Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore SequencingAmplicon-Oxford 나노포어 시퀀싱을 통한 고품질 SARS-CoV-2 게놈의 신속한 획득Article Published on 2021-10-012022-09-11 Journal: Virologica Sinica [Category] SARS, 치료기술, [키워드] acquisition Amplicon amplification Analysis approach complexity comprehensive evaluation conducted correlated COVID-19 pandemic COVID-19 patient Ct value Ct values detect effective error rate evaluated experiment Genetic Genome Genome sequencing genomic Illumina IMPROVE indicated initial less multi Mutation nanopore sequencing nucleic acid Oxford pathogen identification PCR platform Rapid resource SARS-CoV-2 SARS-CoV-2 genome Sequencing shown specimen Stage throat swab transcript Variation Viral load virus were assessed while yielding [DOI] 10.1007/s12250-021-00378-8 PMC 바로가기 [Article Type] Article
Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variantsTools and Resources Published on 2021-09-282022-10-31 Journal: eLife [Category] COVID-19, SARS, [키워드] Affect Amplicon approach cDNA cDNA synthesis ClickSeq clinical sample Complete coronavirus genome Critical Defective RNAs driving event Evolution Final generate Genome genome coverage Genomics identify Illumina junction limitations nanopore sequencing Next-generation sequencing NGS nucleic acid pathogenicity PCR reaction platform primer primer pairs provide RNA RNA recombination robust SARS-CoV-2 SARS-CoV-2 isolate sensitivity sequence Sequencing sgmRNAs single-nucleotide SNV SNVs specificity Structural variant sub-genomic mRNA SVs Tiled-ClickSeq Transmission UMI Unique Molecular Identifier variant variants Variation virus virus genome viruses while [DOI] 10.7554/eLife.68479 PMC 바로가기 [Article Type] Tools and Resources
Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling PipelinesSARS-COV-2 ORF8에서 168- 뉴클레오티드 결실의 다중 발생, 표준 앰플 리콘 시퀀싱 및 변형 호출 파이프 라인에 의해 눈에 띄지 않습니다.Article Published on 2021-09-182022-09-10 Journal: Viruses [Category] SARS, 변종, 치료기술, [키워드] Amplicon Amplicon sequencing amplicons analyzed ARTIC protocol classical coding region Consensus Data analysis database Deletion deletions ENA endemism Genome Genomic surveillance hospital hotspot identify infection chain infection chains investigated Lineage Local Multiple Mutation Nanopore nanopore sequencing nucleotide nucleotides ORF8 ORF8 deletion ORF8 gene outbreak Outbreaks pandemic Physiology Positive selection protocols raw data reported SARS-CoV-2 SARS-CoV-2 genome sequences SARS-CoV-2 pandemic SARS-CoV-2 sequence sequence Sequencing Standard the SARS-CoV-2 viral genomics virus virus genome [DOI] 10.3390/v13091870 PMC 바로가기 [Article Type] Article
Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domainSARS-CoV-2 스파이크 단백질 N-말단 도메인의 중화 항체 에피토프에서 숙주 내 비 동의어 다양성Article Published on 2021-09-012022-09-11 Journal: Clinical microbiology and infection : the official [Category] SARS, 변종, 진단, [키워드] Affect Amino acid amino acid residue binding Clusters collected Course COVID-19 COVID-19 patient COVID-19 patients database deep sequencing demonstrated determine epitope Epitopes Frequency Genetic hotspot Illumina Illumina sequencing Infection Intra-host diversity monoclonal antibodies Mutation mutations N-terminal domain Nanopore nanopore sequencing Neutralizing neutralizing antibody neutralizing epitope neutralizing epitopes Non-synonymous Non-synonymous mutation nucleotide Patient performed respiratory respiratory specimen respiratory tract Saliva Sanger sequencing SARS-CoV-2 SARS-CoV-2 spike protein sequence sequenced sequences Sequencing severe disease single nucleotide polymorphisms specimen spike spike gene Spike protein sputum the spike protein therapeutic efficacy Viral viral genome was performed [DOI] 10.1016/j.cmi.2020.10.030 PMC 바로가기 [Article Type] Article
Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: Lessons learned to optimize future molecular and epidemiological approachesResearch Article Published on 2021-08-012022-10-27 Journal: Bosnian Journal of Basic Medical Sciences [Category] COVID-19, [키워드] acute respiratory syndrome approach Bosnia and Herzegovina center Cluster contribute coronavirus coronavirus disease COVID-19 COVID-19 patient Cyprus England Epidemic epidemiological Epidemiology European events faculty France genome sequence independent indicate Italy Laboratory lesson molecular nanopore sequencing outbreak Phylogenetic tree Phylogeny SARS-CoV-2 sequence the disease viral infections was done Whole genome sequencing [DOI] 10.17305/bjbms.2020.5381 PMC 바로가기 [Article Type] Research Article
Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: Lessons learned to optimize future molecular and epidemiological approachesResearch Article Published on 2021-08-012022-10-27 Journal: Bosnian Journal of Basic Medical Sciences [Category] Coronavirus, COVID-19, Fulltext, MERS, SARS, [키워드] acute respiratory syndrome approach Bosnia and Herzegovina center Cluster contribute coronavirus coronavirus disease COVID-19 COVID-19 patient Cyprus England Epidemic epidemiological Epidemiology European events faculty France genome sequence independent indicate Italy Laboratory lesson molecular nanopore sequencing outbreak Phylogenetic tree Phylogeny SARS-CoV-2 sequence the disease viral infections was done Whole genome sequencing [DOI] 10.17305/bjbms.2020.5381 PMC 바로가기 [Article Type] Research Article
Cross-disciplinary approaches to assist with nucleic acid testing for SARS-CoV-2SARS-CoV-2에 대한 핵산 검사를 지원하기 위한 학제 간 접근 방식Review Published on 2021-08-012022-09-11 Journal: Applied Microbiology and Biotechnology [Category] SARS, 치료기술, [키워드] Accuracy acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 affected Antibody detection approach assist Combination Community compensating Computed tomography coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 COVID-19 diagnosis COVID-19 pandemic COVID-19 patients Critical CT diagnostic test diagnostic tests Efficiency Epidemics epidemiological Epidemiology IMPROVE Improving Infection less limitation Nanopore nanopore sequencing nucleic acid nucleic acid testing pandemic positive sampling SARS-CoV-2 Sequencing significantly spatial epidemiology Transmission [DOI] 10.1007/s00253-021-11498-2 PMC 바로가기 [Article Type] Review
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore SequencingGenetics Published on 2021-07-282022-10-31 Journal: Frontiers in Genetics [Category] COVID-19, [키워드] Analysis ARTIC protocol bioinformatics coronavirus – COVID-19 data set Docker effort generate Genome genomes genotyping Github highlight information lab lineages molecular Nanopore nanopore sequencing Nextflow pandemic parameter Pipeline processed raw sequencing data reconstruction robust SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 sequencing sequence Sequencing Surveillance the SARS-CoV-2 viral evolution [DOI] 10.3389/fgene.2021.711437 PMC 바로가기 [Article Type] Genetics
Genome Sequences of 15 SARS-CoV-2 Sublineage B.1.617.2 Strains in BangladeshGenome Sequences Published on 2021-07-152022-10-29 Journal: Microbiology Resource Announcements [Category] COVID-19, [키워드] acute respiratory syndrome Amplicon sequencing approach ARTIC Network B.1.617.2 Community coronavirus genome sequence India individual nanopore sequencing SARS-CoV-2 sequence strain Travel [DOI] 10.1128/MRA.00560-21 PMC 바로가기 [Article Type] Genome Sequences
A Confirmed Case of SARS-CoV-2 Pneumonia With Negative Routine Reverse Transcriptase-Polymerase Chain Reaction and Virus Variation in Guangzhou, China중국 광저우에서 일상적인 역전사효소-중합효소 연쇄반응과 바이러스 변이를 동반한 SARS-CoV-2 폐렴의 확인된 사례Article Published on 2021-07-152022-09-11 Journal: Clinical Infectious Diseases: An Official Publicat [Category] SARS, 치료기술, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus antibody Antibody detection chain Chain Reaction Clinical diagnosis Confirmed coronavirus diagnosed Diagnosis disease effective false-negative false-negative results Guangzhou, China Nanopore nanopore sequencing negative ORF pathogen Pneumonia reaction reverse transcriptase routine routine RT-PCR RT-PCR RT-PCR diagnosis SARS-CoV-2 SARS-CoV-2 pneumonia Sequencing severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus 2 transcriptase Variation virus virus variation [DOI] 10.1093/cid/ciaa941 PMC 바로가기 [Article Type] Article