2024
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections
Li K, Chaguza C, Stamp J, Chew Y, Chen N, Ferguson D, Pandya S, Kerantzas N, Schulz W, Initiative Y, Hahn A, Ogbunugafor C, Pitzer V, Crawford L, Weinberger D, Grubaugh N. Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology 2024, 20: e1012469. PMID: 39288189, PMCID: PMC11432881, DOI: 10.1371/journal.pcbi.1012469.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle-nucleotide polymorphismsAssociation studiesWhole-genome sequencingAmino acid changesSingle nucleotide polymorphismsPairs of substitutionsViral copiesEpistasis testsGenome sequenceGenetic variationSpike geneAcid changesViral genomeNucleotide polymorphismsSARS-CoV-2Detect interactionsHost factorsVirus copiesCopyInfection dynamicsRT-qPCRPolymorphismOmicron BASARS-CoV-2 infectionCytoskeleton‐associated gelsolin responds to the midgut distention process in saline meal‐fed Aedes aegypti and affects arbovirus dissemination from the midgut
Cui Y, Megawati D, Lin J, Rehard D, Grant D, Liu P, Jurkevich A, Reid W, Mooney B, Franz A. Cytoskeleton‐associated gelsolin responds to the midgut distention process in saline meal‐fed Aedes aegypti and affects arbovirus dissemination from the midgut. The FASEB Journal 2024, 38: e23764. PMID: 39042395, PMCID: PMC11268798, DOI: 10.1096/fj.202302684rr.Peer-Reviewed Original ResearchConceptsApoptotic signalingHost factorsInduction of apoptosisIncreased induction of apoptosisBlood meal ingestionDifferentially expressed proteinsActin filamentsCytoskeleton modulationTime course analysisSecondary tissuesBasal laminaStable knockoutTissue distentionAedes aegyptiMosquito linesFunctional studiesVertebrate hostsSynthesized virionsMosquito midgutMidgut escape barrierCourse analysisGelsolinSurrounding basal laminaMidgutMidgut tissueiGATE analysis improves the interpretability of single-cell immune landscape of influenza infection
Hill B, Zak A, Raja S, Bugada L, Rizvi S, Roslan S, Nguyen H, Chen J, Jiang H, Ono A, Goldstein D, Wen F. iGATE analysis improves the interpretability of single-cell immune landscape of influenza infection. JCI Insight 2024, 9: e172140. PMID: 38814732, PMCID: PMC11383363, DOI: 10.1172/jci.insight.172140.Peer-Reviewed Original ResearchInfluenza infectionImmune cell typesCourse of influenza infectionDefective T cell responsesSurvival of C57BL/6 miceCell typesDecreased IL-10 expressionEffect of host genetic backgroundT cell responsesGenetic backgroundTime-of-flight (CyTOFIL-10 expressionInflammatory cell typesCells in silicoHost genetic backgroundC57BL/6 miceAged miceMouse lungHost genotypeInfection susceptibilityHost factorsEffects of ageMiceHealth burdenInfectionSleep Deficiency and Pain in Persons With Substance Use Disorders
Buonora M, Sharma M, Falker C, Baldassarri S. Sleep Deficiency and Pain in Persons With Substance Use Disorders. Current Addiction Reports 2024, 11: 447-458. DOI: 10.1007/s40429-024-00562-2.Peer-Reviewed Original ResearchSubstance use disordersUse disorderSleep deficiencyPotential tissue damagePatterns of substance useShort sleep durationMaladaptive pattern of substance useTrajectories of substance useSubstance usePainNeurological changesComponents of sleepSleep timeSummaryThis reviewTissue damageClinical practiceHost factorsSleep durationLower sleep qualityDisordersSleepDeficiencyMaladaptive patternsSleep qualityEmotional experienceUpdate on Biomarkers in Renal Cell Carcinoma.
Saliby R, Saad E, Kashima S, Schoenfeld D, Braun D. Update on Biomarkers in Renal Cell Carcinoma. American Society Of Clinical Oncology Educational Book 2024, 44: e430734. PMID: 38207251, DOI: 10.1200/edbk_430734.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsRenal cell carcinomaCell carcinomaMetastatic renal cell carcinomaTumor intrinsic featuresImmune checkpoint inhibitorsRobust predictive biomarkersCheckpoint inhibitorsDurable responsesOverall survivalCare regimensPathological characteristicsPredictive biomarkersTherapeutic responseTreatment paradigmImmune systemHost factorsTranscriptional signatureGenomic alterationsTumor heterogeneityBiomarkersCarcinomaBiomarker discoveryInnovative technological approachesRegimens
2023
2301. Viral Kinetics of Sequential SARS-CoV-2 Infections
Kissler S, Hay J, Fauver J, Mack C, Tai C, Anderson D, Ho D, Grubaugh N, Grad Y. 2301. Viral Kinetics of Sequential SARS-CoV-2 Infections. Open Forum Infectious Diseases 2023, 10: ofad500.1923. PMCID: PMC10677142, DOI: 10.1093/ofid/ofad500.1923.Peer-Reviewed Original ResearchSARS-CoV-2 infectionFaster clearance timesViral clearance timeSecond infectionVaccination statusClearance timeViral kineticsFirst infectionAcute SARS-CoV-2 infectionPrior SARS-CoV-2 infectionVaccine doseDisease coursePatient characteristicsPrior infectionOropharyngeal swabsImmune responseInfection historySubsequent infectionSequential infectionUS populationViral variantsInfectionHost factorsConvenience sampleConflicting resultsA Diagnostic Approach to Fungal Pneumonia An Infectious Diseases Perspective
Azar M. A Diagnostic Approach to Fungal Pneumonia An Infectious Diseases Perspective. CHEST Journal 2023, 165: 559-572. PMID: 37813181, DOI: 10.1016/j.chest.2023.10.005.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsFungal pneumoniaAppropriate diagnostic testingClinical syndromeDiagnostic testingLower respiratory tract infectionsNon-resolving pneumoniaRespiratory tract infectionsInfectious diseases perspectiveTract infectionsRadiographic patternsCommon causeEpidemiologic exposuresCorrect diagnosisRisk populationsPneumoniaDiagnostic approachHost factorsDisease perspectiveConstellation of factorsPatientsSyndromeInfectionEpidemiologyIncidenceDiagnosisViral kinetics of sequential SARS-CoV-2 infections
Kissler S, Hay J, Fauver J, Mack C, Tai C, Anderson D, Ho D, Grubaugh N, Grad Y. Viral kinetics of sequential SARS-CoV-2 infections. Nature Communications 2023, 14: 6206. PMID: 37798265, PMCID: PMC10556125, DOI: 10.1038/s41467-023-41941-z.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionFaster clearance timesPrior SARS-CoV-2 infectionViral clearance timeSecond infectionClearance timeViral kineticsFirst infectionAcute SARS-CoV-2 infectionVaccination statusAnterior naresOropharyngeal swabsImmune responseSubsequent infectionSequential infectionViral variantsInfectionHost factorsConvenience sampleSame variantRT-qPCR measurementsRelative abilityVaccinationSwabsIndividualsGenome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed −1 ribosomal frameshifting
Wei L, Sun Y, Guo J. Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed −1 ribosomal frameshifting. Cell Reports 2023, 42: 112987. PMID: 37581984, DOI: 10.1016/j.celrep.2023.112987.Peer-Reviewed Original ResearchConceptsSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Host factorsSARS-CoV-2 replicationSyndrome coronavirus 2SARS-CoV-2Eukaryotic translation initiation factor 2ACoronavirus 2Viral RNAGenome-wide CRISPR screenFactor 2APositive-strand RNA virusesGenome-wide CRISPRRNA virusesKnockout screensRNAInitiationDYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner
Strine M, Cai W, Wei J, Alfajaro M, Filler R, Biering S, Sarnik S, Chow R, Patil A, Cervantes K, Collings C, DeWeirdt P, Hanna R, Schofield K, Hulme C, Konermann S, Doench J, Hsu P, Kadoch C, Yan Q, Wilen C. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLOS Biology 2023, 21: e3002097. PMID: 37310920, PMCID: PMC10263356, DOI: 10.1371/journal.pbio.3002097.Peer-Reviewed Original ResearchConceptsGenome-wide CRISPR/Cas9 screenCRISPR/Cas9 screenPathogenic human coronavirusesKinase-independent mannerRegulated kinase 1AProviral host factorNovel drug targetsMultiple cell typesDNA accessibilityHost factorsKinase functionHuman coronavirusesHost genesDistal enhancerNovel regulatorCas9 screenKinase 1AGene expressionNeuronal developmentDYRK1ADrug targetsDiverse coronavirusesProviral activityCell typesSevere acute respiratory syndrome coronavirus 2HPV is a cargo for the COPI sorting complex during virus entry
Harwood M, Woo T, Takeo Y, DiMaio D, Tsai B. HPV is a cargo for the COPI sorting complex during virus entry. Science Advances 2023, 9: eadc9830. PMID: 36662862, PMCID: PMC9858521, DOI: 10.1126/sciadv.adc9830.Peer-Reviewed Original ResearchConceptsCoat protein complex ITrans-Golgi networkProtein complex IGene knockdown strategyVirus entryCOPI complexProtein complexesCellular fractionationUnbiased proteomicsRetrograde traffickingCytoplasmic segmentGolgi stacksCellular cargoL2 mutantKnockdown strategyGolgi apparatusComplex IIncoming virusCell surfaceGolgiHost factorsCargoComplexesMutantsEndosomes
2022
CD55 Facilitates Immune Evasion by Borrelia crocidurae, an Agent of Relapsing Fever
Arora G, Lynn GE, Tang X, Rosen CE, Hoornstra D, Sajid A, Hovius JW, Palm NW, Ring AM, Fikrig E. CD55 Facilitates Immune Evasion by Borrelia crocidurae, an Agent of Relapsing Fever. MBio 2022, 13: e01161-22. PMID: 36036625, PMCID: PMC9600505, DOI: 10.1128/mbio.01161-22.Peer-Reviewed Original ResearchConceptsRole of CD55Fever infectionImmune evasionSurface of erythrocytesRosette formationB. crociduraeB. persicaHost factorsBorrelia crociduraeAcute febrile illnessInflammatory cytokine levelsElevated proinflammatory cytokinesExpression of CD55Causative agentErythrocyte rosette formationFacilitates Immune EvasionComplement-mediated lysisHost-pathogen interactionsCytokine levelsFebrile illnessSignificant morbidityProinflammatory cytokinesHigh-throughput screenC5a levelsCD55 expressionGenome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection
Biering SB, Sarnik SA, Wang E, Zengel JR, Leist SR, Schäfer A, Sathyan V, Hawkins P, Okuda K, Tau C, Jangid AR, Duffy CV, Wei J, Gilmore RC, Alfajaro MM, Strine MS, Nguyenla X, Van Dis E, Catamura C, Yamashiro LH, Belk JA, Begeman A, Stark JC, Shon DJ, Fox DM, Ezzatpour S, Huang E, Olegario N, Rustagi A, Volmer AS, Livraghi-Butrico A, Wehri E, Behringer RR, Cheon DJ, Schaletzky J, Aguilar HC, Puschnik AS, Button B, Pinsky BA, Blish CA, Baric RS, O’Neal W, Bertozzi CR, Wilen CB, Boucher RC, Carette JE, Stanley SA, Harris E, Konermann S, Hsu PD. Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Nature Genetics 2022, 54: 1078-1089. PMID: 35879412, PMCID: PMC9355872, DOI: 10.1038/s41588-022-01131-x.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionHost factorsSARS-CoV-2 entry factors ACE2SARS-CoV-2-host interactionsSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Diverse respiratory virusesMild respiratory illnessRespiratory distress syndromeSARS-CoV-2 host factorsHost-directed therapeuticsSyndrome coronavirus 2Coronavirus disease 2019Human lung epithelial cellsRange of symptomsHost defense mechanismsLung epithelial cellsGenome-wide CRISPR knockoutDistress syndromeRespiratory virusesRespiratory illnessCoronavirus 2Cell cycle regulationHigh molecular weight glycoproteins
2021
Knowledge gaps in the epidemiology of severe dengue impede vaccine evaluation
Sharp T, Anderson K, Katzelnick L, Clapham H, Johansson M, Morrison A, Harris E, Paz-Bailey G, Waterman S. Knowledge gaps in the epidemiology of severe dengue impede vaccine evaluation. The Lancet Infectious Diseases 2021, 22: e42-e51. PMID: 34265259, PMCID: PMC11379041, DOI: 10.1016/s1473-3099(20)30871-9.Peer-Reviewed Original ResearchConceptsDengue virus infectionSevere dengueVirus infectionDisease severityAnti-dengue virus antibodiesMajor organ failureHospital admissionOrgan failureVaccine evaluationClinical spectrumVaccine trialsPrevious infectionRisk factorsVirus antibodiesClinical studiesClinical practiceDengue virusStudy participantsInfectionLack of specificityHost factorsVirus characteristicsDengueEpidemiologyRange of agesIn vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission
Haugh KA, Ladinsky MS, Ullah I, Stone HM, Pi R, Gilardet A, Grunst MW, Kumar P, Bjorkman PJ, Mothes W, Uchil PD. In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission. ELife 2021, 10: e64179. PMID: 34223819, PMCID: PMC8298093, DOI: 10.7554/elife.64179.Peer-Reviewed Original ResearchConceptsSentinel macrophagesSiglec-1/CD169Immune surveillance functionCommon host factorMesenteric sacsPeyer's patchesGastrointestinal tractOral routeReporter virusRetrovirus transmissionRetrovirus infectionFrontline cellsRetroviral pathogenesisHost factorsBioluminescence imagingVirus entryIncoming virusInfectionRetrovirus life cycleCD169Early eventsMacrophagesMultiscale imaging approachVirusSurveillance functionAdverse events induced by immune checkpoint inhibitors
Perdigoto AL, Kluger H, Herold KC. Adverse events induced by immune checkpoint inhibitors. Current Opinion In Immunology 2021, 69: 29-38. PMID: 33640598, PMCID: PMC8122053, DOI: 10.1016/j.coi.2021.02.002.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutoantibodiesAutoantigensAutoimmune DiseasesAutoimmunityCytotoxicity, ImmunologicDrug-Related Side Effects and Adverse ReactionsGene-Environment InteractionGenetic Predisposition to DiseaseHumansImmune Checkpoint InhibitorsImmunotherapyLymphocyte ActivationNeoplasmsT-LymphocytesConceptsImmune checkpoint inhibitorsCheckpoint inhibitorsAdverse eventsT cellsImmune related adverse eventsEmergence of autoantibodiesRelated adverse eventsAnti-tumor responseAutoreactive T cellsActivated T cellsAutoimmune mechanismsTreatment of cancerAutoimmune diseasesInflammatory responsePredictive valueHost factorsToxic effectsInhibitorsDirect effectOngoing investigationAutoantibodiesCellsAutoimmunityPathogenesisCancerAssociation of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India
Pandit B, Bhattacharjee S, Bhattacharjee B. Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Infection Genetics And Evolution 2021, 90: 104734. PMID: 33508515, PMCID: PMC7839510, DOI: 10.1016/j.meegid.2021.104734.Peer-Reviewed Original ResearchConceptsIndication of population expansionNegative Tajima's D valuesAllele frequency spectrumTajima's D valuesSARS-CoV-2 sequencesAmino acid changesClade of virusesNucleotide diversityEvolutionary analysisLinkage disequilibriumPopulation expansionContribution of host factorsViral haplotypesClade GAcid changesSARS-CoV-2 variantsViral populationsHost factorsMortality rateVariantsViral factorsNetwork analysisCoronary heart diseaseSARS-CoV-2 virusVirusImaging of abdominal and pelvic infections in the cancer patient
Itani M, Menias CO, Mellnick VM, El Zakhem A, Elsayes K, Katabathina V, Revzin MV. Imaging of abdominal and pelvic infections in the cancer patient. Abdominal Radiology 2021, 46: 2920-2941. PMID: 33386914, PMCID: PMC7778421, DOI: 10.1007/s00261-020-02896-7.Peer-Reviewed Original ResearchConceptsCancer patientsDegree of immunosuppressionTreatment-related factorsPrognosis of infectionMain risk factorsManifestations of infectionClinical background informationSymptoms of infectionIntegrity of barriersAnatomic obstructionPelvic infectionTumor burdenPatient populationRisk factorsClassical signsPatientsInfectionHost factorsPotential mimicsAbdomenPelvisDifferentiating featuresUnderlying typeImmunosuppressionComplicationsTranslational regulation of viral RNA in the type I interferon response
Hsu J, Laurent-Rolle M, Cresswell P. Translational regulation of viral RNA in the type I interferon response. Current Research In Virological Science 2021, 2: 100012. DOI: 10.1016/j.crviro.2021.100012.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsInterferon-stimulated genesViral infectionViral replicationIFN-I responsesType I interferon responseAntigen-independent mannerInnate immune responseVariety of mechanismsI interferon responseImmune responseVirus life cycleInfectious organismsInterferon responseHost factorsInfectionFirst lineViral RNAViral proteinsType IViral translationCommon cellular responseMolecular mechanismsInhibitionCellular responsesTranslation inhibition
2020
Cytidine Monophosphate N-Acetylneuraminic Acid Synthetase and Solute Carrier Family 35 Member A1 Are Required for Reovirus Binding and Infection
Urbanek K, Sutherland DM, Orchard RC, Wilen CB, Knowlton JJ, Aravamudhan P, Taylor GM, Virgin HW, Dermody TS. Cytidine Monophosphate N-Acetylneuraminic Acid Synthetase and Solute Carrier Family 35 Member A1 Are Required for Reovirus Binding and Infection. Journal Of Virology 2020, 95: 10.1128/jvi.01571-20. PMID: 33087464, PMCID: PMC7944449, DOI: 10.1128/jvi.01571-20.Peer-Reviewed Original ResearchConceptsSialic acid expressionMicroglial cellsCell surface expressionReovirus-induced cell deathReovirus infectionSialic acidMurine microglial BV2 cellsReovirus-induced diseaseMember A1Microglial BV2 cellsSurface expressionMurine microglial cellsCell deathReovirus bindingBV2 cellsViral tropismInfectionHost genesLow-level bindingCell surface receptorsHost factorsCell surfaceReceptorsSialic acid synthesisSurface receptors
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