2022
Association between primary or booster COVID-19 mRNA vaccination and Omicron lineage BA.1 SARS-CoV-2 infection in people with a prior SARS-CoV-2 infection: A test-negative case–control analysis
Lind M, Robertson A, Silva J, Warner F, Coppi A, Price N, Duckwall C, Sosensky P, Di Giuseppe E, Borg R, Fofana M, Ranzani O, Dean N, Andrews J, Croda J, Iwasaki A, Cummings D, Ko A, Hitchings M, Schulz W. Association between primary or booster COVID-19 mRNA vaccination and Omicron lineage BA.1 SARS-CoV-2 infection in people with a prior SARS-CoV-2 infection: A test-negative case–control analysis. PLOS Medicine 2022, 19: e1004136. PMID: 36454733, PMCID: PMC9714718, DOI: 10.1371/journal.pmed.1004136.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionBooster vaccinationPrior infectionOmicron infectionPrimary vaccinationMRNA vaccinationOdds ratioAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionPrior SARS-CoV-2 infectionTest-negative case-control analysisYale New Haven Health SystemTest-negative case-control studyCOVID-19 mRNA vaccinationSyndrome coronavirus 2 infectionOmicron variant infectionPrior infection statusCoronavirus 2 infectionCase-control studyCase-control analysisOdds of infectionRisk of infectionRace/ethnicityBooster dosesDate of testUse of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness
Lind M, Copin R, McCarthy S, Coppi A, Warner F, Ferguson D, Duckwall C, Borg R, Muenker M, Overton J, Hamon S, Zhou A, Cummings D, Ko A, Hamilton J, Schulz W, Hitchings M. Use of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness. The Journal Of Infectious Diseases 2022, 227: 663-674. PMID: 36408616, DOI: 10.1093/infdis/jiac453.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesCOVID-19COVID-19 VaccinesHepatitis DHumansImmune EvasionSARS-CoV-2Vaccine EfficacyConceptsVaccine effectivenessImmune evasionDelta infectionVE estimatesSecond doseTest-negative case-control studySevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Whole-genome sequencingCOVID-19 vaccine effectivenessRespiratory syndrome coronavirus 2Syndrome coronavirus 2Case-control studyCoronavirus 2Calendar periodDelta variantInfectionDoseEvasionDaysLow effectivenessImmunityVariantsMIF is a common genetic determinant of COVID-19 symptomatic infection and severity
Shin JJ, Fan W, Par-Young J, Piecychna M, Leng L, Israni-Winger K, Qing H, Gu J, Zhao H, Schulz WL, Unlu S, Kuster J, Young G, Liu J, Ko AI, Garcia A, Sauler M, Wisnewski AV, Young L, Orduña A, Wang A, Klementina O, Garcia AB, Hegyi P, Armstrong ME, Mitchell P, Ordiz DB, Garami A, Kang I, Bucala R. MIF is a common genetic determinant of COVID-19 symptomatic infection and severity. QJM 2022, 116: 205-212. PMID: 36222594, PMCID: PMC9620729, DOI: 10.1093/qjmed/hcac234.Peer-Reviewed Original ResearchConceptsMacrophage migration inhibitory factorLow-expression MIF alleleCOVID-19 infectionMIF allelesCATT7 alleleHealthy controlsCOVID-19Serum macrophage migration inhibitory factorSymptomatic SARS-CoV-2 infectionHigher serum MIF levelsHigh-expression MIF allelesRetrospective case-control studySARS-CoV-2 infectionFunctional polymorphismsAvailable clinical characteristicsMultinational retrospective studySerum MIF levelsUninfected healthy controlsSymptomatic COVID-19Tertiary medical centerHealthy control subjectsCase-control studyMigration inhibitory factorCoronavirus disease 2019Common functional polymorphismsEffectiveness of an inactivated Covid-19 vaccine with homologous and heterologous boosters against Omicron in Brazil
Ranzani OT, Hitchings MDT, de Melo RL, de França GVA, Fernandes CFR, Lind ML, Torres MSS, Tsuha DH, David LCS, Said RFC, Almiron M, de Oliveira RD, Cummings DAT, Dean NE, Andrews JR, Ko AI, Croda J. Effectiveness of an inactivated Covid-19 vaccine with homologous and heterologous boosters against Omicron in Brazil. Nature Communications 2022, 13: 5536. PMID: 36202800, PMCID: PMC9537178, DOI: 10.1038/s41467-022-33169-0.Peer-Reviewed Original ResearchMeSH KeywordsAdultBNT162 VaccineBrazilCase-Control StudiesCOVID-19COVID-19 VaccinesHumansVaccines, InactivatedChange in covid-19 risk over time following vaccination with CoronaVac: test negative case-control study
Hitchings MDT, Ranzani OT, Lind ML, Dorion M, D'Agostini TL, de Paula RC, de Paula OFP, de Moura Villela EF, Scaramuzzini Torres MS, de Oliveira SB, Schulz W, Almiron M, Said R, de Oliveira RD, Vieira da Silva P, de Araújo WN, Gorinchteyn JC, Dean NE, Andrews JR, Cummings DAT, Ko AI, Croda J. Change in covid-19 risk over time following vaccination with CoronaVac: test negative case-control study. The BMJ 2022, 377: e070102. PMID: 35697361, PMCID: PMC9189440, DOI: 10.1136/bmj-2022-070102.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultBrazilCase-Control StudiesCOVID-19COVID-19 TestingCOVID-19 VaccinesHumansSARS-CoV-2VaccinationVaccinesConceptsSymptomatic COVID-19Negative case-control studyCase-control studyHospital admissionOdds ratioCOVID-19Series completionCovid-19 related hospital admissionReverse transcription polymerase chain reaction testingTranscription polymerase chain reaction testingSevere COVID-19 outcomesSARS-CoV-2 infectionPolymerase chain reaction testingInactivated whole virus vaccineDoses of CoronaVacAcute respiratory illnessTest-negative controlsWhole virus vaccineRelated hospital admissionsHealthcare worker statusConditional logistic regressionCOVID-19 outcomesCOVID-19 symptomsMunicipality of residenceSARS-CoV-2Effectiveness of CoronaVac, ChAdOx1 nCoV-19, BNT162b2, and Ad26.COV2.S among individuals with previous SARS-CoV-2 infection in Brazil: a test-negative, case-control study
Cerqueira-Silva T, Andrews JR, Boaventura VS, Ranzani OT, de Araújo Oliveira V, Paixão ES, Júnior JB, Machado TM, Hitchings MDT, Dorion M, Lind ML, Penna GO, Cummings DAT, Dean NE, Werneck GL, Pearce N, Barreto ML, Ko AI, Croda J, Barral-Netto M. Effectiveness of CoronaVac, ChAdOx1 nCoV-19, BNT162b2, and Ad26.COV2.S among individuals with previous SARS-CoV-2 infection in Brazil: a test-negative, case-control study. The Lancet Infectious Diseases 2022, 22: 791-801. PMID: 35366959, PMCID: PMC8971277, DOI: 10.1016/s1473-3099(22)00140-2.Peer-Reviewed Original ResearchMeSH KeywordsAd26COVS1BNT162 VaccineBrazilCase-Control StudiesChAdOx1 nCoV-19COVID-19COVID-19 VaccinesHumansSARS-CoV-2ConceptsPrevious SARS-CoV-2 infectionSARS-CoV-2 infectionChAdOx1 nCoV-19Negative RT-PCR testRT-PCR testVaccine series completionCase-control studySymptomatic infectionCOVID-19 vaccineNCoV-19Symptomatic illnessVaccine seriesSecond doseSevere outcomesSeries completionTwo-dose vaccine seriesPositive RT-PCR testInitial SARS-CoV-2 infectionMultivariable conditional logistic regressionCOVID-19Effectiveness of CoronaVacFull vaccine seriesMore daysOdds of hospitalisationSymptomatic COVID-19Use of Recently Vaccinated Individuals to Detect Bias in Test-Negative Case–Control Studies of COVID-19 Vaccine Effectiveness
Hitchings MDT, Lewnard JA, Dean NE, Ko AI, Ranzani OT, Andrews JR, Cummings DAT. Use of Recently Vaccinated Individuals to Detect Bias in Test-Negative Case–Control Studies of COVID-19 Vaccine Effectiveness. Epidemiology 2022, 33: 450-456. PMID: 35384900, PMCID: PMC9148635, DOI: 10.1097/ede.0000000000001484.Peer-Reviewed Original ResearchConceptsCOVID-19 vaccine effectivenessVaccine effectivenessNegative control exposureObservational studyControl exposurePhase III trialsTest-negative studiesTest-negative casesVaccine effectiveness estimatesCOVID-19 vaccineDemonstration of efficacyCOVID-19 riskIII trialsUnvaccinated individualsClinical trialsControl studyStudy designEffectiveness estimatesCareful study designUnmeasured confoundingSelection biasTrialsConfoundingExposureIndividuals
2021
Effectiveness of ChAdOx1 vaccine in older adults during SARS-CoV-2 Gamma variant circulation in São Paulo
Hitchings MDT, Ranzani OT, Dorion M, D’Agostini T, de Paula RC, de Paula OFP, de Moura Villela EF, Torres MSS, de Oliveira SB, Schulz W, Almiron M, Said R, de Oliveira RD, Silva PV, de Araújo WN, Gorinchteyn JC, Andrews JR, Cummings DAT, Ko AI, Croda J. Effectiveness of ChAdOx1 vaccine in older adults during SARS-CoV-2 Gamma variant circulation in São Paulo. Nature Communications 2021, 12: 6220. PMID: 34711813, PMCID: PMC8553924, DOI: 10.1038/s41467-021-26459-6.Peer-Reviewed Original ResearchMeSH KeywordsAgedBrazilCase-Control StudiesCOVID-19COVID-19 VaccinesFemaleHumansMaleMiddle AgedSARS-CoV-2ConceptsSingle doseOxford-AstraZeneca COVID-19 vaccineTest-negative case-control studySevere COVID-19 outcomesCOVID-19COVID-19-related deathsTwo-dose scheduleTwo-dose regimenCase-control studyCOVID-19 outcomesInter-dose intervalCOVID-19 hospitalizationCOVID-19 vaccineSARS-CoV-2ChAdOx1 vaccinePrimary endpointSecondary endpointsFirst doseSecond doseHigh prevalenceElderly individualsElderly populationVariant prevalenceVaccine supplyHospitalizationEffectiveness of the CoronaVac vaccine in older adults during a gamma variant associated epidemic of covid-19 in Brazil: test negative case-control study
Ranzani OT, Hitchings MDT, Dorion M, D'Agostini TL, de Paula RC, de Paula OFP, Villela EFM, Torres MSS, de Oliveira SB, Schulz W, Almiron M, Said R, de Oliveira RD, Vieira da Silva P, de Araújo WN, Gorinchteyn JC, Andrews JR, Cummings DAT, Ko AI, Croda J. Effectiveness of the CoronaVac vaccine in older adults during a gamma variant associated epidemic of covid-19 in Brazil: test negative case-control study. The BMJ 2021, 374: n2015. PMID: 34417194, PMCID: PMC8377801, DOI: 10.1136/bmj.n2015.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overBrazilCase-Control StudiesCOVID-19COVID-19 Nucleic Acid TestingCOVID-19 VaccinesFemaleHumansMaleSARS-CoV-2Treatment OutcomeConceptsSymptomatic COVID-19Negative case-control studyCase-control studyHospital admissionVaccine effectivenessSecond doseDose regimenElderly populationCOVID-19Reverse transcription polymerase chain reaction testingTranscription polymerase chain reaction testingPolymerase chain reaction testingGamma variantInactivated whole virus vaccineAdjusted vaccine effectivenessTest-negative controlsWhole virus vaccineCOVID-19 statusCOVID-19 symptomsYounger age groupsMunicipality of residenceSARS-CoV-2RT-PCR testSelf-reported raceCoronaVac vaccineMaternal outcomes and risk factors for COVID-19 severity among pregnant women
Vouga M, Favre G, Martinez-Perez O, Pomar L, Acebal LF, Abascal-Saiz A, Hernandez MRV, Hcini N, Lambert V, Carles G, Sichitiu J, Salomon L, Stirnemann J, Ville Y, de Tejada BM, Goncé A, Hawkins-Villarreal A, Castillo K, Solsona EG, Trigo L, Cleary B, Geary M, Bartels H, Al-Kharouf F, Malone F, Higgins M, Keating N, Knowles S, Poncelet C, Ribeiro-do-Valle CC, Surita F, Dantas-Silva A, Borrelli C, Luz AG, Fuenzalida J, Carvajal J, Canales MG, Hernandez O, Grechukhina O, Ko AI, Reddy U, Figueiredo R, Moucho M, Pinto PV, De Luca C, De Santis M, de Campos DA, Martins I, Garabedian C, Subtil D, Bohrer B, Da Rocha Oppermann ML, Wender MCO, Schuler-Faccini L, Sanseverino MTV, Giugliani C, Friedrich L, Scherer MH, Mottet N, Ducarme G, Pelerin H, Moreau C, Breton B, Quibel T, Rozenberg P, Giannoni E, Granado C, Monod C, Mueller D, Hoesli I, Bassler D, Heldstab S, Kölble NO, Sentilhes L, Charvet M, Deprest J, Richter J, Van der Veeken L, Eggel-Hort B, Plantefeve G, Derouich M, Calvache AJN, Lopez-Giron MC, Burgos-Luna JM, Escobar-Vidarte MF, Hecher K, Tallarek AC, Hadar E, Haratz KK, Amikam U, Malinger G, Maymon R, Yogev Y, Schäffer L, Toussaint A, Rossier MC, De Sa RAM, Grawe C, Aebi-Popp K, Radan AP, Raio L, Surbek D, Böckenhoff P, Strizek B, Kaufmann M, Bloch A, Boulvain M, Johann S, Heldstab SA, Bernasconi MT, Grant G, Feki A, Brochut AM, Giral M, Sedille L, Papadia A, Brugger RC, Weber B, Fischer T, Kahlert C, Saines KN, Cambou M, Kanellos P, Chen X, Yin M, Haessig A, Ackermann S, Baud D, Panchaud A. Maternal outcomes and risk factors for COVID-19 severity among pregnant women. Scientific Reports 2021, 11: 13898. PMID: 34230507, PMCID: PMC8260739, DOI: 10.1038/s41598-021-92357-y.Peer-Reviewed Original ResearchConceptsSevere maternal outcomesPregnant womenRisk factorsMaternal outcomesPulmonary comorbiditiesHypertensive disordersNeonatal outcomesSevere complicationsHigh riskSevere acute respiratory syndrome coronavirus 2Severe coronavirus disease-19Severe COVID-19 diseaseAcute respiratory syndrome coronavirus 2Neonatal intensive care unitSARS-CoV-2 infectionRespiratory syndrome coronavirus 2Immediate neonatal outcomeIntensive care unitSyndrome coronavirus 2COVID-19 severityCase-control studyCoronavirus disease-19SARS-CoV-2COVID-19 diseaseMaternal diseaseKynurenic acid may underlie sex-specific immune responses to COVID-19
Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Yan H, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh JE, Silva J, Wong P, team Y, Ko AI, Khan SA, Iwasaki A, Johnson CH. Kynurenic acid may underlie sex-specific immune responses to COVID-19. Science Signaling 2021, 14: eabf8483. PMID: 34230210, PMCID: PMC8432948, DOI: 10.1126/scisignal.abf8483.Peer-Reviewed Original ResearchConceptsKynurenic acidImmune responseClinical outcomesSex-specific immune responsesT cell responsesPoor clinical outcomeCOVID-19 patientsCoronavirus disease 2019COVID-19Sex-related differencesMale patientsCytokine abundanceInflammatory cytokinesKynurenine ratioSerum metabolomeDisease 2019Sex-specific linkKynurenine aminotransferaseCell responsesOld malePatientsMalesOutcomesResponseMetabolitesDiverse functional autoantibodies in patients with COVID-19
Wang EY, Mao T, Klein J, Dai Y, Huck JD, Jaycox JR, Liu F, Zhou T, Israelow B, Wong P, Coppi A, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Zheng NS, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Dela Cruz C, Farhadian S, Schulz W, Ma S, Grubaugh N, Ko A, Iwasaki A, Ring A. Diverse functional autoantibodies in patients with COVID-19. Nature 2021, 595: 283-288. PMID: 34010947, DOI: 10.1038/s41586-021-03631-y.Peer-Reviewed Original ResearchConceptsPeripheral immune cell compositionSARS-CoV-2 infectionCOVID-19Effects of autoantibodiesTissue-associated antigensSpecific clinical characteristicsInnate immune activationImmune cell compositionCOVID-19 exhibitCOVID-19 manifestsAnalysis of autoantibodiesSARS-CoV-2Functional autoantibodiesMouse surrogateClinical characteristicsVirological controlClinical outcomesImmune activationMild diseaseAsymptomatic infectionAutoantibody reactivityDisease progressionHealthcare workersHigh prevalenceAutoantibodiesHousehold rat infestation in urban slum populations: Development and validation of a predictive score for leptospirosis
Costa F, Zeppelini CG, Ribeiro GS, Santos N, Reis RB, Martins RD, Bittencourt D, Santana C, Brant J, Reis MG, Ko AI. Household rat infestation in urban slum populations: Development and validation of a predictive score for leptospirosis. PLOS Neglected Tropical Diseases 2021, 15: e0009154. PMID: 33657101, PMCID: PMC7959339, DOI: 10.1371/journal.pntd.0009154.Peer-Reviewed Original Research
2020
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Team Y, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND, Iwasaki A. Detection of SARS-CoV-2 RNA by multiplex RT-qPCR. PLOS Biology 2020, 18: e3000867. PMID: 33027248, PMCID: PMC7571696, DOI: 10.1371/journal.pbio.3000867.Peer-Reviewed Original ResearchMeSH KeywordsBetacoronavirusCase-Control StudiesClinical Laboratory TechniquesCoronavirus InfectionsCOVID-19COVID-19 TestingDNA PrimersHEK293 CellsHumansLimit of DetectionMultiplex Polymerase Chain ReactionNasopharynxPandemicsPneumonia, ViralReagent Kits, DiagnosticReverse Transcriptase Polymerase Chain ReactionRNA, ViralSARS-CoV-2United StatesConceptsSARS-CoV-2 RNAMultiplex RT-qPCRRT-qPCRSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testingSARS-CoV-2Quantitative reverse transcription PCRCycle threshold valuesReverse transcription-PCRRT-qPCR assaysDisease controlMultiplex RT-qPCR assayTranscription-PCRAssaysSingle assayLow copy number
2002
Population-based case-control investigation of risk factors for leptospirosis during an urban epidemic.
Sarkar U, Nascimento S, Barbosa R, Martins R, Nuevo H, Kalofonos I, Kalafanos I, Grunstein I, Flannery B, Dias J, Riley L, Reis M, Ko A. Population-based case-control investigation of risk factors for leptospirosis during an urban epidemic. American Journal Of Tropical Medicine And Hygiene 2002, 66: 605-10. PMID: 12201599, DOI: 10.4269/ajtmh.2002.66.605.Peer-Reviewed Original ResearchConceptsRisk factorsUrban epidemicPopulation-based case-control studyPopulation-based case-control investigationIndependent risk factorLaboratory-confirmed casesHealthy neighbourhood controlsCase-control investigationCase-control studyCases of leptospirosisSevere leptospirosisWeil's syndromeWorkplace exposuresNeighborhood controlsHigh endemicityLeptospirosisFocused interventionsMore ratsSyndromeRatsEpidemicEnvironmental sourcesComplicationsFactorsMortality