RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysisArticle Published on 2022-11-022022-11-16 Journal: PLoS ONE [Category] SARS, 변종, 치료기술, [키워드] acting Analysis assessment automatically COVID-19 pandemic dataset datasets detect evaluate Evolution Genome Genome sequences genomes genomic include Intensive Lineage lineages molecular Mutation natural selection Notation object pathogen Phylogenetic Rapid SARS-CoV-2 selected Selection selective sensitivity sequence Sequence analysis sequencing error Surveillance underlie unmet need variants of concern whole genes yielding [DOI] 10.1371/journal.pone.0275623 PMC 바로가기
Genomic surveillance: Circulating lineages and genomic variation of SARS-CoV-2 in early pandemic in Ceará state, Northeast BrazilArticle Published on 2022-11-012022-11-16 Journal: Virus research [Category] SARS, 변종, 유전자 메커니즘, 치료기술, [키워드] B.1 B.1.1 B.1.1.28 B.1.1.33 Brazil circulating compose COVID-19 dataset death rate genetic diversity Genome Genome sequences genomes sequenced genomic genomic variation GISAID database impacted Lineage Missense Missense mutations Mutation mutations mutations. Other lineage P.1 P.2 pandemic polymorphism prevalent prevalent lineage SARS-CoV-2 SARS-CoV-2 sequencing sequence sequenced single-nucleotide SNPs Surveillance synonymous virus [DOI] 10.1016/j.virusres.2022.198908 PMC 바로가기
Molecular diversity and phenotypic pleiotropy of ancient genomic regulatory loci derived from human endogenous retrovirus type H (HERVH) promoter LTR7 and HERVK promoter LTR5_Hs and their contemporary impacts on pathophysiology of Modern HumansArticle Published on 2022-11-012022-11-15 Journal: Molecular genetics and genomics : MGG [Category] SARS, 유전자 메커니즘, 진단, [키워드] affected analysis Ape apes azoospermia Brain brain regions Cancer Cell cell type cells Central nervous system cognitive Consensus conserved coronavirus COVID-19 COVID-19 pandemic database defined disorders DNA sequence dominant element embryogenesis event Evidence Evolution expressed expression fetal functional gene signature Genes genes encoding Genome genomic germline global pandemic Glutamatergic GSEA HERV HERVs Human human cell Human embryogenesis human endogenous retrovirus Human endogenous retrovirus type H (HERVH) Human endogenous retrovirus type K (HERVK) human physiology Human spermatogenesis identification Impact implicated include Infection inheritance insertion Interaction Lineage loci LTR LTR5_Hs LTR7 subfamilies majority mammalian Mammalian offspring survival genes marker Metastasis Monkey morphological feature morphologically MOS naïve neoplasm Neoplasm metastasis Neural Neuron neurons New World non-human primates observation offspring Oligospermia pathogen pathology pathophysiology Phenotypes phenotypic physiological Pleiotropy Population population-level effect primate Primate evolution promoter protein-protein interaction Protein–protein interactions at synapses proteomics Quantitative Radial rare disease recessive regulated Regulatory regulatory element regulatory sequence Release replicate representing Retrotransposition retroviral retrovirus SARS-CoV-2 SARS-CoV-2 coronavirus Schizophrenia sequence significantly Spread Stage survival synaptic Synaptic transmission Synaptic transmission. target the SARS-CoV-2 timeline traits Transmission trigeminal undergo viral genome viral infection viral infections virus viruses [DOI] 10.1007/s00438-022-01954-7 PMC 바로가기
A computational approach to biological pathogenicityArticle Published on 2022-11-012022-11-15 Journal: Molecular genetics and genomics : MGG [Category] 바이오마커, [키워드] Accuracy adverse impact approach assessment Biochemistry Biomarkers clinical trial COVID-19 death Digital Digital genomic signature DNA DNA sequence energy event feature genomic Gibbs energy h-distance. Health Host humans hybridization machine machine learning machine learning model methodology microbe mitigate new strain oligonucleotide Other pandemic pathogen pathogenic Pathogenic relationship pathogenicity Pathogens/nonpathogens Perspective predict Quality reducing sensitivity Sensitivity and specificity Sickness specificity structural property [DOI] 10.1007/s00438-022-01951-w PMC 바로가기
An outlook on potential protein targets of COVID-19 as a druggable siteArticle Published on 2022-11-012022-11-15 Journal: Molecular biology reports [Category] COVID19(2023년), SARS, 변종, 치료제, [키워드] approved cause claimed clinical trial combating contagious COVID-19 COVID-19 disease Cryo-electron microscopy Delta Efficacy feature genomic help host cell host protein infecting inhibit mechanism of action MERS-CoV Mutation non-structural proteins omicron pandemic Protein Protein target proteolytic cleavage raised Repurposed drug required SARS-CoV SARS-CoV-2 SARS-CoV-2 entry SARS-CoV-2 protein shown similarity spike Spike protein strain suggested the vaccine therapeutic drugs therapeutic interventions Vaccines. variants of SARS-CoV-2 viral infection virus Wuhan X-ray diffraction [DOI] 10.1007/s11033-022-07724-3 PMC 바로가기
Bioinformatics pipeline unveils genetic variability to synthetic vaccine design for Indian SARS-CoV-2 genomesArticle Published on 2022-11-012022-11-15 Journal: International immunopharmacology [Category] SARS, 치료기술, 치료제, [키워드] aligned amino acid change antigenic antigenic epitopes B-cell epitope bioinformatics bioinformatics pipeline can be used clade clades conserved conserved regions criteria epitope Evolution genetic variability genomic HLA allele identify immunogenic MAFFT MHC-I MHC-II Multiple sequence alignment Mutation Nextstrain Non-synonymous Non-Synonymous Signature SNP performed Phylogenetic analysis primer probe Protein Region regions reported resulting SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 pandemic selected SNP SNPs T-cell T-cell epitope T-cell epitopes T-cell epitopes. unique Vaccine Vaccine design virus virus detection virus genome [DOI] 10.1016/j.intimp.2022.109224 PMC 바로가기
The evaluation of an automated mariPOC SARS-CoV-2 antigen test compared to RT-qPCR SARS-CoV-2 assay and comparison of its sensitivity in Delta- and Omicron-variant samplesArticle Published on 2022-11-012022-11-16 Journal: Influenza and Other Respiratory Viruses [Category] SARS, 변종, [키워드] 95% CI 95% confidence interval Affect analysed Antigen antigen testing assays Asymptomatic automated circulating clinical samples cycle threshold Delta diagnostics evaluate evaluated genomic investigated lineages material mild respiratory symptom Mutation Nasopharyngeal swab omicron oropharyngeal swabs performed positive retrospective RT-qPCR SARS-CoV-2 SARS-CoV-2 antigen sensitivities sensitivity Sensitivity and specificity Sensitivity. specificity subject the SARS-CoV-2 variant variants [DOI] 10.1111/irv.13048 PMC 바로가기
SARS-CoV-2 BA.1 and BA.2 coinfection detected by genomic surveillance in Brazil, January 2022Article Published on 2022-11-012022-11-16 Journal: Archives of Virology [Category] COVID19(2023년), SARS, 유전자 메커니즘, 치료기술, [키워드] Brazil genomic Patient SARS-CoV-2 Surveillance surveillance network [DOI] 10.1007/s00705-022-05532-5 PMC 바로가기
One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021Article Published on 2022-10-312022-11-16 Journal: PLoS ONE [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, [키워드] analyses clade Clinical data clone collected Community conducted contributed defined Delta Evidence facilitate Genome genomic genomic data Genomic surveillance Health identify infectious disease outbreak Lineage local public health Mutation new SARS-CoV-2 occurred one health outbreak phylogenetic analysis positive provided public health RT-qPCR SARS-CoV-2 SARS-CoV-2 genome secondary transmission sequenced single mutation Spread spread of COVID-19 subsequent subset Surveillance targeted interventions the SARS-CoV-2 through contact variant variants was tested wastewater were used [DOI] 10.1371/journal.pone.0272830 PMC 바로가기
Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletionArticle Published on 2022-10-272022-11-15 Journal: Virology Journal [Category] COVID19(2023년), SARS, 변종, 치료기술, 치료제, [키워드] Accuracy Algorithm Amino acid amplification BA.1 BA.4 BA.5 Cluster COVID-19 pandemic database detect diagnostic downstream epidemiological example faster genomic knowledge melting curve analysis Mutation mutations next generation sequencing Next-generation sequencing NGS omicron over overcome PCR PCR assay Point mutation probe SARS-CoV-2 SARS-CoV-2 variant sequence Spain specific mutation Surveillance temperature time-consuming variant Variant-specific PCR. while [DOI] 10.1186/s12985-022-01883-2 PMC 바로가기