (T478K and T95I). Regarding the comparison between the frequency of mutations for each variant concerning the vaccination groups, there were no changes in mutations for each group. In conclusion, the study showed a temporal increase in mutations and subvariants for characterized strains. Furthermore, the vaccination profile did not impact significant changes in the mutational profile yet remains a determining factor for severe disease.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/88/5a/10.1177_11779322231186477.PMC10350575.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9886260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}