Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France일상적인 게놈 감시 동안 병원 클러스터에서 검출된 SARS-CoV-2 ORF6 결실 변이체의 특성화, 프랑스 리옹Coronaviruses Published on 2021-01-272022-09-10 Journal: Emerging Microbes & Infections [Category] SARS, 변종, 치료기술, [키워드] Analysis Care CCL2 center characterization Cluster coding collected comparable replication Cytokines Deletion deletion variant disease severity fecal Frame France genomic Genomic surveillance Health Health care high plasma level high plasma levels hospital Host immune response host immune responses immune responses Infection Inflammation Inflammatory cytokine Inflammatory cytokines interferon-stimulated gene interferon-stimulated genes MCP1 molecular MONITOR nasopharyngeal sample NF-kB NF-kB pathway no difference nosocomial nosocomial cluster Nosocomial transmission Occurrence one health Open reading frame ORF6 overexpression Patient patients hospitalized performed Ptx3 reference respiratory respiratory viruses SARS-CoV-2 sequence severe COVID-19 Stool suggested Surveillance TNFα Transmission upregulated variants viruses while wild-type [DOI] 10.1080/22221751.2021.1872351 PMC 바로가기 [Article Type] Coronaviruses
Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene네바다 환자의 게놈 감시는 RdRp 유전자에 돌연변이가 있는 독특한 SARS-CoV-2 변이체의 유행을 나타냈습니다Article Published on 2021-01-202022-09-11 Journal: Journal of genetics and genomics = Yi chuan xue ba [Category] 변종, [키워드] accessory protein accessory proteins amplification association changed circulating circulation Community COVID-19 COVID-19 patient Culture determine diagnostic domain Evolution Frequency genome coverage Genome enrichment Genomic surveillance geographic locations humans Mutation Nsp12 Occurrence ORF1b orf1b 314. other variant other variants outbreak Patient Phenylalanine Phylogenetic relationship platform polymerase Prevalence proline public health RdRP RdRp gene reported required RNA RNA-dependent RNA polymerase robust RT-PCR SARS-CoV-2 SARS-CoV-2 variant SARS-CoV-2 variants sequenced Sequencing specimen swabs tested unique variant variants variants of SARS-CoV-2 Viral viral loads Wuhan-Hu-1 [DOI] 10.1016/j.jgg.2021.01.004 PMC 바로가기 [Article Type] Article
Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a태국에서 SARS-CoV-2의 게놈 감시는 혼합된 수입 개체군, 지역 혈통 확장 및 잘린 ORF7a가 있는 바이러스를 보여줍니다Article Published on 2021-01-152022-09-11 Journal: Virus research [Category] Coronavirus, SARS, 변종, 유전자 메커니즘, [키워드] coronavirus disease Coronavirus disease 2019 country COVID-19 diagnostic Genomic surveillance global public health Host Lineage Local ORF7a populations predominant reveal SARS-CoV-2 Thailand the SARS-CoV-2 truncated ORF7a virus [DOI] 10.1016/j.virusres.2020.198233 PMC 바로가기 [Article Type] Article
An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa서아프리카 베냉에서 SARS-CoV-2 분자 진단에 대한 관찰 실험실 기반 평가Observational Study Published on 2021-01-132022-09-10 Journal: mSphere [Category] MERS, 변종, 임상, 진단, 치료기술, 치료제, [키워드] activities acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 African Amplicon sequencing Analytical specificity assessment average B.1 Benin cell culture supernatant characterized Chinese circulation clinical samples clinical sensitivity comparable coronavirus coronavirus disease country COVID-19 COVID-19 pandemic D614G diagnostic diagnostics domain endemic human coronavirus endemic human coronaviruses Europe European foundation genomic Genomic surveillance HCoVs in vitro increase in introduced Jack Ma Laboratory Month N gene N genes National ORF1 ORF1ab overload pandemic performed positive sample reaction regions respiratory resulting RT-PCR RT-PCR kit SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genomes SARS-CoV-2 genomic surveillance SARS-CoV-2 lineage SARS-CoV-2 test SARS-CoV-2 tests severe acute respiratory syndrome Coronavirus similarity spike mutation Spike protein Spread Support target target region target regions test results Transmissibility variant West Africa [DOI] 10.1128/mSphere.00979-20 PMC 바로가기 [Article Type] Observational Study
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal포르투갈에서 SARS-CoV-2 Spike Y839 변종의 대규모 보급Research Article Published on 2020-11-252022-09-10 Journal: Emerging Microbes & Infections [Category] MERS, SARS, 변종, 유전자 메커니즘, 치료기술, 치료제, [키워드] anti-viral drug Anti-viral drugs collaboration confirmed case contributing to country COVID-19 COVID-19 case D839Y dissemination Effect Epidemic Epidemics experimental validation exponential phase Frequency functional fusion peptide Genetic variant Genome genomes Genomic epidemiology Genomic surveillance Italy massive motif Mutation peptide Portugal prevalent Region relative frequency required SARS-CoV-2 SARS-CoV-2 spike SARS-CoV-2 variant selective Sequencing spike spike variants Spread Support Surveillance the epidemic the Spike variant variants [DOI] 10.1080/22221751.2020.1844552 PMC 바로가기 [Article Type] Research Article
Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America남미에서 순환하는 SARS-CoV-2의 스파이크 및 뉴클레오캡시드 단백질의 치환Article Published on 2020-11-012022-09-11 Journal: Infection, genetics and evolution : journal of mol [Category] SARS, 치료법, [키워드] ACE Algorithm Amino acid Betacoronavirus Brazil circulating collected conserved country COVID-19 diagnostic assay COVID-19 pandemic D614G diagnostic tests Ecuador Epidemic Frequency genetic variability Genome genomes genomic Genomic surveillance genus genus Betacoronavirus high affinity human population Illumina Miseq immunogenic infect information Lower respiratory tract muscle N protein Non-synonymous substitutions nucleocapsid nucleotide nucleotide sequence Oxford pandemic Protein Proteins protocol receptor replaced REPLACED BY reported respiratory responsible SARS-CoV-2 SARS-CoV-2 pandemic sequence sequences Seven South South America spike Spike protein structural protein structural proteins Substitution substitutions Surveillance synonymous substitutions the SARS-CoV-2 the spike protein Therapeutics Vaccines virus [DOI] 10.1016/j.meegid.2020.104557 PMC 바로가기 [Article Type] Article
Genomic surveillance of COVID-19 cases in BeijingArticle Published on 2020-10-302022-10-04 Journal: Nature Communications [Category] MERS, SARS, 변종, 치료기술, 치료법, [키워드] Beijing Cluster collected comparison COVID-19 case effective Evolution Features genomic genomic sequence Genomic surveillance genomic variation groups identify implication indels isolate Local mandatory no significant difference outbreak phylogenetics Prevent quarantine random SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 isolate sequenced genome Seven Single nucleotide polymorphism single nucleotide variation SNPs Spread surveillance data Tolerance Transmission triggered Vaccines viral infection Wuhan [DOI] 10.1038/s41467-020-19345-0 PMC 바로가기 [Article Type] Article
The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencingResearch Article Published on 2020-08-112022-10-31 Journal: Emerging Microbes & Infections [Category] COVID-19, MERS, SARS, [키워드] Analysis assumption Brazil Chinese Complete confirmed case Consequences coronavirus country COVID-19 epidemic Epidemic epidemiological data estimate examined Genome genomic Genomic epidemiology Genomic surveillance geographical distribution highlight independent Italy lombardy Minas Gerais pandemic public health reduction in reported reproductive returned SARS-CoV-2 SARS-CoV-2 genome sequenced Sequencing southeast Brazil Spread Surveillance sustained the epidemic the SARS-CoV-2 virus transmission whole genome Wuhan [DOI] 10.1080/22221751.2020.1803146 PMC 바로가기 [Article Type] Research Article
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisationRapid Communication Published on 2020-07-052022-10-28 Journal: Virus Evolution [Category] COVID-19, [키워드] Amplicon sequencing amplicon-based enrichment approach ARTIC Network bioinformatics capture method characterisation Complete consensus sequence Coverage COVID-19 COVID-19 outbreak DNA enrichment evaluated Genome genome coverage genomes Genomic surveillance Genomics identity Illumina metagenomic metagenomic sequencing next generation sequencing NGS ONT ORF6 Oxford Nanopore Technology Panel performed producing protocol reference sequence Region required respiratory respiratory sample SARS-CoV-2 sequenced Sequencing SNP threshold Viral load WGS whole-genome sequencing [DOI] 10.1093/ve/veaa075 PMC 바로가기 [Article Type] Rapid Communication
SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle EastResearch Article Published on 2020-07-032022-10-31 Journal: Emerging Microbes & Infections [Category] COVID-19, MERS, SARS, [키워드] acute respiratory syndrome addition Americas clade clades contributed coronavirus COVID-19 Culture dominant Europe First wave Frame Genome sequencing Genomic surveillance genomic variation Infection Iran Local Middle East mutant Mutation ORF8 ORF8 deletion Patient performed Phylogenetic analysis Phylogeny SARS-CoV-2 SARS-CoV-2 genomic surveillance SARS-CoV-2 strain SARS-CoV-2 transmission second wave sequenced Sequencing strain Strains Taiwan trajectory Transmission Travel Turkey virus Wuhan [DOI] 10.1080/22221751.2020.1782271 PMC 바로가기 [Article Type] Research Article