Application of a high-throughput quantitative PCR system for simultaneous monitoring of SARS-CoV-2 variants and other pathogenic viruses in wastewaterArticle Published on 2022-12-202022-11-15 Journal: The Science of the total environment [Category] COVID19(2023년), SARS, 변종, 치료기술, 치료제, [키워드] acute respiratory syndrome Alpha variant analyzed application applied assays can be used collected Community coronavirus coronavirus disease COVID-19 delta variant demonstrated detect eight epidemiologically FIVE Health High-throughput qPCR highlighting increase Japan L452R labor-intensive likelihood Mie N501Y nine nucleotide nucleotide substitution pathogenic virus pathogenic viruses Pathogenic viruses, SARS-CoV-2 Patient PCR positive prevalent qPCR quantitative PCR quarantine reported RNA RT-qPCR SARS-CoV-2 SARS-CoV-2 spike SARS-CoV-2 variant separated Surveillance target tested time-consuming Treatment virus viruses Volume wastewater Yokkaichi [DOI] 10.1016/j.scitotenv.2022.158659 PMC 바로가기
A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus StrainsSARS-CoV-2 바이러스 균주 검출 시 Illumina 차세대 시퀀싱 시스템 강화를 위한 생물정보학 파이프라인 비교Comparative Study Published on 2022-07-262022-09-11 Journal: Genes [Category] COVID19(2023년), SARS, 치료기술, 치료제, [키워드] acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 Algorithm Amino acid bioinformatics bioinformatics pipeline capture method characterization coronavirus 2 coronavirus disease Coronavirus disease 2019 Coverage COVID-19 Critical Deletion downstream enrichment enrichment. full-length SARS-CoV-2 genome Generation Hope Human genome Illumina Indonesia insertion limitation Major mapped mapping metagenomic mutations next generation sequencing NGS normal nucleotide nucleotide substitution nucleotide substitutions pandemic Panel Previous studies previous study reads respiratory respiratory virus respiratory viruses SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 strain SARS-CoV-2 strains sequence Severe acute respiratory syndrome severe acute respiratory syndrome Coronavirus situation SNPs strain Strains System table the SARS-CoV-2 genome utilization Variation virus worldwide pandemic worsening [DOI] 10.3390/genes13081330 PMC 바로가기 [Article Type] Comparative Study
First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France프랑스 마르세유에서 21L/BA.2 오미크론 변종 첫 감염 사례Article Published on 2022-07-012022-09-11 Journal: Journal of medical virology [Category] COVID19(2023년), SARS, 변종, [키워드] Amino acid amino acid substitution amino acid substitutions Clinical outcome Cluster country deletions Denmark deviation diagnosed distribution emergence England facilitate flattening France Genome genomes incidence Infection initial Interaction Marseille MONITOR N-terminal domain Nepal Next-generation sequencing nucleotide nucleotide substitution nucleotide substitutions omicron Omicron variant Phylogeny predominant qPCR remained resulting SARS-CoV-2 Singapore South Africa southern France Spike protein Surveillance the spike protein Travel variant viral genome viral genomes [DOI] 10.1002/jmv.27695 PMC 바로가기 [Article Type] Article
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein스파이크 단백질에서 N501Y 및 E484K 치환을 모두 담은 새로운 SARS-COV-2 변형의 프랑스 남부의 출현Annotated Sequence Record Published on 2022-02-182022-09-10 Journal: Archives of Virology [Category] COVID19(2023년), Fulltext, MERS, SARS, 변종, [키워드] Amino acid amino acid substitution amino acid substitutions Atypical Combination Deletion deletions E484K emergence epidemiological escape example France genome sequence Genome sequences Genotype geographical area index case isolate Lineage lineages Mutation N501Y new SARS-CoV-2 Next-generation sequencing nine nucleotide nucleotide substitution Oxford Nanopore Technologies Oxford Nanopore Technology pangolin Pangolin lineage Phylogenetic qPCR test resulting risk SARS-CoV-2 variant SARS-CoV-2 variants SARS-CoV-2-positive patient Spike protein Substitution supplementary material the spike protein These data Travel Vaccine-induced immunity variant Virological [DOI] 10.1007/s00705-022-05385-y PMC 바로가기 [Article Type] Annotated Sequence Record
Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organsArticle Published on 2022-02-152022-10-04 Journal: Virus research [Category] COVID19(2023년), MERS, SARS, 변종, [키워드] Abstract Analysis appear CoV COVID-19 Critical Divergent selection evade Evolution Evolutionary rate favor genetic data Host human ACE2 receptor Image increase indicate Infection Invasion Lineage Mutation Neutral nonsynonymous mutation nucleotide substitution organ organs RaTG13 residue RNA virus S1 protein SARS-CoV2 SARS-CoV2 genome Substitution synonymous Temporal virus [DOI] 10.1016/j.virusres.2022.198712 PMC 바로가기 [Article Type] Article
Genomic diversity and molecular dynamics interaction on mutational variances among RB domains of SARS-CoV-2 interplay drug inactivationSARS-CoV-2 상호 작용 약물 비활성화의 RB 도메인 간의 돌연변이 변이에 대한 게놈 다양성 및 분자 역학 상호 작용Article Published on 2022-01-012022-09-11 Journal: Infection, genetics and evolution : journal of mol [Category] SARS, 변종, 유전자 메커니즘, 치료제, [키워드] America Analysis Asia binding affinity conformational change country docking domain drug and vaccine development effective Efficiency Europe facilitate Genome genomes genomic genomic sequence inactivation Interaction investigated lowest molecular molecular docking molecular dynamics Molecular dynamics simulation molecular feature molecular features Mutation mutational analysis mutations nucleotide nucleotide substitution occurred performed Phylogenomic diversity Positive selection predicted prevalent Protein RBD RBD domain reference sequence Region Remdesivir Research retrieved S protein SARS-CoV-2 SARS-CoV-2 genomes Scientific community similarity spike the RBD the SARS-CoV-2 the SARS-CoV-2 genome USA Vaccine development [DOI] 10.1016/j.meegid.2021.105128 PMC 바로가기 [Article Type] Article
Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in CoronavirusesDiscoveries Published on 2021-12-102022-10-29 Journal: Molecular Biology and Evolution [Category] COVID-19, SARS, [키워드] Analysis Combination Complete complex conservation Coronaviral Coronaviruses data set detect disrupt elements evolutionary dynamics examined exceptional feature frameshift Genome genomic genomic data nucleotide nucleotide substitution ORF1a ORF1a/b ORF1b overlap performed Phylogenetic provide SARS-CoV-2 SARS-CoV-2 sequencing secondary structure sequence sequencing data specificity translation [DOI] 10.1093/molbev/msab265 PMC 바로가기 [Article Type] Discoveries
Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoringArticle Published on 2021-11-302022-10-31 Journal: Communications Biology [Category] COVID-19, SARS, [키워드] Affect Analysis antigenic B.1.1.7 B.1.351 B.1.617.2 consensus genome Course COVID-19 pandemic Deletion duplication Effect escaped Evidence furin site Genome informatics genomes higher infectivity identify insertion mechanism N-terminal domain Neutralizing antibodies new SARS-CoV-2 nucleotide substitution pandemic pathogenicity polymerase predicted Protein researcher SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 variants Sequencing subgenomic RNAs switching T-cell immunity Template the S protein the SARS-CoV-2 the Spike thought unique variant variants virulence virus [DOI] 10.1038/s42003-021-02858-9 PMC 바로가기 [Article Type] Article
A Comparative Study between Spanish and British SARS-CoV-2 Variants스페인과 영국 SARS-CoV-2 변종 간의 비교 연구Comparative Study Published on 2021-11-162022-09-11 Journal: Curr Issues Mol Biol [Category] SARS, 변종, [키워드] ACE2 ACE2 receptor Affect alignment angiotensin Angiotensin-converting enzyme angiotensin-converting enzyme 2 antigenicity binding binding affinity changes in Comparative Computational docking COVID-19 deletions docking domain energy fitness genome sequence genome variant genomics characterization homology host cell identity in silico infective Interaction interfere Ligand Mutation N501Y nucleotide nucleotide substitution predicted Predictive produced Protein Proteins reason reason for receptor SARS-CoV-2 SARS-CoV-2 spike protein SARS-CoV-2 variant sequence sequenced similarity Spanish Spike protein stability the RBD the SARS-CoV-2 the Spike the spike protein variant virus [DOI] 10.3390/cimb43030140 PMC 바로가기 [Article Type] Comparative Study
Genomic diversity of SARS-CoV-2 in MalaysiaBioinformatics Published on 2021-11-032022-10-28 Journal: PeerJ [Category] COVID-19, [키워드] A701V accumulated Algorithm analysed analyses approved Asian association circulating Clustering complexes Consequences Continuous country COVID-19 pandemic D614G distribution Emergency use epidemiological examined Genes Genetic genetic change genetic diversity Genome genomic GISAID Health help immune evasion isolate Lineage lineages Linkage disequilibrium Malaysia massive minimum Mutation mutations new SARS-CoV-2 Non-synonymous nucleotide substitution ORF1ab performed populations Public ranged researchers Result SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 virus sequence sequenced Seven Spread Surveillance tree Vaccine variant viral genome Viral genome sequencing viral nucleotide virus [DOI] 10.7717/peerj.12449 PMC 바로가기 [Article Type] Bioinformatics