Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samplesResearch Published on 2021-07-122022-10-28 Journal: BMC veterinary research [Category] COVID-19, [키워드] Amplicon Amplicon sequencing amplicon-based sequencing bovine BVDV BVDV-1 BVDV-2 cattle clinical presentation clinical sample Complete Covering diarrhea genetic variability Genome genome coverage genomes identify limitation MinION Molecular epidemiology Nanopore nanopore sequencing outbreak pathogen PCR Pestivirus Phylogenetic analysis plasma presenting produced Protein protocol responsible Result sequence sequence information Sequencing strain Strains subtype Subtypes supplementary material the disease Tiling PCR titre variety Viral load virus was performed whole genomes whole-genome sequencing [DOI] 10.1186/s12917-021-02945-3 PMC 바로가기 [Article Type] Research
COVID-19: first long-term care facility outbreak in the Netherlands following cross-border introduction from Germany, March 2020COVID-19: 2020년 3월 독일에서 국경을 넘어 도입된 후 네덜란드에서 첫 번째 장기 요양 시설 발생Research Article Published on 2021-05-042022-09-10 Journal: BMC Infectious Diseases [Category] SARS, 치료기술, [키워드] activity an area approach Asymptomatic asymptomatic infections Care chain Chain Reaction Cluster community transmission conducted coronavirus COVID-19 COVID-19 case COVID-19 cases COVID-19 epidemic COVID-19 patient COVID-19 patients criteria cross-sectional Ct-values determine disease District epidemiological data epidemiologically Germany Health care Health care worker health care workers highlight hospital Hospitalized implementation infection control information limit Local Long-term care measure microbiologically nanopore sequencing Nasopharyngeal swab nasopharyngeal swabs National Netherland Netherlands nursing home Observational outbreak polymerase chain reaction positive random reaction real-time polymerase chain reaction reported Result SARS-CoV-2 sequenced Sequencing Signs and symptoms spread of COVID-19 supplementary material survey Symptom symptomatic tested the District took place Transmission virus was performed whole genome Whole genome sequencing [DOI] 10.1186/s12879-021-06093-9 PMC 바로가기 [Article Type] Research Article
Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infectionArticle Published on 2021-04-232023-06-14 Journal: Cell Reports [Category] MERS, SARS, [키워드] coronavirus COVID-19 differential expression direct cDNA sequencing Direct RNA sequencing discontinuous transcription nanopore sequencing poly(A) tail RNA modification SARS-CoV-2 [DOI] 10.1016/j.celrep.2021.109108 PMC 바로가기 [Article Type] Article
The wastewater microbiome: A novel insight for COVID-19 surveillance폐수 미생물군집: COVID-19 감시를 위한 새로운 통찰력Article Published on 2021-04-102022-09-11 Journal: The Science of the total environment [Category] SARS, 치료기술, [키워드] 16S rRNA appear Bacteria Bacterial Care collected Community condition correlated COVID-19 COVID-19 outbreak Evidence expelled full-length Health Health care Indicator individual infected with SARS-CoV-2 manifestation Microbiome microbiota mitigate nanopore sequencing nanopore technology Patient positive profile quarantine reported residential care risk factor Risk factors rRNA SARS-CoV-2 SARS-CoV-2 detection SARS-CoV-2 surveillance Sequencing sewage Surveillance the SARS-CoV-2 wastewater [DOI] 10.1016/j.scitotenv.2020.142867 PMC 바로가기 [Article Type] Article
Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing신속한 현장 배포 시퀀싱을 통한 SARS-CoV-2 및 다중 호흡기 바이러스의 동시 탐지 및 돌연변이 감시Clinical Advances Published on 2021-03-312022-09-14 Journal: Med (New York, N.Y.) [Category] MERS, SARS, 변종, 진단, 치료기술, [키워드] Abstract acute respiratory syndrome Adenovirus Analysis Antonio clinical sample Co-infection combating complex Context coronavirus coronavirus disease COVID-19 detect detection Detection limit determine develop diagnose education Effectiveness Epidemiology finding funding help identify Infection Influenza influenza A isothermal isothermal amplification Mild MONITOR multiplex Mutation mutation surveillance Nanopore nanopore sequencing nucleic acid offer office other respiratory virus pandemic provide reagents real time real-time pathogen detection respiratory virus SARS-CoV-2 Sensitivity and specificity Sequencing Simultaneous Spread spread of COVID-19 Strategy supported Surveillance Vaccines variant variant virus sequencing viral amplification viral genomes viral infection viral mutation Viral mutations Viral RNA virus viruses wastewater [DOI] 10.1016/j.medj.2021.03.015 PMC 바로가기 [Article Type] Clinical Advances
Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing루프 매개 등온 증폭과 나노포어 시퀀싱을 결합한 고처리량 플랫폼인 LamPORE를 사용한 SARS-CoV-2 감염 진단Virology Published on 2021-03-292022-09-10 Journal: Journal of Clinical Microbiology [Category] SARS, 치료기술, [키워드] 95% confidence interval acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 approach clinical samples collected coronavirus Diagnosis diagnosis of SARS-CoV-2 diagnostic diagnostic sensitivity diagnostic specificity evaluated extracted RNA Genome Infection isothermal amplification LamPORE limit limit of detection Loop-mediated isothermal amplification Nanopore nanopore sequencing nose and throat offer Pathogens Patient per day platform produced reduction reproducibility respiratory respiratory pathogen respiratory sample reverse transcriptase reverse transcriptase PCR RNA RT-PCR SARS-CoV-2 SARS-COV-2 infection sensitivity Sequencing severe acute respiratory syndrome Coronavirus specificity specimen specimens Swab symptomatic infection symptomatic patient Symptomatic patients throat swabs UK hospitals [DOI] 10.1128/JCM.03271-20 PMC 바로가기 [Article Type] Virology
Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa남아프리카 케이프타운에 SARS-CoV-2의 여러 초기 도입Article Published on 2021-03-222022-09-10 Journal: Viruses [Category] SARS, 치료기술, [키워드] 95% confidence interval addition Analysis B.1 Bayesian method Bayesian methods Betacoronavirus Cape Cape Town clade CLOCK Cluster Contact coronavirus disease Coronavirus disease 2019 COVID-19 determine Epidemic Genome sequencing genomes Genomic surveillance likelihood Lineage lineages Local Maximum likelihood molecular Molecular epidemiology Multiple Mutation Nanopore nanopore sequencing Netherland Netherlands nine occurred outbreak pandemic Patient Phylogenetic phylogenetic inference phylogenetics produced SARS-CoV-2 sequence sequences Sequencing South Africa Spread Support town Transmission were used Western Cape Province whole genomes [DOI] 10.3390/v13030526 PMC 바로가기 [Article Type] Article
Genome Sequences of 10 SARS-CoV-2 Viral Strains Obtained by Nanopore Sequencing of Nasopharyngeal Swabs in MaltaGenome Sequences Published on 2021-01-282022-10-29 Journal: Microbiology Resource Announcements [Category] COVID-19, [키워드] acute respiratory syndrome Amplicon sequencing analyzed approach assigned B.1 lineage circulating coronavirus Europe Genome genome sequence Malta nanopore sequencing network pangolin SARS-CoV-2 sequence strain [DOI] 10.1128/MRA.01375-20 PMC 바로가기 [Article Type] Genome Sequences
Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital뉴욕시 병원에서 COVID-19 위기 동안 2차 감염을 유발하는 Carbapenemase 생성 EnterobacteralesArticle Published on 2021-01-192022-09-11 Journal: Journal of Antimicrobial Chemotherapy [Category] 유전자 메커니즘, 치료기술, 치료제, [키워드] Antibiotic resistance antibiotic resistance gene Bacterial infections Clinical characteristics collected COVID-19 crisis COVID-19 patients CPE Culture declined Enterobacter cloacae complex genotyping global pandemic hospital Illumina Increased increased risk isolate isolates Klebsiella pneumoniae KPC Lineage MDR mechanism mitigate MOST Most patient Most patients Nanopore nanopore sequencing New York City pathogen Pathogens Patient patients patients with COVID-19 Phylogenetic analysis pneumoniae positive Prevalence respiratory SARS-CoV-2 secondary bacterial infection Secondary bacterial infections Secondary infection secondary infections Sequencing sequencing data Surveillance Treatment treatment approach treatment failure wake WGS while with COVID-19 [DOI] 10.1093/jac/dkaa466 PMC 바로가기 [Article Type] Article
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysisArticle Published on 2020-12-092022-10-04 Journal: Nature Communications [Category] MERS, SARS, 변종, 유전자 메커니즘, [키워드] Accuracy Analysis controls coronavirus 2 Coverage COVID-19 Critical detect elevated error rate Evidence Evolution facilitate frequencies Illumina improvement INDEL International Local Nanopore nanopore sequencing National Next-generation sequencing ONT Oxford Nanopore Technology Patient platform Precision provide public health respiratory RNA SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 surveillance sensitivity sequence Sequencing sequencing reads short-read sequencing Single nucleotide variant SNVs specimen Structural variation supported Transmission Validity variant Viral genetics WGS whole-genome sequencing widespread [DOI] 10.1038/s41467-020-20075-6 PMC 바로가기 [Article Type] Article