2023
Transmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics
Dodd P, Shaweno D, Ku C, Glaziou P, Pretorius C, Hayes R, MacPherson P, Cohen T, Ayles H. Transmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics. Nature Communications 2023, 14: 1639. PMID: 36964130, PMCID: PMC10037365, DOI: 10.1038/s41467-023-37314-1.Peer-Reviewed Original ResearchConceptsHigh HIV prevalence settingsEstimation of burdenHIV prevalence settingsGeneralized HIV epidemicsTB transmission modelAntiretroviral therapyTB infectionTB incidenceHIV prevalenceTB prevalencePrevalence settingsTB epidemicHIV epidemicHigh burdenBurden estimatesNotification dataAnnual riskSingle pathogenIntervention impactTherapy effectsTuberculosisPrevalenceEpidemicBurdenAfrican countries
2022
Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model
Chitwood MH, Russi M, Gunasekera K, Havumaki J, Klaassen F, Pitzer VE, Salomon JA, Swartwood NA, Warren JL, Weinberger DM, Cohen T, Menzies NA. Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model. PLOS Computational Biology 2022, 18: e1010465. PMID: 36040963, PMCID: PMC9467347, DOI: 10.1371/journal.pcbi.1010465.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionCOVID-19 casesIncident SARS-CoV-2 infectionCOVID-19 disease burdenSymptomatic COVID-19 casesLocal epidemiological trendsSARS-CoV-2 transmissionBayesian evidence synthesis modelCOVID-19 outcomesEvidence synthesis modelMagnitude of infectionCOVID-19 deathsCumulative incidenceDisease burdenExcess mortalityCase ascertainmentEpidemiological trendsSeroprevalence estimatesUnderlying incidenceUS populationDisease trendsViral transmission dynamicsInfectionEpidemiological driversCOVID-19 epidemic
2021
The Impact of Changes in Diagnostic Testing Practices on Estimates of COVID-19 Transmission in the United States
Pitzer VE, Chitwood M, Havumaki J, Menzies NA, Perniciaro S, Warren JL, Weinberger DM, Cohen T. The Impact of Changes in Diagnostic Testing Practices on Estimates of COVID-19 Transmission in the United States. American Journal Of Epidemiology 2021, 190: 1908-1917. PMID: 33831148, PMCID: PMC8083380, DOI: 10.1093/aje/kwab089.Peer-Reviewed Original ResearchConceptsSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Diagnostic testingRespiratory syndrome coronavirus 2Reproductive numberPercentage of patientsSyndrome coronavirus 2Coronavirus disease 2019Diagnostic testing practicesFraction of casesCOVID-19 transmissionEffective reproductive numberCoronavirus 2Disease 2019Testing practicesCoronavirus diseaseBasic reproductive numberLevel of interventionEstimates of R0Daily number
2020
Post-tuberculosis mortality and morbidity: valuing the hidden epidemic
Quaife M, Houben RMGJ, Allwood B, Cohen T, Coussens AK, Harries AD, van Kampen S, Marx FM, Sweeney S, Wallis RS, Menzies NA. Post-tuberculosis mortality and morbidity: valuing the hidden epidemic. The Lancet Respiratory Medicine 2020, 8: 332-333. PMID: 32057300, DOI: 10.1016/s2213-2600(20)30039-4.Peer-Reviewed Original Research
2019
Cost-Effectiveness of Alternative Uses of Polyvalent Meningococcal Vaccines in Niger: An Agent-Based Transmission Modeling Study
Arifin SMN, Zimmer C, Trotter C, Colombini A, Sidikou F, LaForce FM, Cohen T, Yaesoubi R. Cost-Effectiveness of Alternative Uses of Polyvalent Meningococcal Vaccines in Niger: An Agent-Based Transmission Modeling Study. Medical Decision Making 2019, 39: 553-567. PMID: 31268405, PMCID: PMC6786941, DOI: 10.1177/0272989x19859899.Peer-Reviewed Original ResearchConceptsReactive campaignsSerogroup replacementConjugate vaccineOne-time catchPolyvalent meningococcal vaccineRoutine infant vaccinationMeningococcal conjugate vaccineMeningococcal polysaccharide vaccineRoutine infant immunizationCurrent vaccination practicesImportant health benefitsCost-effectiveness thresholdStandard cost-effectiveness thresholdsAgent-based transmission modelVaccination seriesImmunization seriesInfant vaccinationInfant immunizationPolysaccharide vaccineMeningococcal vaccineVaccination practicesPolyvalent vaccineLaboratory confirmationMenAfriVacSerogroups A
2018
Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models
Zimmer C, Leuba SI, Cohen T, Yaesoubi R. Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models. Statistical Methods In Medical Research 2018, 28: 3591-3608. PMID: 30428780, PMCID: PMC6517086, DOI: 10.1177/0962280218805780.Peer-Reviewed Original ResearchConceptsFilter degeneracyParameter estimatesPosterior distributionStochastic transmission-dynamic modelParameter posterior distributionsEpidemic compartmental modelKey epidemic parametersStochastic compartmental modelStochastic systemsPrediction intervalsCompartmental modelMultiple shootingArt calibration methodsEpidemic parametersDegeneracyDynamic modelInfluenza modelMSS approachLong-term predictionTransmission dynamic modelSimulation experimentsCalibration methodUncertaintyEstimatesCompetitive performanceUse of daily Internet search query data improves real-time projections of influenza epidemics
Zimmer C, Leuba SI, Yaesoubi R, Cohen T. Use of daily Internet search query data improves real-time projections of influenza epidemics. Journal Of The Royal Society Interface 2018, 15: 20180220. PMID: 30305417, PMCID: PMC6228485, DOI: 10.1098/rsif.2018.0220.Peer-Reviewed Original ResearchTuberculosis control interventions targeted to previously treated people in a high-incidence setting: a modelling study
Marx FM, Yaesoubi R, Menzies NA, Salomon JA, Bilinski A, Beyers N, Cohen T. Tuberculosis control interventions targeted to previously treated people in a high-incidence setting: a modelling study. The Lancet Global Health 2018, 6: e426-e435. PMID: 29472018, PMCID: PMC5849574, DOI: 10.1016/s2214-109x(18)30022-6.Peer-Reviewed Original ResearchConceptsHigh-incidence settingsIsoniazid preventive therapyPreventive therapyTuberculosis treatmentActive casesHIV prevalenceTuberculosis controlControl interventionsIncident tuberculosis casesPrevious tuberculosis treatmentTuberculosis control interventionsTB case notificationHigh-risk groupTransmission dynamic modelTuberculosis deathsHigh tuberculosisRecurrent diseasePrevalent tuberculosisTuberculosis casesTuberculosis incidenceCase notificationTreatment outcomesTuberculosis morbidityTuberculosis epidemicAdditional interventionsRisk ratios for contagious outcomes
Morozova O, Cohen T, Crawford FW. Risk ratios for contagious outcomes. Journal Of The Royal Society Interface 2018, 15: 20170696. PMID: 29343627, PMCID: PMC5805970, DOI: 10.1098/rsif.2017.0696.Peer-Reviewed Original Research
2017
A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
Zimmer C, Yaesoubi R, Cohen T. A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLOS Computational Biology 2017, 13: e1005257. PMID: 28095403, PMCID: PMC5240920, DOI: 10.1371/journal.pcbi.1005257.Peer-Reviewed Original ResearchConceptsParameter estimationStochastic modelLinear noise approximationStochastic transmission-dynamic modelEnsemble Kalman filter methodReal-time parameter estimationKey epidemic parametersParticle filtering methodInfectious individualsStochastic systemsCompartmental epidemic modelLikelihood approximationMultiple shootingNoise approximationBenchmark methodsEpidemic modelPoisson observationsKalman filter methodUnobserved numberAccurate estimatesEpidemic parametersLikelihood approachFiltering methodDynamic modelApproximationPriority-Setting for Novel Drug Regimens to Treat Tuberculosis: An Epidemiologic Model
Kendall EA, Shrestha S, Cohen T, Nuermberger E, Dooley KE, Gonzalez-Angulo L, Churchyard GJ, Nahid P, Rich ML, Bansbach C, Forissier T, Lienhardt C, Dowdy DW. Priority-Setting for Novel Drug Regimens to Treat Tuberculosis: An Epidemiologic Model. PLOS Medicine 2017, 14: e1002202. PMID: 28045934, PMCID: PMC5207633, DOI: 10.1371/journal.pmed.1002202.Peer-Reviewed Original ResearchConceptsEase of adherenceTB mortalityTB incidenceNovel drug regimensTB regimenNovel regimenDrug regimensRegimen characteristicsTreatment durationTreatment efficacyRR-TB treatmentTB treatment efficacyRifampicin-resistant TBTB treatment durationDynamic transmission modelTB regimensNew regimensRR-TBTB treatmentMedical contraindicationsPatients' qualitySafety profileBaseline prevalenceTB epidemicTuberculosis treatment
2016
Connectivity of diagnostic technologies: improving surveillance and accelerating tuberculosis elimination
Andre E, Isaacs C, Affolabi D, Alagna R, Brockmann D, de Jong BC, Cambau E, Churchyard G, Cohen T, Delmee M, Delvenne JC, Farhat M, Habib A, Holme P, Keshavjee S, Khan A, Lightfoot P, Moore D, Moreno Y, Mundade Y, Pai M, Patel S, Nyaruhirira AU, Rocha LE, Takle J, Trébucq A, Creswell J, Boehme C. Connectivity of diagnostic technologies: improving surveillance and accelerating tuberculosis elimination. The International Journal Of Tuberculosis And Lung Disease 2016, 20: 999-1003. PMID: 27393530, PMCID: PMC4937753, DOI: 10.5588/ijtld.16.0015.Peer-Reviewed Original ResearchIdentifying cost‐effective dynamic policies to control epidemics
Yaesoubi R, Cohen T. Identifying cost‐effective dynamic policies to control epidemics. Statistics In Medicine 2016, 35: 5189-5209. PMID: 27449759, PMCID: PMC5096998, DOI: 10.1002/sim.7047.Peer-Reviewed Original ResearchConceptsNet health benefitHighest net health benefitHealth benefitsTransmission-reducing interventionsDynamic policiesNovel viral pathogensCurrent interventionsHealth policyMathematical decision modelViral pathogensMonetary outcomesPolicy makersInterventionPolicyDecision modelStatic policyEpidemicEpidemic dataVaccinationVaccinePerformance measures
2014
How can mathematical models advance tuberculosis control in high HIV prevalence settings?
Houben RM, Dowdy DW, Vassall A, Cohen T, Nicol MP, Granich RM, Shea JE, Eckhoff P, Dye C, Kimerling ME, White RG, . How can mathematical models advance tuberculosis control in high HIV prevalence settings? The International Journal Of Tuberculosis And Lung Disease 2014, 18: 509-514. PMID: 24903784, PMCID: PMC4436821, DOI: 10.5588/ijtld.13.0773.Peer-Reviewed Original ResearchConceptsHigh HIV prevalence settingsHIV prevalence settingsTB-HIVTuberculosis controlPrevalence settingsHigh human immunodeficiency virus (HIV) prevalenceHuman immunodeficiency virus (HIV) prevalenceTB ModellingHealth policy makersDifficult diagnosisDisease progressionHigh riskHigh mortalityHealth systemNatural progressionVirus prevalencePublic healthProgressionMortalityPrevalenceSettingAnalysis ConsortiumDiagnosisExpert discussion
2013
Identifying dynamic tuberculosis case-finding policies for HIV/TB coepidemics
Yaesoubi R, Cohen T. Identifying dynamic tuberculosis case-finding policies for HIV/TB coepidemics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 9457-9462. PMID: 23690585, PMCID: PMC3677479, DOI: 10.1073/pnas.1218770110.Peer-Reviewed Original ResearchConceptsUndiagnosed casesHigh-burden settingsSmear-negative casesTB control programsDuration of roundsBurden settingsTB suspectsTB transmissionAggressive approachOnward transmissionIncremental yieldPopulation healthIncremental benefitInfectious individualsDiagnostic toolControl programsICFPassive caseSymptomsCasesSettingDiagnosis