2025
Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US
Chen N, Pham K, Chaguza C, Lopes R, Klaassen F, Kalinich C, Initiative Y, Kerantzas N, Pandya S, Ferguson D, Schulz W, Weinberger D, Pitzer V, Warren J, Grubaugh N, Hahn A. Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US. Viruses 2025, 17: 1020. PMID: 40733636, PMCID: PMC12299087, DOI: 10.3390/v17071020.Peer-Reviewed Original ResearchConceptsDominant lineageHost-pathogen dynamicsGenomic surveillance programsResponse to previous infectionsSequence dataVariant fitnessLineage replacementCopy numberDynamic fitness landscapesLineagesSARS-CoV-2Integrated analysisViral copy numberFitness landscapeReplacement dynamicsReproductive rateOmicron lineagesGrowth rateImmune escapeAntigen exposureVariant emergenceViral sheddingPrevious infectionEpidemiological dataInfection
2024
Clinical features and outcomes in kidney transplant recipients with COVID-19 pneumonia: a single center retrospective cohort study
Xu L, Chen X, Yang X, Chen S, Yang M, Yuan Z, Chen R, Wang J, Jiang H, Xu J, Wang Y. Clinical features and outcomes in kidney transplant recipients with COVID-19 pneumonia: a single center retrospective cohort study. Frontiers In Cellular And Infection Microbiology 2024, 14: 1392491. PMID: 39211792, PMCID: PMC11358093, DOI: 10.3389/fcimb.2024.1392491.Peer-Reviewed Original ResearchConceptsKidney transplant recipientsCOVID-19 pneumoniaViral shedding timeRetrospective cohort studyShort-term prognosisTransplant recipientsClinical featuresAntiviral drugsAntiviral medicationsCohort studyShort-term renal functionAdministration of antiviral drugsAssociated with better therapeutic outcomesSevere COVID-19 pneumoniaConcurrent coronavirus disease 2019Diagnosis of COVID-19 pneumoniaTransplanted kidney functionStatistically significant reductionShedding timeRenal functionSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Clinical symptomsKidney functionInitial symptomsA retrospective cohort study of Paxlovid efficacy depending on treatment time in hospitalized COVID-19 patients
Du Z, Wang L, Bai Y, Liu Y, Lau E, Galvani A, Krug R, Cowling B, Meyers L. A retrospective cohort study of Paxlovid efficacy depending on treatment time in hospitalized COVID-19 patients. ELife 2024, 13: e89801. PMID: 38622989, PMCID: PMC11078542, DOI: 10.7554/elife.89801.Peer-Reviewed Original ResearchConceptsViral sheddingHospitalized COVID-19 patientsSARS-CoV-2Retrospective cohort studyRisk of reboundCOVID-19 patientsViral reboundTime of treatmentTreated patientsPreventing severe illnessEarly treatmentCohort studyHospitalized patientsPatientsViral replicationReducing infectiousnessSevere illnessTimely treatmentViral dynamicsHealth record dataTreatmentTransmission riskTransmission of SARS-CoV-2EfficacySymptoms
2021
Modeling SARS-CoV-2 propagation using rat coronavirus-associated shedding and transmission
Zeiss CJ, Asher JL, Vander Wyk B, Allore HG, Compton SR. Modeling SARS-CoV-2 propagation using rat coronavirus-associated shedding and transmission. PLOS ONE 2021, 16: e0260038. PMID: 34813610, PMCID: PMC8610237, DOI: 10.1371/journal.pone.0260038.Peer-Reviewed Original ResearchConceptsViral sheddingSialodacryoadenitis virusSARS-CoV-2Prior natural infectionSARS-CoV-2 propagationSeropositive animalsLow-level sheddingNaive recipient ratsCOVID-19Cycle threshold valuesDirect contact exposureSeroconversion ratesReinfected animalsRecipient ratsImmune protectionHigh riskNaive animalsSusceptible individualsInitial infectionGlobal immunityExposure paradigmRat coronavirusNatural infectionInfectionRatsViral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies
Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLOS Biology 2021, 19: e3001333. PMID: 34252080, PMCID: PMC8297933, DOI: 10.1371/journal.pbio.3001333.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionViral RNA concentrationClearance phaseAcute SARS-CoV-2 infectionReverse transcription-PCR testingPeak viral concentrationPersistent viral RNAPositive PCR testTranscription-PCR testingViral proliferationPublic health strategiesRNA concentrationViral concentrationInfection stagesCycle threshold valuesAcute infectionAsymptomatic individualsTest turnaround timeSymptomatic individualsClinical measuresHealth strategiesPatient progressPCR testingInfectionViral dynamicsA new positive SARS-CoV-2 test months after severe COVID-19 illness: reinfection or intermittent viral shedding?
Tuan J, Spichler-Moffarah A, Ogbuagu O. A new positive SARS-CoV-2 test months after severe COVID-19 illness: reinfection or intermittent viral shedding? BMJ Case Reports 2021, 14: e240531. PMID: 33542020, PMCID: PMC8098910, DOI: 10.1136/bcr-2020-240531.Peer-Reviewed Case Reports and Technical NotesConceptsSARS-CoV-2 RNA testSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2SARS-CoV-2 reinfectionSevere COVID-19 illnessRespiratory syndrome coronavirus 2COVID-19 reinfectionLong asymptomatic periodCOVID-19 illnessSyndrome coronavirus 2Intermittent viral sheddingAsymptomatic periodViral sheddingRNA testCoronavirus 2Clinical managementPersistent infectionDisease 4Molecular testingReinfectionRNA PCRCurrent presentationPotential casesMonthsPatients
2018
An Infant Mouse Model of Influenza Virus Transmission Demonstrates the Role of Virus-Specific Shedding, Humoral Immunity, and Sialidase Expression by Colonizing Streptococcus pneumoniae
Ortigoza M, Blaser S, Zafar M, Hammond A, Weiser J. An Infant Mouse Model of Influenza Virus Transmission Demonstrates the Role of Virus-Specific Shedding, Humoral Immunity, and Sialidase Expression by Colonizing Streptococcus pneumoniae. MBio 2018, 9: 10.1128/mbio.02359-18. PMID: 30563897, PMCID: PMC6299224, DOI: 10.1128/mbio.02359-18.Peer-Reviewed Original ResearchConceptsInfluenza A virusSusceptible to influenza A virusesInfluenza A virus transmissionInfant mouse modelUpper respiratory tractInfluenza A virus sheddingHumoral immunityMouse modelInfluenza A virus strainsTransmission of influenza A virusesAnimal modelsVirus strainsInfluenza virus strainsUpper respiratory tract floraGuinea pig modelAntagonizing transmissionAdult miceSusceptible recipientsA virusMarker of infectiousnessSialidase expressionPandemic potentialViral sheddingRespiratory tractPig model
2017
Duration of viral shedding and factors associated with prolonged shedding among inpatients with influenza treated with oseltamivir: a prospective cohort study
Khoury J, Szwarcwort M, Kra-oz Z, Saffuri M, Seh K, Yahalomi T, Braun E, Azzam Z, Paul M, Neuberger A. Duration of viral shedding and factors associated with prolonged shedding among inpatients with influenza treated with oseltamivir: a prospective cohort study. European Journal Of Clinical Microbiology & Infectious Diseases 2017, 37: 319-323. PMID: 29143145, DOI: 10.1007/s10096-017-3135-0.Peer-Reviewed Original ResearchConceptsRisk factorsBlood pressureDiagnostic yieldDay 2Lower diastolic blood pressureNegative PCR testIndependent risk factorProspective cohort studyProspective observational studyDiastolic blood pressureLower blood pressurePCR testInitiation of treatmentLow diagnostic yieldFirst positive testEvaluable patientsInfluenza PCROseltamivir administrationOseltamivir treatmentCohort studyMedian ageAdult inpatientsViral sheddingPositive PCRPCR positivityNorovirus Cell Tropism Is Determined by Combinatorial Action of a Viral Non-structural Protein and Host Cytokine
Lee S, Wilen CB, Orvedahl A, McCune BT, Kim KW, Orchard RC, Peterson ST, Nice TJ, Baldridge MT, Virgin HW. Norovirus Cell Tropism Is Determined by Combinatorial Action of a Viral Non-structural Protein and Host Cytokine. Cell Host & Microbe 2017, 22: 449-459.e4. PMID: 28966054, PMCID: PMC5679710, DOI: 10.1016/j.chom.2017.08.021.Peer-Reviewed Original ResearchConceptsIntestinal epithelial cellsViral surface proteinsCellular tropismPersistent viral infectionNon-structural protein NS1Expression of NS1MNoV infectionSurface proteinsHost cytokinesAntiviral immunityHost determinantsInterferon lambdaViral infectionKey host determinantsViral non-structural proteinsCell tropismFecal sheddingNon-structural proteinsTropism determinantsEpithelial cellsGlobal causeInfectionTropismProtein NS1MNoV
2014
Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body
Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP. Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body. PLOS Pathogens 2014, 10: e1004092. PMID: 24811311, PMCID: PMC4014458, DOI: 10.1371/journal.ppat.1004092.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2013
Effect of immunodeficiency on MPV shedding and transmission.
Macy JD, Paturzo FX, Compton SR. Effect of immunodeficiency on MPV shedding and transmission. Journal Of The American Association For Laboratory Animal Science 2013, 52: 467-74. PMID: 23849445, PMCID: PMC3725932.Peer-Reviewed Original Research
2012
Polyomavirus JC Urinary Shedding in Kidney and Liver Transplant Recipients Associated With Reduced Creatinine Clearance
Kusne S, Vilchez RA, Zanwar P, Quiroz J, Mazur MJ, Heilman RL, Mulligan D, Butel JS. Polyomavirus JC Urinary Shedding in Kidney and Liver Transplant Recipients Associated With Reduced Creatinine Clearance. The Journal Of Infectious Diseases 2012, 206: 875-880. PMID: 22802433, PMCID: PMC3501156, DOI: 10.1093/infdis/jis469.Peer-Reviewed Original ResearchConceptsJohn Cunningham virusSolid organ transplant recipientsLiver transplant recipientsOrgan transplant recipientsTransplant recipientsBK virusTransplant patientsUrinary sheddingKidney recipientsCreatinine clearanceReduced creatinine clearanceKidney transplant patientsLiver transplant patientsOrgan transplant patientsPolyomavirus BK virusJCV loadLiver recipientsPolyomavirus reactivationRenal dysfunctionSignificant morbidityPatient groupCrCl valuesLiver patientsPatientsKidney
2011
An addition to the effect of treating co-infections on HIV-1 viral load
Modjarrad K, Vermund SH. An addition to the effect of treating co-infections on HIV-1 viral load. The Lancet Infectious Diseases 2011, 11: 81. PMID: 21272789, DOI: 10.1016/s1473-3099(11)70013-5.Peer-Reviewed Original Research
2004
Transmission of enterotropic mouse hepatitis virus from immunocompetent and immunodeficient mice.
Compton SR, Ball-Goodrich LJ, Paturzo FX, Macy JD. Transmission of enterotropic mouse hepatitis virus from immunocompetent and immunodeficient mice. Journal Of The American Association For Laboratory Animal Science 2004, 54: 29-35. PMID: 15027615.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Outbred StrainsFecesFemaleHepatitis, Viral, AnimalImmunocompetenceImmunocompromised HostInfectious Disease Transmission, VerticalMiceMice, Inbred StrainsMurine hepatitis virusReverse Transcriptase Polymerase Chain ReactionRNA, ViralRodent DiseasesSentinel SurveillanceSpecies SpecificityVirus SheddingConceptsCell-deficient miceEnterotropic mouse hepatitis virusT cell-deficient miceMouse hepatitis virusInfected miceIntestinal infectionsC57BL/6 miceHepatitis virusB cell-deficient miceViral RNABALB/c miceSevere disseminated diseaseNon-infectious RNADisseminated diseaseNaive miceC miceMHV infectionImmunodeficient miceSentinel miceBALB/ cViral transmissionInfectionMiceVirus RNAWeeks
2001
An Effective AIDS Vaccine Based on Live Attenuated Vesicular Stomatitis Virus Recombinants
Rose N, Marx P, Luckay A, Nixon D, Moretto W, Donahoe S, Montefiori D, Roberts A, Buonocore L, Rose J. An Effective AIDS Vaccine Based on Live Attenuated Vesicular Stomatitis Virus Recombinants. Cell 2001, 106: 539-549. PMID: 11551502, DOI: 10.1016/s0092-8674(01)00482-2.Peer-Reviewed Original ResearchMeSH KeywordsAcquired Immunodeficiency SyndromeAIDS VaccinesAnimalsCD4 Lymphocyte CountCD4-Positive T-LymphocytesEnzyme-Linked Immunosorbent AssayGene Products, envGene Products, gagHIVHIV AntibodiesHumansImmunization, SecondaryMacaca mulattaMiceNeutralization TestsPilot ProjectsRecombinant Fusion ProteinsSAIDS VaccinesSimian Acquired Immunodeficiency SyndromeSimian immunodeficiency virusT-Lymphocytes, CytotoxicTime FactorsVaccines, AttenuatedVaccines, SyntheticVesicular stomatitis Indiana virusViral LoadVirus Shedding
1998
Public Health Implications of Antiretroviral Therapy and HIV Drug Resistance
Wainberg M, Friedland G. Public Health Implications of Antiretroviral Therapy and HIV Drug Resistance. JAMA 1998, 279: 1977-1983. PMID: 9643862, DOI: 10.1001/jama.279.24.1977.Peer-Reviewed Original ResearchConceptsHuman immunodeficiency virusDrug-resistant variantsDrug-resistant virusesHIV drug resistanceAntiviral therapyPublic health implicationsDrug resistanceGenital secretionsHealth implicationsPublic health importanceAntiretroviral therapyViral burdenAntiretroviral agentsPatient adherenceTreatment failureViral loadImmunodeficiency virusResistant virusesSustained reductionHealth importanceTherapyVirusChild routeBloodSecretion
1992
Recurrent Genital Infection in the Guinea Pig: Differences between Herpes Simplex Types 1 and 2
Landry M, Myerson D, Bull C. Recurrent Genital Infection in the Guinea Pig: Differences between Herpes Simplex Types 1 and 2. Intervirology 1992, 34: 169-179. PMID: 1339184, DOI: 10.1159/000150279.Peer-Reviewed Original ResearchConceptsHSV-2 strainsHSV-2HSV-1Genital infectionRecurrence rateHSV-1 McKrae strainType 1Herpes simplex virus type 2Simplex virus type 2Recurrent genital infectionsHerpes simplex type 1Guinea pig modelHSV type 1Simplex type 1HSV-1 strainsVirus type 2Vaginal virusAcute infectionLesion recurrenceOcular infectionsMcKrae strainGenital tractNervous systemType 2Guinea pigs
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