The use of next-generation sequencing in personalized medicineArticle Published on 2024-03-062024-09-05 Journal: ArXiv [Category] update2024, [키워드] deep sequencing High-throughput sequencing massively parallel sequencing Next-generation sequencing Personalized medicine second generation sequencing ultra-high-throughput sequencing PMC 바로가기 [Article Type] Article
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirusResources Published on 2024-02-072024-09-05 Journal: Virus Evolution [Category] update2024, [키워드] deep sequencing intrahost single nucleotide variant (iSNV) machine learning sequencing error VCFgenie [DOI] 10.1093/ve/veae013 PMC 바로가기 [Article Type] Resources
Genome stability assessment of PRRS vaccine strain with new ARTIC-style sequencing protocolVeterinary Science Brief Research Report Published on 2024-01-082024-09-05 Journal: Frontiers in Veterinary Science [Category] update2024, [키워드] deep sequencing genetic variability Porcilis MLV porcine reproductive and respiratory syndrome virus single nucleotide variation tiling amplicon sequencing [DOI] 10.3389/fvets.2023.1327725 PMC 바로가기 [Article Type] Veterinary Science Brief Research Report
Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domainArticle Published on 2022-10-132022-11-15 Journal: Cell [Category] COVID19(2023년), SARS, 변종, 진단, [키워드] ACE2 ACE2 binding antibody antibody treatment artificial intelligence COVID-19 COVID-19 pandemic deep deep learning deep sequencing develop directed evolution domain Evolution of SARS-CoV-2 machine learning mutated variant Mutation mutations Neutralizing antibodies neutralizing antibody omicron predict Predictive Protein protein engineering RBD RBD variants representing SARS-CoV-2 variant Selection sequence the SARS-CoV-2 therapeutic Trajectories Vaccine variant variants viral escape viral spike protein yeast yeast display [DOI] 10.1016/j.cell.2022.08.024 PMC 바로가기
A key F27I substitution within HCDR1 facilitates the rapid maturation of P2C-1F11-like neutralizing antibodies in a SARS-CoV-2-infected donorArticle Published on 2022-09-132022-11-15 Journal: Cell Reports [Category] SARS, 진단, [키워드] Analysis anti-SARS-CoV-2 antibodies antibody antibody repertoire Bioactivity characterized contribute CP: Immunology deep sequencing developmental Donor early infection elicit event facilitate immunogen information Lineage longitudinal maturation monoclonal NAb neutralizing antibody P2C-1F11 lineage pathway reveal SARS-CoV-2 SARS-COV-2 infection SARS-CoV-2-specific antibody sequence significantly viral infection [DOI] 10.1016/j.celrep.2022.111335 PMC 바로가기
SARS-CoV-2 and post-donation information: a one-year experience of the French haemovigilance networkArticle Published on 2022-09-012022-11-15 Journal: Blood transfusion = Trasfusione del sangue [Category] SARS, 치료기술, [키워드] antigenic applied Blood blood donor COVID-19 symptom Culture deep sequencing demographic data Diagnosis Donor donors Duration elapsed Evidence experiment fraction French highlight Hypothesis information investigated material molecular MOST nasopharyngeal no difference parameter Paris PCR test PDI plasma plasmas positive questionnaire Region reported Repository RNA RNA sequencing SARS-CoV-2 SARS-CoV-2 RNA screened Sequencing Support Symptom tested Vero E6 cell Viral transmission Virological virus isolation was collected was determined [DOI] 10.2450/2022.0266-21 PMC 바로가기
SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patientArticle Published on 2022-09-012022-11-16 Journal: International Journal of Infectious Diseases [Category] COVID19(2023년), SARS, 변종, 치료기술, [키워드] Amino acid approach changes in chronic infection Combination deep sequencing deletions demonstrated Evolution favor Genetic Host immune evasion Immunocompromised immunocompromised individual Immunocompromised patient Infection intra-host evolution investigated Mutation Nasopharyngeal swab new SARS-CoV-2 Patient Prolonged Prolonged infection Protein SARS-CoV-2 SARS-CoV-2 evolution SARS-CoV-2 lineage Sequencing suggested the SARS-CoV-2 the Spike variant variants with HIV [DOI] 10.1016/j.ijid.2022.06.023 PMC 바로가기
RT-qPCR and ATOPlex sequencing for the sensitive detection of SARS-CoV-2 RNA for wastewater surveillance폐수 감시를 위한 SARS-CoV-2 RNA의 민감한 검출을 위한 RT-qPCR 및 ATOPlex 시퀀싱Article Published on 2022-07-152022-09-11 Journal: Water research [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, 치료기술, 치료제, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 appear approach assays assessment China CDC Combination Concentration Concentration method condition coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 deep sequencing detect detection Detection limit detection rate Detection sensitivity enveloped virus greater handling impacted less limit of detection MONITOR multiplex Mutation N1 and N2 nucleic acid nucleic acid extraction offer ORF1ab pandemic PCR platform powerful tool Probability promise quantitation quantitative PCR recovery required Result reverse transcription RT-qPCR RT-qPCR assay RT-qPCR assays SARS-CoV-2 SARS-CoV-2 RNA Sequencing severe acute respiratory syndrome Coronavirus shown Spread Surveillance US CDC variants variants of concern viral genome virus VoC wastewater [DOI] 10.1016/j.watres.2022.118621 PMC 바로가기 [Article Type] Article
Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site상부 및 하부 호흡기에서 SARS-CoV-2 유사종의 비교 분석은 스파이크 절단 부위에서 진행 중인 진화를 보여줍니다Article Published on 2022-07-022022-09-11 Journal: Virus research [Category] COVID19(2023년), SARS, 변종, 치료기술, [키워드] ACE2 acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 Cell cleavage site Comparative analysis coronavirus deep deep sequencing Deleterious mutations evidenced Evolution explained genomic humans incidence INDEL indels intensive care intensive care unit locus Lower respiratory tract LRT Macrophage Minority variants Mutation Next-generation sequencing Non-synonymous mutation Patient phagocytosis Quasispecies quasispecy Result S gene SARS-CoV-2 selective severe acute respiratory syndrome Coronavirus specimens spike Spike protein spillover the Spike upper and lower respiratory tract upper respiratory tract URT variant variants viral quasispecy virus was performed [DOI] 10.1016/j.virusres.2022.198786 PMC 바로가기 [Article Type] Article
Comprehensive fitness landscape of SARS-CoV-2 M pro reveals insights into viral resistance mechanismsSARS-CoV-2 M pro의 종합적인 피트니스 환경은 바이러스 저항 메커니즘에 대한 통찰력을 보여줍니다Article Published on 2022-06-202022-09-11 Journal: eLife [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, 치료제, [키워드] active site acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus-2 addition Amino acid amino acid changes amino acids analyzed Anti-viral drugs can be used cleave Complete Comprehensive conserved contribute Coronavirus-2 correlated Critical deep mutational scanning deep sequencing defined drug drug design drug resistance Effect effective elicit evade Evolution Evolutionary biology expression functional human population Infectious disease inhibitor inhibitors life cycle M pro main protease mechanism Microbiology MPro Mutation network new strain performed physically protease Protein reduced reveal S. cerevisiae SARS-CoV-2 SARS-CoV-2 main protease selection pressure Severe acute respiratory syndrome severe acute respiratory syndrome Coronavirus Toxicity Vaccines variant viral life cycle Viral resistance virulent yeast [DOI] 10.7554/eLife.77433 PMC 바로가기 [Article Type] Article