Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients인플루엔자 유사 질병(ILI) 환자에서 SARS-CoV-2의 스파이크, RdRp 및 Orf3a 유전자 돌연변이의 구조적 매핑Article Published on 2021-01-192022-09-10 Journal: Viruses [Category] 치료기술, [키워드] Affect ambulatory patients Amino acid amino acid substitution Analysis binding site cause characterized China clade Clustering collected community transmission confirmation conformational change COVID-19 COVID-19 case COVID-19 illness D614G epidemiological link Extracellular followed by functional ILI illness incidence independent indicated Influenza influenza like illness influenza vaccine isolate Like mapping membrane mild COVID-19 illness mitigate Nasopharyngeal swab nasopharyngeal swabs next generation sequencing NGS oligomerization overlap P323L pandemic Patient PCR Public health interventions Q57H RdRP replaced SARS-CoV-2 SARS-CoV-2 RNA SARS-CoV-2 virus Sequencing silent silent transmission spike spike gene Substitution Surveillance thought Transcription Transmission transmission of SARS-CoV-2 virus virus replication [DOI] 10.3390/v13010136 PMC 바로가기 [Article Type] Article
Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, AustraliaArticle Published on 2021-01-192022-10-28 Journal: Viruses [Category] COVID-19, [키워드] acute respiratory syndrome Analysis changed changes in collected coronavirus COVID-19 pandemic dataset determine Diversity effort epidemiological Epidemiology etiological agent Evidence Factor Genes Genetic genetic bottleneck genomic sequence glycoprotein greater highlighting Host Intra-host diversity Intra-host variant iSNVs less lineages magnitude MONITOR N genes Next-generation sequencing NGS nonsynonymous nonsynonymous iSNVs nonsynonymous variant ORF1a ORF1b pathogen phylodynamic Phylogenetic Quasispecies quasispecy real time RNA virus SARS-CoV-2 SARS-CoV-2 gene single-nucleotide state Transmission variant Victoria virus [DOI] 10.3390/v13010133 PMC 바로가기 [Article Type] Article
Monitoring COVID-19 Transmission Risks by Quantitative Real-Time PCR Tracing of Droplets in Hospital and Living EnvironmentsResearch Article Published on 2021-01-062022-10-30 Journal: mSphere [Category] COVID-19, MERS, [키워드] accumulated acute respiratory syndrome amplicons association Asymptomatic carriers biofluid biological fluid biological fluids collected communicable disease Contamination coronavirus coronavirus disease COVID COVID-19 creating Critical droplet droplets Environment environmental contamination evaluated fecal fomite highest hospital hospital ward identify infections Influenza marker microbiota monitoring multiplex nasopharyngeal NGS occur pandemic Patient patients PCR public health qPCR quantitative real-time PCR released risk Saliva SARS-CoV-2 searched secretion selected Sequencing significantly Spread Support surface swabs trace tracing Transmission Viral RNA virus was performed widespread [DOI] 10.1128/mSphere.01070-20 PMC 바로가기 [Article Type] Research Article
Nucleic Acid-Based Diagnostic Tests for the Detection SARS-CoV-2: An UpdateReview Published on 2021-01-012022-10-31 Journal: Diagnostics [Category] COVID-19, [키워드] 2019-nCoV acute respiratory syndrome amplification caused CDC Characteristics Cluster coronavirus coronavirus disease country COVID-19 COVID-19 case CRISPR death detection Diagnosis diagnostic test diagnostics disadvantage drug Effect effort Emergency use authorization EUA FDA feature food Healthcare system highlight Impact isothermal LAMP lateral flow less limit NGS notable pandemic Panel Perspective pneumonia case POC protocol quarantine Rapid test recorded RT-PCR SARS-CoV-2 Sequencing Test Transmission virus Wuhan, China [DOI] 10.3390/diagnostics11010053 PMC 바로가기 [Article Type] Review
Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, IndonesiaBioinformatics Published on 2020-12-212022-10-28 Journal: PeerJ [Category] COVID-19, [키워드] Analysis appear applied Asia circulating clade Cluster collected Complete COVID-19 COVID-19 patient COVID-19 situation D614G mutation dataset dissemination distribution Europe full-length full-length genome sequence Genome GISAID Hospitalized Illumina Miseq Indonesia NC_045512.2 Next-generation sequencing NGS Patient Phylogenetic analysis reference genome Region Result retrieved SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 virus SARS-CoV-2 virus strain sequence severity variant virus virus genome virus sample was performed WGS Whole genome sequencing [DOI] 10.7717/peerj.10575 PMC 바로가기 [Article Type] Bioinformatics
Can Coronaviruses Steal Genes from the Host as Evidenced in Western European Hedgehogs by EriCoV Genetic Characterization?Article Published on 2020-12-202022-10-28 Journal: Viruses [Category] COVID-19, MERS, SARS, [키워드] Erinaceus coronavirus Eulipotyphla adaptive ancestor Asia bat Betacoronavirus Betacoronavirus infection betacoronaviruses Can cascade CD200 CD200 glycoprotein CD200 ortholog circulating collected Complete coronavirus correlation CoV eight EriCoV Erinaceus Erinaceus europaeus Eurasia Europe European Evolution Fecal sample genes encoding genetics genomes global pandemic hedgehog hedgehogs Host host gene Human involved Italy living cells MERS-CoV Middle East NGS ORF ORF3a ortholog pandemic Pathogens Phylogenetic Protein Proteins reported reservoir RT-PCR Sanger sequencing SARS-CoV SARS-CoV-2 sequence Sequence analysis Sequencing Steal strain the Spike viral strain virus viruses were used zoonotic [DOI] 10.3390/v12121471 PMC 바로가기 [Article Type] Article
Evolution of viral quasispecies during SARS-CoV-2 infectionArticle Published on 2020-11-012023-07-12 Journal: Clinical microbiology and infection : the official [Category] SARS, [키워드] Infection follow-up Minority variants NGS Quasispecies SARS-CoV-2 [DOI] 10.1016/j.cmi.2020.07.032 PMC 바로가기
Identification of a Novel Pathogen Using Family-Wide PCR: Initial Confirmation of COVID-19 in ThailandFamily-Wide PCR을 사용한 새로운 병원체 식별: 태국의 COVID-19 초기 확인Public Health Published on 2020-10-072022-09-11 Journal: Frontiers in Public Health [Category] MERS, SARS, 치료기술, [키워드] Chain Reaction characterized collected confirmation coronavirus COVID-19 disease disease outbreak Early detection Efficacy facilitate family-wide PCR Genome identification individual initial next generation sequencing NGS novel novel pathogen nucleotide outbreak pathogen Pathogens PCR PCR assay polymerase chain polymerase chain reaction positive result respiratory SARS-CoV-2 secretion sequence similarity Thailand whole genome sequence Wuhan Wuhan, China [DOI] 10.3389/fpubh.2020.555013 PMC 바로가기 [Article Type] Public Health
Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome AnalysisCommunication Published on 2020-09-292022-10-31 Journal: Diagnostics [Category] COVID-19, [키워드] Analysis genome analysis genome variant GISAID Illumina initiative library limitation Next-generation sequencing NGS outbreak Paragon performance Perspective preparation required SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genome sequence solution the SARS-CoV-2 Twist variant [DOI] 10.3390/diagnostics10100769 PMC 바로가기 [Article Type] Communication
Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patientsResearch Article Published on 2020-09-022022-10-31 Journal: Emerging Microbes & Infections [Category] COVID-19, MERS, SARS, [키워드] accumulate ACE2 receptor binding Burn circulation Complete COVID19 patient Deletion deletions described Diversity facilitate frameshift generate Genome host cell Infection insertions Mild Mutation rates natural selection Naturally Neutralizing antibodies NGS other coronaviruses Patient Protein Quasispecies Recombination reducing released respiratory virus S1 protein S1/S2 cleavage site SARS-CoV-2 SARS-CoV-2 S gene SARS-CoV-2 spike severe COVID-19 severe COVID-19 patients severity stop codon tissue damage Transmission Treatment upstream Vaccine development viral particle viral quasispecy virus [DOI] 10.1080/22221751.2020.1806735 PMC 바로가기 [Article Type] Research Article