IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoringTechnical Note Published on 2020-10-152022-10-31 Journal: GigaScience [Category] COVID-19, MERS, SARS, [키워드] Analysis bioinformatics categories Clinicians cloud-based contig COVID-2019 Critical Data analysis data interpretation dataset determine facilitate filtration finding Host Hypothesis Intensive knowledge Local metagenomic metagenomics microbe microbial nasopharyngeal swab sample Next-generation sequencing pathogen detection pathogen-specific Pathogens portal processed reagents reduce reported Research resources SARS-CoV-2 Support viral sequence virus virus detection Wuhan, China [DOI] 10.1093/gigascience/giaa111 PMC 바로가기 [Article Type] Technical Note
Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100 TM SystemMicrobiology Published on 2020-09-252022-10-31 Journal: Frontiers in Microbiology [Category] COVID-19, [키워드] amplicon-based sequencing approach characterization Chinese clinical sample consensus genome COVID-19 Direct Genome sequencing Health help human diseases Illumina increasingly involved iSeq100TM system Laboratory MERS Middle East MinION next-generation sequencer pathogen Pneumonia public health measures Rapid real-time genome sequencing respiratory SARS-CoV-2 System Threats viral outbreak viral sequence Wuhan [DOI] 10.3389/fmicb.2020.571328 PMC 바로가기 [Article Type] Microbiology
In silico identification of conserved cis -acting RNA elements in the SARS-CoV-2 genomeShort Communication Published on 2020-07-292022-10-31 Journal: Future Virology [Category] COVID-19, [키워드] cis-acting RNA elements 3′ end acute respiratory syndrome Analysis Antiviral conserved coronavirus element Genome genomic material ORF1ab predict RNA RNA secondary structure RNA sequence RNA structure RNA virus SARS-CoV SARS-CoV-2 Structure the SARS-CoV-2 the SARS-CoV-2 genome therapeutic Vaccine viral sequence were used [DOI] 10.2217/fvl-2020-0163 PMC 바로가기 [Article Type] Short Communication
Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL pro targeting repurposed drug candidatesResearch Published on 2020-07-092022-10-30 Journal: Journal of Translational Medicine [Category] COVID-19, SARS, [키워드] 3CL pro acute respiratory syndrome African analysed anti-malarial drug Anti-viral bat-CoV Clustal Omega collected Complete Compound cysteine protease database drug candidate enzyme fatality Genetic Genome genomic sequence GISAID high mutation rate host genome host immunity identity implication in silico analysis in silico approaches in-depth analysis individual infection rate inhibitor initiative Interaction isolate Local Multiple mutagenic mutations occurred pandemic Pandemics pangolin-CoV pathogen pathogenicity pharmacological populations provide recurrent mutation reference genome regulate reported Repurposed drug Result RNA SARS Coronavirus SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 infected patients SARS-CoV2 sequence South South America the SARS-CoV-2 unique viral genome viral pathogenicity viral replication viral sequence was collected was used Wuhan [DOI] 10.1186/s12967-020-02448-z PMC 바로가기 [Article Type] Research
Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from TurkeyArticle Published on 2020-06-212022-10-29 Journal: Turkish Journal of Biology [Category] COVID-19, [키워드] acute respiratory syndrome analyzed Asia coronavirus coronavirus disease country COVID-19 diagnosed Europe evaluated Evolution GISAID database Haplotype identification Mutation North America nucleotide substitution Oceania pandemic SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 sequence shown the disease Turkey viral isolate viral sequence viral strain Wuhan [DOI] 10.3906/biy-2005-69 PMC 바로가기 [Article Type] Article
Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome1001 Published on 2020-06-102022-10-28 Journal: Royal Society Open Science [Category] COVID-19, [키워드] 2019-nCoV acute respiratory syndrome Analysis approach binding bioinformatics Clinicians conducted coronavirus coronavirus SARS-CoV-2 COVID-19 COVID-19 pandemic Diagnosis diagnostic Genome in silico information Laboratory Patient PCR PCR assay PCR assays polymerase chain Polymerase chain reaction (PCR) Presence primer–template mismatch professional Region responsible SARS-CoV-2 sequence variability sequence variation target region viral genome viral sequence viral sequences was performed WHO World Health Organization [DOI] 10.1098/rsos.200636 PMC 바로가기 [Article Type] 1001
A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data AnalysisOriginal Paper Published on 2020-06-012022-10-31 Journal: JMIR Public Health and Surveillance [Category] COVID-19, SARS, [키워드] acute respiratory syndrome affecting Analysis available data coronavirus COVID-19 data set determine dissemination distress effort Evolution genetic heterogeneity genetics Genome genome sequence GISAID Infectious disease information initiative limitation limitations objective pandemic Phylogenetic phylogenetics plethora released required Result robust SARS-CoV-2 SARS-CoV-2 sequence Scientific community sequence spatiotemporal Spread the epidemic tracing tracking Transmission transmission cluster viral sequence virus [DOI] 10.2196/19170 PMC 바로가기 [Article Type] Original Paper
VADR: validation and annotation of virus sequence submissions to GenBankSoftware Published on 2020-05-242022-10-27 Journal: BMC Bioinformatics [Category] Coronavirus, Fulltext, MERS, [키워드] added alignment Analysis annotation annotations automatically Biotechnology center Characteristics checked curated Dengue GenBank hidden markov model identify IMPROVE incrementally Influenza virus Intervention Local mapped NCBI ncRNA Norovirus nucleotide nucleotide sequence Other Protein RefSeq researcher Result SARS-CoV-2 sequence sequence submission viral sequence viral sequences virus [DOI] 10.1186/s12859-020-3537-3 PMC 바로가기 [Article Type] Software
Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequencesArticle Published on 2018-07-032022-10-29 Journal: Scientific Reports [Category] Coronavirus, [키워드] applied approach Comparative conserved coronavirus correlated dinucleotide Diseases Frequency gene sequences Host influenza A virus influenza A viruses investigated K -mer pandemic predict Rabies virus Sample size sequence spike gene Support Surveillance SVM time-consuming Variability viral sequence virus viruses [DOI] 10.1038/s41598-018-28308-x PMC 바로가기 [Article Type] Article
Genetics and Pathogenesis of Feline Infectious Peritonitis VirusResearch Published on 2009-09-012022-10-31 Journal: Emerging Infectious Diseases [Category] Coronavirus, [키워드] addition amino acid residue Analysis avirulent circulating clinically colonies coronavirus diagnostic disease Endemic exhibit feline form functional Genes Genetic healthy hypotheses in vivo Infection infectious infectious peritonitis marker Maryland membrane membrane protein mutate outbreak pathogenic peritonitis phylogenetic analyses Population populations Protein Research sequence sick strain Uncertainty USA viral sequence virulence virulent viruses [DOI] 10.3201/eid1509.081573 PMC 바로가기 [Article Type] Research