2024
A ~40-kb flavi-like virus does not encode a known error-correcting mechanism
Petrone M, Grove J, Mélade J, Mifsud J, Parry R, Marzinelli E, Holmes E. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2403805121. PMID: 39018195, PMCID: PMC11287256, DOI: 10.1073/pnas.2403805121.Peer-Reviewed Original ResearchConceptsFlavi-like virusGenome sizeRNA virusesRNA virus genomesNucleic acid metabolismGenome lengthPhylogenetic inferenceDeleterious mutationsExonuclease domainGenomeVirus genomeProofreading mechanismPopulation extinctionMutation rateRNAAcid metabolismExonucleaseMutationsVirusMetatranscriptomicsStructural analysisLineagesProofreadingMechanismMetabolismDengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specific
2023
Evidence for an ancient aquatic origin of the RNA viral order Articulavirales
Petrone M, Parry R, Mifsud J, Van Brussel K, Voorhees I, Richards Z, Holmes E. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2310529120. PMID: 37906647, PMCID: PMC10636315, DOI: 10.1073/pnas.2310529120.Peer-Reviewed Original ResearchConceptsEvolutionary historyAquatic-terrestrial transitionsDeep phylogenetic historiesVirus-host codivergenceMajor evolutionary transitionsLong-term evolutionary processesTotal RNA sequencingClose phylogenetic relationshipTranscriptome data miningPhylogenetic diversityEvolutionary transitionsPhylogenetic historyPhylogenetic relationshipsInfluenza virus lineagesPhylum CnidariaDivergent familiesPutative familiesRNA sequencingAquatic animalsEvolutionary processesNew hostAquatic originDisease-causing virusesEmergence of virusesVirus lineages
2016
Effect of HIV Antibody VRC01 on Viral Rebound after Treatment Interruption
Bar KJ, Sneller MC, Harrison LJ, Justement JS, Overton ET, Petrone ME, Salantes DB, Seamon CA, Scheinfeld B, Kwan RW, Learn GH, Proschan MA, Kreider EF, Blazkova J, Bardsley M, Refsland EW, Messer M, Clarridge KE, Tustin NB, Madden PJ, Oden K, O'Dell SJ, Jarocki B, Shiakolas AR, Tressler RL, Doria-Rose NA, Bailer RT, Ledgerwood JE, Capparelli EV, Lynch RM, Graham BS, Moir S, Koup RA, Mascola JR, Hoxie JA, Fauci AS, Tebas P, Chun TW. Effect of HIV Antibody VRC01 on Viral Rebound after Treatment Interruption. New England Journal Of Medicine 2016, 375: 2037-2050. PMID: 27959728, PMCID: PMC5292134, DOI: 10.1056/nejmoa1608243.Peer-Reviewed Original ResearchConceptsPlasma viral reboundHuman immunodeficiency virusAntiretroviral therapyViral reboundViral suppressionHIV infectionPassive immunizationHistorical controlsWeek 8Interruption of ARTNeutralization-resistant virusesOpen-label trialSide effect profileART interruptionSingle bNAbsTreatment interruptionAdverse eventsMedian timeImmunodeficiency virusNIH trialPassive administrationHIV CD4Week 4Antibody VRC01Trial participants