2025
Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts
Petrone M, Grove J, Parry R, Van Brussel K, Mifsud J, Dindar Z, Mei S, Shi M, Turnbull O, Marzinelli E, Holmes E. Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts. Current Biology 2025 PMID: 40472852, DOI: 10.1016/j.cub.2025.05.032.Peer-Reviewed Original ResearchRNA virusesCo-divergenceEvolution of structural genesVirus-host co-divergenceRNA-dependent RNA polymeraseRNA virus evolutionNegative-sense virusesPhylogenetic relationshipsSister groupEarly chordatesRNA polymeraseStructural geneAnimal evolutionEvolutionary historyTransitional taxaRNA librariesEvolutionary timescalesInvertebrate relativesVirus evolutionVirus lineagesMultiple lineagesRNAVertebratesChordatesTunicates
2024
No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota
Parry R, Lytras S, Petrone M, Wille M, Crits-Christoph A, Gifford R, Saito A, Smura T, Peacock T. No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota. Journal Of Virology 2024, 98: e01468-24. PMID: 39494907, PMCID: PMC11650967, DOI: 10.1128/jvi.01468-24.Peer-Reviewed Original ResearchBacterial sequencesViral RNA-dependent RNA polymeraseRNA-dependent RNA polymeraseSARS-CoV-2 variantsBacterial protein sequencesSARS-CoV-2 proteinsEvolution of mutationsRNA polymeraseIntrahost diversityProtein sequencesHomologous fragmentsNucleotide sequenceProtein databaseTemplate-switchingGut microbiotaSARS-CoV-2 VOCsViral genomeSARS-CoV-2Mutated fragmentsAmino acidsRdRpMutationsSequenceViral replicationProtein
2022
Translocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2’s RNA polymerase complexes
Shi Y, Wang J, Batista V. Translocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2’s RNA polymerase complexes. Frontiers In Molecular Biosciences 2022, 9: 999291. PMID: 36387272, PMCID: PMC9640752, DOI: 10.3389/fmolb.2022.999291.Peer-Reviewed Original ResearchDe novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report
Gandhi S, Klein J, Robertson AJ, Peña-Hernández MA, Lin MJ, Roychoudhury P, Lu P, Fournier J, Ferguson D, Mohamed Bakhash SAK, Catherine Muenker M, Srivathsan A, Wunder EA, Kerantzas N, Wang W, Lindenbach B, Pyle A, Wilen CB, Ogbuagu O, Greninger AL, Iwasaki A, Schulz WL, Ko AI. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Nature Communications 2022, 13: 1547. PMID: 35301314, PMCID: PMC8930970, DOI: 10.1038/s41467-022-29104-y.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionVirologic responsePersistent SARS-CoV-2 infectionResistance mutationsPre-treatment specimensB-cell deficiencyRemdesivir resistanceRemdesivir therapyViral sheddingCase reportAntiviral agentsPatientsCombinatorial therapyInfectionTherapyWhole-genome sequencingTreatmentImportance of monitoringDe novo emergenceFold increaseRNA-dependent RNA polymeraseNovo emergencePotential benefitsMutationsIndolentInsights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations
Wang J, Shi Y, Reiss K, Allen B, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Insights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations. Biochemistry 2022, 61: 424-432. PMID: 35199520, PMCID: PMC8887646, DOI: 10.1021/acs.biochem.1c00755.Peer-Reviewed Original ResearchConceptsReplication-transcription complexPriming reactionRNA duplexesTemplate strandRNA templateHigher-order oligomerizationRNA-dependent RNA polymeraseCryo-EM structureRNA primaseViral RNA templateRNA polymerasePrimer synthesisViral transcriptionSecondary structureViral genomeSubunitsMolecular dynamics simulations
2021
Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir
Wang J, Reiss K, Shi Y, Lolis E, Lisi GP, Batista VS. Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir. Biochemistry 2021, 60: 1869-1875. PMID: 34110129, PMCID: PMC8204756, DOI: 10.1021/acs.biochem.1c00292.Peer-Reviewed Original Research
2003
RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong
Chen X, Feng Q, Wu Z, Liu Y, Huang K, Shi R, Chen S, Lu W, Ding M, Collins R, Fung Y, Lau L, Yu A, Chen J. RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong. Biochemical And Biophysical Research Communications 2003, 308: 899-905. PMID: 12927804, DOI: 10.1016/s0006-291x(03)01511-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBase SequenceCloning, MolecularConserved SequenceDNA-Directed RNA PolymerasesFoot-and-Mouth Disease VirusGenetic VariationHong KongModels, GeneticMolecular Sequence DataMutationPhylogenyProtein Structure, TertiaryReverse Transcriptase Polymerase Chain ReactionRNA, ViralRNA-Dependent RNA PolymeraseSequence Analysis, DNASequence Homology, Amino AcidConceptsRNA-dependent RNA polymerase gene sequencesNucleotide sequenceRNA polymerase gene sequencesViral RNA-dependent RNA polymeraseRNA-dependent RNA polymeraseAmino acid sequenceAmino acid residuesMouth disease virusPolymerase gene sequencesCommon ancestorEvolutionary treeRNA polymeraseGene sequencesSequence comparisonAcid sequenceSame geneN-terminusDisease virusAcid residuesGenesFunctional relevanceRepresentative isolatesHost immune systemFMDV isolatesHKN/2002
1987
Rhabdovirus Genomes and Their Products
Rose J, Schubert M. Rhabdovirus Genomes and Their Products. The Viruses 1987, 129-166. DOI: 10.1007/978-1-4684-7032-1_4.Peer-Reviewed Original ResearchGenomic RNANucleocapsid coreRNA-dependent RNA polymeraseVirus particlesMembrane-enveloped virusesSingle glycoprotein speciesRhabdovirus genomesRNA polymeraseRNA genomeMembrane envelopeMatrix proteinsMessenger RNAGlycoprotein speciesRhabdovirusRNAGenomeProteinMembraneInvertebratesVertebratesBacilliformPolymeraseSpeciesPlantsNegative sense
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