Featured Publications
Cytokinopathy with aberrant cytotoxic lymphocytes and profibrotic myeloid response in SARS-CoV-2 mRNA vaccine–associated myocarditis
Barmada A, Klein J, Ramaswamy A, Brodsky N, Jaycox J, Sheikha H, Jones K, Habet V, Campbell M, Sumida T, Kontorovich A, Bogunovic D, Oliveira C, Steele J, Hall E, Pena-Hernandez M, Monteiro V, Lucas C, Ring A, Omer S, Iwasaki A, Yildirim I, Lucas C. Cytokinopathy with aberrant cytotoxic lymphocytes and profibrotic myeloid response in SARS-CoV-2 mRNA vaccine–associated myocarditis. Science Immunology 2023, 8: eadh3455-eadh3455. PMID: 37146127, PMCID: PMC10468758, DOI: 10.1126/sciimmunol.adh3455.Peer-Reviewed Original ResearchConceptsMRNA vaccinesSARS-CoV-2 mRNA vaccinesSARS-CoV-2 mRNA vaccinationC-reactive protein levelsB-type natriuretic peptidePeripheral blood mononuclear cellsCardiac tissue inflammationDeep immune profilingSerum soluble CD163Vaccine-associated myocarditisCohort of patientsBlood mononuclear cellsCytotoxic T cellsLate gadolinium enhancementHypersensitivity myocarditisElevated troponinMRNA vaccinationImaging abnormalitiesNK cellsImmune profilingKiller cellsMyeloid responseNatriuretic peptideHumoral mechanismsInflammatory cytokinesSARS-CoV-2 mRNA vaccines decouple anti-viral immunity from humoral autoimmunity
Jaycox J, Lucas C, Yildirim I, Dai Y, Wang E, Monteiro V, Lord S, Carlin J, Kita M, Buckner J, Ma S, Campbell M, Ko A, Omer S, Lucas C, Speake C, Iwasaki A, Ring A. SARS-CoV-2 mRNA vaccines decouple anti-viral immunity from humoral autoimmunity. Nature Communications 2023, 14: 1299. PMID: 36894554, PMCID: PMC9996559, DOI: 10.1038/s41467-023-36686-8.Peer-Reviewed Original ResearchConceptsVaccine-associated myocarditisAutoimmune patientsAutoantibody reactivitySARS-CoV-2 mRNA vaccinationVaccine-related adverse effectsSARS-CoV-2 immunitySARS-CoV-2 infectionAcute COVID-19Development of autoantibodiesCOVID-19 patientsAnti-viral immunityVirus-specific antibodiesCOVID-19 vaccineCOVID-19Humoral autoimmunityMRNA vaccinationAutoantibody responsePost vaccinationAutoantibody developmentAutoimmune diseasesHumoral responseHealthy individualsPatientsAntigen profilingAdverse effectsNonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants
Petrone M, Lucas C, Menasche B, Breban M, Yildirim I, Campbell M, Omer S, Holmes E, Ko A, Grubaugh N, Iwasaki A, Wilen C, Vogels C, Fauver J. Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biology And Evolution 2023, 15: evad052. PMID: 36974986, PMCID: PMC10113931, DOI: 10.1093/gbe/evad052.Peer-Reviewed Original ResearchEvidence of leaky protection following COVID-19 vaccination and SARS-CoV-2 infection in an incarcerated population
Lind M, Dorion M, Houde A, Lansing M, Lapidus S, Thomas R, Yildirim I, Omer S, Schulz W, Andrews J, Hitchings M, Kennedy B, Richeson R, Cummings D, Ko A. Evidence of leaky protection following COVID-19 vaccination and SARS-CoV-2 infection in an incarcerated population. Nature Communications 2023, 14: 5055. PMID: 37598213, PMCID: PMC10439918, DOI: 10.1038/s41467-023-40750-8.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionPrior infectionHybrid immunityInfection riskCOVID-19 vaccinationNon-pharmaceutical interventionsInfected residentsVaccinationInfectionDocumented exposureDelta periodCell exposureIncarcerated populationsExposureImmunityRiskAssociationPotential benefitsCorrectional facilitiesCrowded settingsResidentsPeriodDistinguishing features of long COVID identified through immune profiling
Klein J, Wood J, Jaycox J, Dhodapkar R, Lu P, Gehlhausen J, Tabachnikova A, Greene K, Tabacof L, Malik A, Silva Monteiro V, Silva J, Kamath K, Zhang M, Dhal A, Ott I, Valle G, Peña-Hernández M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Song E, McCarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng T, Xu L, Geraghty A, Monje M, Yildirim I, Shon J, Medzhitov R, Lutchmansingh D, Possick J, Kaminski N, Omer S, Krumholz H, Guan L, Dela Cruz C, van Dijk D, Ring A, Putrino D, Iwasaki A. Distinguishing features of long COVID identified through immune profiling. Nature 2023, 623: 139-148. PMID: 37748514, PMCID: PMC10620090, DOI: 10.1038/s41586-023-06651-y.Peer-Reviewed Original ResearchConceptsLong COVIDSARS-CoV-2Infection syndromeExaggerated humoral responseSoluble immune mediatorsEpstein-Barr virusPost-exertional malaiseCross-sectional studyHigher antibody responseImmune mediatorsImmune phenotypingImmune profilingHumoral responseAntibody responseLymphocyte populationsCOVID statusUnbiased machineCortisol levelsLC statusRelevant biomarkersViral pathogensSyndromeCOVIDFuture studiesBiological featuresPrevalence of Chronic Diseases, Depression, and Stress Among US Childcare Professionals During the COVID-19 Pandemic
Elharake JA, Shafiq M, Cobanoglu A, Malik AA, Klotz M, Humphries JE, Murray T, Patel KM, Wilkinson D, Yildirim I, Diaz R, Rojas R, Cohen A, Lee A, Omer SB, Gilliam WS. Prevalence of Chronic Diseases, Depression, and Stress Among US Childcare Professionals During the COVID-19 Pandemic. Preventing Chronic Disease 2022, 19: e61. PMID: 36137183, PMCID: PMC9541678, DOI: 10.5888/pcd19.220132.Peer-Reviewed Original ResearchConceptsPhysical health conditionsMental healthHealth conditionsChronic diseasesDepression ratesCOVID-19 pandemicSex/gender disparityPublic health officialsChildcare professionalsSevere asthmaHeart diseaseUS adultsAsthma ratesSociodemographic characteristicsHealth officialsDepressionDiseaseNational representativenessLinear regression modelsPrevalenceHealthRegression modelsPandemicProfessionalsGender disparitiesCOVID-19 Vaccine Acceptance and Hesitancy Among Health Care Workers in Lebanon
Youssef N, Tfaily N, Moumneh M, Boutros C, Elharake J, Malik A, McFadden S, Galal B, Yildirim I, Khoshnood K, Omer S, Memish Z, Dbaibo G. COVID-19 Vaccine Acceptance and Hesitancy Among Health Care Workers in Lebanon. Journal Of Epidemiology And Global Health 2023, 13: 55-66. PMID: 36735184, PMCID: PMC9896451, DOI: 10.1007/s44197-023-00086-4.Peer-Reviewed Original ResearchConceptsHealth care workersCOVID-19 vaccine acceptanceVaccine acceptancePrevious infectionCare workersPrevious SARS-CoV-2 infectionSARS-CoV-2 infectionMethodsA cross-sectional studyCOVID-19 vaccination ratesCOVID-19 vaccinationCross-sectional studyCOVID-19 vaccineHealth care authoritiesVaccine uptakeVaccination ratesOrder of PhysiciansVaccine hesitancyGeneral populationHealthcare providersVaccineCare authoritiesInfectionCOVID-19 informationTrusted sourceCOVID-19 pandemic
2023
Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose
Filardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.Peer-Reviewed Original ResearchMeSH KeywordsAgedAntibodies, ViralAntibody FormationBNT162 VaccineCOVID-19HumansImmunoglobulin GSARS-CoV-2ConceptsBooster doseAntibody responseNeutralization titersVirus-specific IgG titersOlder adultsAntiviral humoral immunityPlasma antibody responsesHigh-risk populationSARS-CoV-2 spikeYears of ageAge-dependent impairmentHeterologous regimensBooster dosesBooster vaccineCoronaVac vaccineIgG titersProtective immunityHumoral immunityHumoral responseCoronaVacOmicron waveBooster strategyAge groupsEarly controlVaccine
2022
No evidence of fetal defects or anti-syncytin-1 antibody induction following COVID-19 mRNA vaccination
Lu-Culligan A, Tabachnikova A, Pérez-Then E, Tokuyama M, Lee HJ, Lucas C, Monteiro V, Miric M, Brache V, Cochon L, Muenker MC, Mohanty S, Huang J, Kang I, Dela Cruz C, Farhadian S, Campbell M, Yildirim I, Shaw AC, Ma S, Vermund SH, Ko AI, Omer SB, Iwasaki A. No evidence of fetal defects or anti-syncytin-1 antibody induction following COVID-19 mRNA vaccination. PLOS Biology 2022, 20: e3001506. PMID: 35609110, PMCID: PMC9129011, DOI: 10.1371/journal.pbio.3001506.Peer-Reviewed Original ResearchConceptsCOVID-19 mRNA vaccinationMRNA vaccinationEarly pregnancyFetal sizeCoronavirus disease 2019 (COVID-19) mRNA vaccinationSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Maternal antibody statusAdverse neonatal outcomesSyndrome coronavirus 2Birth defectsPolyinosinic-polycytidylic acidCrown-rump lengthGross birth defectsUnvaccinated adultsMaternal illnessNeonatal outcomesVaccinated adultsAntibody statusTLR3 agonistEarly immunizationMurine pregnancyAntibody inductionCoronavirus 2The balancing role of distribution speed against varying efficacy levels of COVID-19 vaccines under variants
Kim D, Keskinocak P, Pekgün P, Yildirim İ. The balancing role of distribution speed against varying efficacy levels of COVID-19 vaccines under variants. Scientific Reports 2022, 12: 7493. PMID: 35523832, PMCID: PMC9075929, DOI: 10.1038/s41598-022-11060-8.Peer-Reviewed Original ResearchConceptsOverall public health impactInfection attack rateCOVID-19 vaccineSARS-CoV-2Public health impactVaccine effectivenessAdverse outcomesMultiple vaccinesInitial efficacySuccessful immunization strategyImmunization strategiesVaccineLow-income countriesAttack rateEfficacyCOVID-19COVID-19 pandemicHealth impactsInfection spreadRecovered-deceased [SI(Q/F)RD] modelEfficacy levelsPandemicHospitalizationVaccinationVariantsNeutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccination
Pérez-Then E, Lucas C, Monteiro VS, Miric M, Brache V, Cochon L, Vogels CBF, Malik AA, De la Cruz E, Jorge A, De los Santos M, Leon P, Breban MI, Billig K, Yildirim I, Pearson C, Downing R, Gagnon E, Muyombwe A, Razeq J, Campbell M, Ko AI, Omer SB, Grubaugh ND, Vermund SH, Iwasaki A. Neutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccination. Nature Medicine 2022, 28: 481-485. PMID: 35051990, PMCID: PMC8938264, DOI: 10.1038/s41591-022-01705-6.Peer-Reviewed Original ResearchConceptsTwo-dose regimenOmicron variantVaccine boosterMRNA vaccinesNeutralization activityDelta variantTwo-dose mRNA vaccinesVirus-specific antibody levelsSARS-CoV-2 Omicron variantMRNA vaccine boosterNeutralization of OmicronNumerous spike mutationsSARS-CoV-2 DeltaPotent neutralization activityInfection-induced immunityCOVID-19 vaccineBNT162b2 boosterBooster vaccinationPrime vaccinationAntibody levelsAntibody titersHumoral immunityImmune escapeInactivated vaccinesVaccineAssociation of Child Masking With COVID-19–Related Closures in US Childcare Programs
Murray TS, Malik AA, Shafiq M, Lee A, Harris C, Klotz M, Humphries JE, Patel KM, Wilkinson D, Yildirim I, Elharake JA, Diaz R, Reyes C, Omer SB, Gilliam WS. Association of Child Masking With COVID-19–Related Closures in US Childcare Programs. JAMA Network Open 2022, 5: e2141227. PMID: 35084484, PMCID: PMC8796014, DOI: 10.1001/jamanetworkopen.2021.41227.Peer-Reviewed Original ResearchConceptsCOVID-19 casesLower riskImportant public health policy implicationsCOVID-19-related closuresPublic health policy implicationsChildren 2 yearsElectronic survey studyCenter-based childcare programsHealth policy implicationsSARS-CoV-2Survey studyChildcare professionalsMAIN OUTCOMEProgram closureHealth policyStudy periodRobust SEsBaselineChildcare programsCOVID-19Young childrenChildcare settingsChildrenPhysical distancingAssociation
2021
Resource allocation for different types of vaccines against COVID-19: Tradeoffs and synergies between efficacy and reach
Kim D, Pekgün P, Yildirim İ, Keskinocak P. Resource allocation for different types of vaccines against COVID-19: Tradeoffs and synergies between efficacy and reach. Vaccine 2021, 39: 6876-6882. PMID: 34688498, PMCID: PMC8520874, DOI: 10.1016/j.vaccine.2021.10.025.Peer-Reviewed Original ResearchMeSH KeywordsCOVID-19COVID-19 VaccinesHumansPandemicsResource AllocationSARS-CoV-2VaccinationVaccinesConceptsInfection attack rateVaccine typesDifferent vaccine typesResource-limited countriesHigh-efficacy vaccinesDifferent study parametersVaccine shortageEfficacy vaccineHealth outcomesLife-saving vaccinesVaccineVaccine distributionLow efficacyAttack rateStudy parametersEfficacyHigh efficacyCOVID-19COVID-19 pandemicDeceased (SIRD) modelDifferent resource allocation decisionsLimited accessImpact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity
Lucas C, Vogels CBF, Yildirim I, Rothman JE, Lu P, Monteiro V, Gehlhausen JR, Campbell M, Silva J, Tabachnikova A, Peña-Hernandez MA, Muenker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Shaw A, Ko A, Omer S, Grubaugh N, Iwasaki A. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature 2021, 600: 523-529. PMID: 34634791, PMCID: PMC9348899, DOI: 10.1038/s41586-021-04085-y.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 variantsMRNA vaccine-induced immunityT-cell activation markersSARS-CoV-2 antibodiesSecond vaccine doseVaccine-induced immunityCell activation markersT cell responsesHigh antibody titresSARS-CoV-2Vaccine boosterVaccine doseActivation markersVaccine dosesHumoral immunityAntibody titresMRNA vaccinesVitro stimulationNeutralization capacityNeutralization responseCell responsesE484KNucleocapsid peptideAntibody-binding sitesGreater reductionCOVID-19 Vaccine Acceptance among Health Care Workers in the Kingdom of Saudi Arabia
Elharake JA, Galal B, Alqahtani SA, Kattan RF, Barry MA, Temsah MH, Malik AA, McFadden SM, Yildirim I, Khoshnood K, Omer SB, Memish ZA. COVID-19 Vaccine Acceptance among Health Care Workers in the Kingdom of Saudi Arabia. International Journal Of Infectious Diseases 2021, 109: 286-293. PMID: 34242765, PMCID: PMC8260488, DOI: 10.1016/j.ijid.2021.07.004.Peer-Reviewed Original ResearchConceptsHealth care workersCOVID-19 vaccineCOVID-19 vaccine acceptanceVaccine acceptanceCare workersPublic health messaging campaignsCOVID-19 vaccine concernsPotential side effectsHealth care authoritiesVaccine concernsGeneral populationSide effectsVaccineCare authoritiesSaudi ArabiaHealth officialsMessaging campaignsDemographic characteristicsCOVID-19 informationKSA MinistryDemographic differencesParticipantsSignificance of SARS-CoV-2 specific antibody testing during COVID-19 vaccine allocation
Fujimoto AB, Keskinocak P, Yildirim I. Significance of SARS-CoV-2 specific antibody testing during COVID-19 vaccine allocation. Vaccine 2021, 39: 5055-5063. PMID: 34274126, PMCID: PMC8233959, DOI: 10.1016/j.vaccine.2021.06.067.Peer-Reviewed Original ResearchConceptsInfection attack rateAntibody testingSARS-CoV-2-specific antibodiesSpecific antibody testingAttack rateCOVID-19 vaccineSingle-dose vaccineCOVID-19 vaccine allocationDose vaccineSerology testingLimited vaccinesEligible individualsVaccine deploymentVaccination planVaccine supplySusceptible individualsNumber of casesRecovered (SIR) compartmental modelPeak dayUse of antibodiesVaccine allocationVaccinePeak infectionVaccinationSpecific antibodiesDelayed production of neutralizing antibodies correlates with fatal COVID-19
Lucas C, Klein J, Sundaram ME, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Vogels CBF, Muenker MC, Chang CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie A, Campbell M, Lee A, Chun H, Grubaugh N, Schulz W, Farhadian S, Dela Cruz C, Ring A, Shaw A, Wisnewski A, Yildirim I, Ko A, Omer S, Iwasaki A. Delayed production of neutralizing antibodies correlates with fatal COVID-19. Nature Medicine 2021, 27: 1178-1186. PMID: 33953384, PMCID: PMC8785364, DOI: 10.1038/s41591-021-01355-0.Peer-Reviewed Original ResearchConceptsDeceased patientsAntibody levelsAntibody responseDisease severityAnti-S IgG levelsCOVID-19 disease outcomesFatal COVID-19Impaired viral controlWorse clinical progressionWorse disease severitySevere COVID-19Length of hospitalizationImmunoglobulin G levelsHumoral immune responseCoronavirus disease 2019COVID-19 mortalityCOVID-19Domain (RBD) IgGSeroconversion kineticsDisease courseIgG levelsClinical parametersClinical progressionHumoral responseDisease onsetFast Development of High-Quality Vaccines in a Pandemic
Pischel L, Yildirim I, Omer SB. Fast Development of High-Quality Vaccines in a Pandemic. CHEST Journal 2021, 160: e1-e3. PMID: 33848535, PMCID: PMC8102080, DOI: 10.1016/j.chest.2021.03.063.Commentaries, Editorials and Letters
2020
Severe COVID‐19 disease in two pediatric oncology patients
Stokes CL, Patel PA, Sabnis HS, Mitchell SG, Yildirim IB, Pauly MG. Severe COVID‐19 disease in two pediatric oncology patients. Pediatric Blood & Cancer 2020, 67: e28432. PMID: 32779861, PMCID: PMC7361273, DOI: 10.1002/pbc.28432.Peer-Reviewed Original ResearchSevere Pediatric COVID-19 Presenting With Respiratory Failure and Severe Thrombocytopenia
Patel PA, Chandrakasan S, Mickells GE, Yildirim I, Kao CM, Bennett CM. Severe Pediatric COVID-19 Presenting With Respiratory Failure and Severe Thrombocytopenia. Pediatrics 2020, 146: e20201437. PMID: 32366611, PMCID: PMC7329259, DOI: 10.1542/peds.2020-1437.Peer-Reviewed Original ResearchConceptsSevere acute respiratory distress syndromeSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Syndrome coronavirus 2Coronavirus disease 2019Respiratory failureSevere thrombocytopeniaCoronavirus 2Disease 2019Pediatric coronavirus disease 2019Airway pressure release ventilationAcute respiratory distress syndromeBroad antiviral agentPediatric COVID-19Respiratory distress syndromeUnderlying medical conditionsPast medical historySignificant clinical benefitIntravenous immunoglobulinElevated markersClinical courseDistress syndromePrompt improvementSevere morbidity