Featured Publications
Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2
Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. New England Journal Of Medicine 2020, 383: 1283-1286. PMID: 32857487, PMCID: PMC7484747, DOI: 10.1056/nejmc2016359.Peer-Reviewed Original ResearchMeasurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics
Peccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M, Warren JL, Weinberger DM, Arnold W, Omer SB. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nature Biotechnology 2020, 38: 1164-1167. PMID: 32948856, PMCID: PMC8325066, DOI: 10.1038/s41587-020-0684-z.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 positive test resultsSARS-CoV-2 RNAPositive test resultsHospital admissionSpecimen collectionCOVID-19 hospital admissionsLocal hospital admissionsSARS-CoV-2 RNA concentrationsCoronavirus disease 2019 (COVID-19) outbreakRNA concentrationDisease 2019 outbreakClinical test resultsInfection surveillanceInfection dynamicsPositive testPopulation-wide levelCommunity infection dynamicsAdmissionNew HavenAssessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United States
Paltiel AD, Zheng A, Walensky RP. Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United States. JAMA Network Open 2020, 3: e2016818. PMID: 32735339, PMCID: PMC7395236, DOI: 10.1001/jamanetworkopen.2020.16818.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionSymptom-based screeningTrue-positive resultsCost-effectiveness analysisHypothetical cohortCumulative infectionsAsymptomatic SARS-CoV-2 infectionSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Safe returnCoronavirus disease 2019 (COVID-19) pandemicSyndrome coronavirus 2Case fatality riskCOVID-19 infectionDisease 2019 pandemicResidential college campusCoronavirus 2Additional infectionsMAIN OUTCOMEBudget impactInfectionBehavioral interventionsCohortFall 2020 semesterEstimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020
Weinberger DM, Chen J, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C. Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020. JAMA Internal Medicine 2020, 180: 1336-1344. PMID: 32609310, PMCID: PMC7330834, DOI: 10.1001/jamainternmed.2020.3391.Peer-Reviewed Original ResearchConceptsCOVID-19Excess deathsOfficial COVID-19 deathsCoronavirus disease 2019Entire US populationPublic health impactCOVID-19 diagnostic testsCOVID-19 burdenCOVID-19 deathsCause deathReported deathsMortality burdenObservational studyDisease 2019Influenza activityMAIN OUTCOMEDeath AssociatedWeekly deathsTotal deathsUS deathsMore deathsDeath recordsUS populationHealth StatisticsTest availabilityCoast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell 2020, 181: 990-996.e5. PMID: 32386545, PMCID: PMC7204677, DOI: 10.1016/j.cell.2020.04.021.Peer-Reviewed Original ResearchConceptsSARS-CoV-2Federal travel restrictionsSARS-CoV-2 transmissionCOVID-19 patientsCoronavirus SARS-CoV-2SARS-CoV-2 introductionsEarly SARS-CoV-2 transmissionPattern of spreadSustained transmissionLocal surveillanceEarly epidemicInternational importationCOVID-19 outbreakUnited StatesViral genomeInternational travel patternsPatientsCritical needTravel restrictions
2025
Moving Forward From the COVID-19 Pandemic
Steinberg D, Molenberghs G, Bathke A, Brinks R, Huppert A, Maggino F, Mukherjee B. Moving Forward From the COVID-19 Pandemic. The American Statistician 2025, 1-8. DOI: 10.1080/00031305.2025.2562891.Peer-Reviewed Original ResearchChanges in pneumococcal deaths in the United States following the COVID-19 pandemic
Shang L, Perniciaro S, Weinberger D. Changes in pneumococcal deaths in the United States following the COVID-19 pandemic. International Journal Of Infectious Diseases 2025, 108020. PMID: 40886796, DOI: 10.1016/j.ijid.2025.108020.Peer-Reviewed Original ResearchGlobal Prevalence of Long COVID, Its Subtypes, and Risk Factors: An Updated Systematic Review and Meta-analysis
Hou Y, Gu T, Ni Z, Shi X, Ranney M, Mukherjee B. Global Prevalence of Long COVID, Its Subtypes, and Risk Factors: An Updated Systematic Review and Meta-analysis. Open Forum Infectious Diseases 2025, 12: ofaf533. PMID: 41018705, PMCID: PMC12461872, DOI: 10.1093/ofid/ofaf533.Peer-Reviewed Original ResearchPrevalence of long COVIDGlobal prevalenceRisk factorsLong COVIDWell-designed follow-up studiesRisk of bias analysisEffects of risk factorsYears of follow-upUpdate systematic reviewsWeb of ScienceHigh prevalence rateHeterogeneity of estimatesAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 infectionHealth challengesSystematic reviewPrevalence ratesDerSimonian-Laird estimatorCoronavirus 2 infectionFollow-up studyBias analysisFemale sexMeta-analysisGeneral fatiguePre-Omicron variantsQuantifying disruptions to tuberculosis case detection in Brazilian states during the COVID-19 pandemic
Chitwood M, Menzies N, Bartholomay P, Pelissari D, de Barros Silva Júnior J, Harada L, Johansen F, Maciel E, Castro M, Sanchez M, Warren J, Cohen T. Quantifying disruptions to tuberculosis case detection in Brazilian states during the COVID-19 pandemic. International Journal Of Epidemiology 2025, 54: dyaf146. PMID: 40838691, DOI: 10.1093/ije/dyaf146.Peer-Reviewed Original ResearchConceptsPre-pandemic levelsTB casesCase detectionCOVID-19 pandemicBrazilian healthcare systemTB notification ratesTB case detectionHealth system disruptionsTuberculosis case detectionCase detection rateMortality dataHealthcare systemIncident TBMeta-regression frameworkTB incidenceNotification ratesSymptomatic TBCase notificationCOVID-19TB controlTB diagnosisBrazilian statesPandemicCareIndividualsThe role of financial stress, food insecurity, and COVID-19-related illness concerns shaping mental health in five South Asian countries during the pandemic (2020–2022): A secondary analysis of the online COVID-19 Trends and Impact Survey (CTIS) data
Yang Y, Zimmermann L, Pramanik S, Wahl B, Mukherjee B. The role of financial stress, food insecurity, and COVID-19-related illness concerns shaping mental health in five South Asian countries during the pandemic (2020–2022): A secondary analysis of the online COVID-19 Trends and Impact Survey (CTIS) data. PLOS Global Public Health 2025, 5: e0004704. PMID: 40779535, PMCID: PMC12334018, DOI: 10.1371/journal.pgph.0004704.Peer-Reviewed Original ResearchFood insecurityOdds ratioIllness concernsMental healthSurvey-weighted logistic regression modelsImpact SurveyCalendar timeFinancial stressMental health worldwidePandemic-related worriesRandom-effects meta-analysisMental health resilienceMiddle-income countriesAssociated with depressionLevels of depressionLogistic regression modelsSocioeconomic stressorsAsian LMICsSecondary analysisHealth resiliencePost-changeLMICsCountry-specific analysisResidential statusSurvey designAssociation of COVID-19 outcomes with measures of institutional and interpersonal trust: an ecological analysis using national data from 61 countries
Rountree L, Tong G, Bu F, Ranney M, Mukherjee B. Association of COVID-19 outcomes with measures of institutional and interpersonal trust: an ecological analysis using national data from 61 countries. Scientific Reports 2025, 15: 26393. PMID: 40691221, PMCID: PMC12280113, DOI: 10.1038/s41598-025-09758-6.Peer-Reviewed Original ResearchIntegrated 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 dataInfectionType 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort
Jayavelu N, Qi J, Milliren C, Ozonoff A, Liu S, Levy O, Baden L, Melamed E, McComsey G, Cairns C, Schaenman J, Shaw A, Hafler D, Corry D, Kheradmand F, Atkinson M, Brakenridge S, Higuita N, Metcalf J, Hough C, Messer W, Pulendran B, Nadeau K, Davis M, Geng L, Sesma A, Simon V, Krammer F, Bime C, Calfee C, Bosinger S, Eckalbar W, Steen H, Maecker H, Becker P, Augustine A, Holland S, Rosen L, Lee S, Vaysman T, Ozonoff A, Diray-Arce J, Chen J, Kho A, Milliren C, Hoch A, Chang A, McEnaney K, Barton B, Lentucci C, Murphy M, Saluvan M, Shaheen T, Liu S, Syphurs C, Albert M, Hayati A, Bryant R, Abraham J, Thomas S, Cooney M, Karoly M, Altman M, Jayavelu N, Presnell S, Kohr B, Jancsyk T, Arnett A, Peters B, Overton J, Vita R, Westendorf K, Overton J, Levy O, Steen H, van Zalm P, Fatou B, Smolen K, Viode A, van Haren S, Jha M, Stevenson D, Odumade O, Baden L, Mendez K, Lasky-Su J, Tong A, Rooks R, Desjardins M, Sherman A, Walsh S, Mitre X, Cauley J, Li X, Evans B, Montesano C, Licona J, Krauss J, Issa N, Chang J, Izaguirre N, Hutton S, Michelotti G, Wong K, Tebbutt S, Shannon C, Sekaly R, Fourati S, McComsey G, Harris P, Sieg S, Ribeiro S, Cairns C, Haddad E, Kutzler M, Bernui M, Cusimano G, Connors J, Woloszczuk K, Joyner D, Edwards C, Lee E, Lin E, Melnyk N, Powell D, Kim J, Goonewardene I, Simmons B, Smith C, Martens M, Croen B, Semenza N, Bell M, Furukawa S, McLin R, Tegos G, Rogowski B, Mege N, Ulring K, Schearer P, Sheidy J, Nagle C, Seyfert-Margolis V, Rouphael N, Bosinger S, Boddapati A, Tharp G, Pellegrini K, Johnson B, Panganiban B, Huerta C, Anderson E, Samaha H, Sevransky J, Bristow L, Beagle E, Cowan D, Hamilton S, Hodder T, Bechnak A, Cheng A, Mehta A, Ciric C, Spainhour C, Carter E, Scherer E, Usher J, Hellmeister K, Hussaini L, Hewitt L, Mcnair N, Ribeiro S, Wimalasena S, Fernandez-Sesma A, Simon V, Krammer F, Van Bakel H, Kim-Schulze S, Reiche A, Qi J, Lee B, Carreño J, Singh G, Raskin A, Tcheou J, Khalil Z, van de Guchte A, Farrugia K, Khan Z, Kelly G, Srivastava K, Eaker L, Bermúdez-González M, Mulder L, Beach K, Saksena M, Altman D, Kojic E, Sominsky L, Azad A, Bielak D, Kawabata H, Yellin T, Fried M, Sullivan L, Morris S, Kleiner G, Stadlbauer D, Dutta J, Xie H, Patel M, Nie K, Rahman A, Messer W, Hough C, Siegel S, Sullivan P, Lu Z, Brunton A, Strand M, Lyski Z, Coulter F, Micheleti C, Maecker H, Pulendran B, Nadeau K, Rosenberg-Hasson Y, Leipold M, Sigal N, Rogers A, Fernandes A, Manohar M, Do E, Chang I, Lee A, Blish C, Din H, Roque J, Geng L, Artandi M, Davis M, Ahuja N, Yang S, Chinthrajah S, Hagan T, Reed E, Schaenman J, Salehi-Rad R, Rivera A, Pickering H, Sen S, Elashoff D, Ward D, Brook J, Sanchez E, Llamas M, Perdomo C, Magyar C, Fulcher J, Erle D, Calfee C, Hendrickson C, Kangelaris K, Nguyen V, Lee D, Chak S, Ghale R, Gonzalez A, Jauregui A, Leroux C, Altamirano L, Rashid A, Willmore A, Woodruff P, Krummel M, Carrillo S, Ward A, Langelier C, Patel R, Wilson M, Dandekar R, Alvarenga B, Rajan J, Eckalbar W, Schroeder A, Fragiadakis G, Tsitsiklis A, Mick E, Guerrero Y, Love C, Maliskova L, Adkisson M, Leligdowicz A, Beagle A, Rao A, Sigman A, Samad B, Curiel C, Shaw C, Tietje-Ulrich G, Milush J, Singer J, Vasquez J, Tang K, Betancourt L, Santhosh L, Pierce L, Paz M, Matthay M, Thakur N, Rodriguez N, Sutter N, Jones N, Sinha P, Prasad P, Lota R, Rashid S, Asthana S, Bhide S, Lea T, Abe-Jones Y, Hafler D, Montgomery R, Shaw A, Kleinstein S, Gygi J, Pawar S, Konstorum A, Chen E, Cotsapas C, Wang X, Xu L, Dela Cruz C, Iwasaki A, Mohanty S, Nelson A, Zhao Y, Farhadian S, Asashima H, Chaudhary O, Coppi A, Fournier J, Muenker M, Nelson A, Raddassi K, Rainone M, Ruff W, Salahuddin S, Shulz W, Vijayakumar P, Wang H, Wunder E, Young H, Ko A, Wang X, Duchen D, Esserman D, Guan L, Brito A, Rothman J, Grubaugh N, Corry D, Kheradmand F, Song L, Nelson E, Metcalf J, Higuita N, Sinko L, Booth J, Drevets D, Brown B, Kraft M, Bime C, Mosier J, Erickson H, Schunk R, Kimura H, Conway M, Francisco D, Molzahn A, Wilson C, Schunk R, Hughes T, Sierra B, Atkinson M, Brakenridge S, Ungaro R, Manning B, Moldawer L, Oberhaus J, Guirgis F, Borresen B, Anderson M, Ehrlich L, Melamed E, Maguire C, Wylie D, Rousseau J, Hurley K, Geltman J, Siles N, Rogers J, Augustine A, Diray-Arce J, Haddad E, Sekaly R, Kraft M, Woodruff P, Erle D, Ehrlich L, Montgomery R, Becker P, Altman M, Fourati S. Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort. Journal Of Allergy And Clinical Immunology Global 2025, 4: 100515. PMID: 40709330, PMCID: PMC12284355, DOI: 10.1016/j.jacig.2025.100515.Peer-Reviewed Original ResearchT2 immune responseClinical outcomesVirus loadImmune responseSARS-CoV-2Primary siteSusceptibility to respiratory viral infectionsType 2 immune responsesAntibody titersCellular markersPrimary site of infectionSeverity of respiratory illnessRespiratory viral infectionsIL-13 levelsDegree of respiratory supportAssociated with less severe COVID-19Site of infectionLow virus loadSevere COVID-19Effects of SARS-CoV-2Severe coronavirus diseaseDiagnosis of asthmaRespiratory supportCoronavirus severe acute respiratory syndrome coronavirus 2Blood cytometryEvaluating the association between routine pneumococcal vaccination and COVID-19 severity among older adults in the United States: A case control study
Prunas O, Tiu A, Shioda K, Bansal S, Weinberger D. Evaluating the association between routine pneumococcal vaccination and COVID-19 severity among older adults in the United States: A case control study. Vaccine X 2025, 24: 100622. DOI: 10.1016/j.jvacx.2025.100622.Peer-Reviewed Original ResearchCOVID-19 patientsCase-control studyIntensive care unitSevere respiratory symptomsPneumococcal vaccineSevere outcomesRespiratory symptomsOdds of progressionReceipt of pneumococcal vaccinationCOVID-19 severitySevere COVID-19 outcomesLogistic regression modelsSevere acute respiratory syndrome coronavirus 2Streptococcus pneumoniaeAcute respiratory syndrome coronavirus 2Non-severeRespiratory syndrome coronavirus 2Care unitControlled studiesPatientsSyndrome coronavirus 2COVID-19 outcomesSARS-CoV-2VaccineCoronavirus 2Early Release - Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States - Volume 31, Supplement—May 2025 - Emerging Infectious Diseases journal - CDC
Pham K, Chaguza C, Lopes R, Cohen T, Taylor-Salmon E, Wilkinson M, Katebi V, Grubaugh N, Hill V. Early Release - Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States - Volume 31, Supplement—May 2025 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2025, 31: s45-s56. PMID: 40359081, PMCID: PMC12078544, DOI: 10.3201/eid3113.240981.Peer-Reviewed Original ResearchChanges in incarceration and tuberculosis notifications from prisons during the COVID-19 pandemic in Europe and the Americas: a time-series analysis of national surveillance data
Zheng A, Faust L, Harries A, Avedillo P, Akodu M, Galvan M, Barreto-Duarte B, Andrade B, Ugarte-Gil C, Garcia-Basteiro A, Espinal M, Warren J, Martinez L. Changes in incarceration and tuberculosis notifications from prisons during the COVID-19 pandemic in Europe and the Americas: a time-series analysis of national surveillance data. The Lancet Public Health 2025, 10: e285-e294. PMID: 40175010, PMCID: PMC11962358, DOI: 10.1016/s2468-2667(24)00325-6.Peer-Reviewed Original ResearchConceptsPrison populationCOVID-19 pandemicPrisonIncarcerationTuberculosis notificationsPan American Health OrganizationNotificationCOVID-19WHO EuropeEuropePandemic yearCountriesAffected peoplePandemicTime series analysisAmericaWorld regionsAnalysis of national surveillance dataHealth OrganizationCOVID-19 pandemic yearPeopleReporting of Fairness Metrics in Clinical Risk Prediction Models Used for Precision Health: Scoping Review
Rountree L, Lin Y, Liu C, Salvatore M, Admon A, Nallamothu B, Singh K, Basu A, Bu F, Mukherjee B. Reporting of Fairness Metrics in Clinical Risk Prediction Models Used for Precision Health: Scoping Review. Online Journal Of Public Health Informatics 2025, 17: e66598. PMID: 39962044, PMCID: PMC11966066, DOI: 10.2196/66598.Peer-Reviewed Original ResearchClinical risk prediction modelsRisk prediction modelFairness metricsSex-stratified modelsEthnicity dataPrecision healthClinical risk predictionSensitive featuresStudy populationCardiovascular diseaseRisk predictionEvaluate potential disparitiesTraining dataPotential disparitiesEmpirical evaluationPrediction modelPrimary preventionInformatics systemsHigh-impact publicationsCOVID-19Metrics usageStudy cohortGoogle ScholarImplementation frameworkCOVID-19 modelEffect of Air Pollution Reductions on Mortality During the COVID-19 Lockdowns in Early 2020.
Chen K, Ma Y, Marb A, Nobile F, Dubrow R, Stafoggia M, Breitner S, Kinney P. Effect of Air Pollution Reductions on Mortality During the COVID-19 Lockdowns in Early 2020. Research Report 2025, 2025: 1-47. PMID: 40551404, PMCID: PMC12185919.Peer-Reviewed Original ResearchConceptsAir pollution changesAir pollutionPollution changesShort-term exposure to PM2.5Air qualityExposure to PM2.5Natural-causeMeteorological normalization techniqueFine particulate matterDaily air pollutionImprove air qualityAir pollutant emissionsAir pollution reductionEmission control strategiesSouthern ItalyQuantify changesAir pollution-mortality relationshipPollution-mortality relationshipCOVID-19 lockdownShort-term exposureNOParticulate matterMeteorological impactsNitrogen dioxidePollution reductionSocial mixing patterns of United States healthcare personnel at a quaternary health center: a prospective observational study
Pischel L, Aguolu O, Ahmed N, Campbell M, Borg R, Duckwall C, Willebrand K, Zaleski A, Paintsil E, Muenker M, Malik A, Kiti M, Warren J, Jenness S, Lopman B, Belsky J, Martinello R, Yildirim I, Ko A, Omer S. Social mixing patterns of United States healthcare personnel at a quaternary health center: a prospective observational study. Infection Control And Hospital Epidemiology 2025, 46: 289-297. PMID: 39880795, PMCID: PMC11883655, DOI: 10.1017/ice.2024.234.Peer-Reviewed Original ResearchHealthcare personnelUnited States healthcare systemStates healthcare systemCOVID-19 pandemicNurse aidesContact diariesHealth centersHealthcare systemWorking-age populationImaging technologistsLow-contact groupNursesRegression modelsPandemic responseWork environmentSocial contactCOVID-19Job typeThree-hundredWorking daysDiaryParticipantsPersonnelInfectious disease transmissionContact groupThe WHO Disease Outbreak News during the Covid-19 pandemic
Weets C, Carlson C, Robertson H, Toole K, McGivern L, Graeden E, Katz R. The WHO Disease Outbreak News during the Covid-19 pandemic. PLOS Global Public Health 2025, 5: e0004025. PMID: 39869635, PMCID: PMC11771871, DOI: 10.1371/journal.pgph.0004025.Peer-Reviewed Original Research
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