2025
Unraveling the role of viral interference in disrupting biennial RSV epidemics in northern Stockholm
Li K, Hamrin J, Nilsson A, Weinberger D, Pitzer V. Unraveling the role of viral interference in disrupting biennial RSV epidemics in northern Stockholm. Nature Communications 2025, 16: 8137. PMID: 40885786, PMCID: PMC12398580, DOI: 10.1038/s41467-025-63654-1.Peer-Reviewed Original ResearchConceptsRespiratory syncytial virusRespiratory syncytial virus activityViral interferenceH1N1 pandemic influenza virusPandemic H1N1 virusPandemic influenza virusNorthern StockholmBiennial patternH1N1 virusInfluenza virusIn vivo studiesRespiratory virusesSyncytial virusInfluenza pandemicRSV epidemicsBirth rateInfluenzaPublic health interventionsWinter outbreaksVirusAdmission dataH1N1InfantsOlder adultsHealth interventionsHow well do disease-specific studies and WHO-CHOICE cost estimates align? Example of estimating cost per episode of diarrhoea and respiratory syncytial virus in 128 low-income and middle-income countries
Li X, Bilcke J, Asare E, Wenger C, Kwon J, Bont L, Beutels P, Pitzer V. How well do disease-specific studies and WHO-CHOICE cost estimates align? Example of estimating cost per episode of diarrhoea and respiratory syncytial virus in 128 low-income and middle-income countries. BMJ Global Health 2025, 10: e016784. PMID: 40850784, PMCID: PMC12382583, DOI: 10.1136/bmjgh-2024-016784.Peer-Reviewed Original ResearchConceptsRespiratory syncytial virusRSV-related diseaseWHO-CHOICE estimatesEpisodes of diarrheaLower middle-incomeWHO-CHOICELow-incomeUpper middle-incomeSyncytial virusRSV studiesInpatient costsMiddle-incomeDiarrhoeal diseaseEconomic evaluationCost studiesMiddle-income countriesDisease-specific diagnosisRSV-specificDisease-specific costsCost-effectiveness studiesDisease-specific studiesOutpatient costsEmpirical studiesDiarrheaCountry-specific dataInterplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model
Ashton P, Mageiros L, Meiring J, Chunga-Chirambo A, Khanam F, Dongol S, Banda H, Karkey A, Preciado-Llanes L, Thomaides-Brears H, Gibani M, Rajib N, Rahman N, Biswas P, Bhuiyan M, Kay S, Auger K, Seret O, Thomson N, Pollard A, Baker S, Basnyat B, Clemens J, Dolecek C, Dunstan S, Dougan G, Heyderman R, Pitzer V, Qadri F, Gordon M, Holt K, Darton T. Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model. Microbiome 2025, 13: 168. PMID: 40696437, PMCID: PMC12281769, DOI: 10.1186/s40168-025-02125-7.Peer-Reviewed Original ResearchConceptsMetabolic gene clustersShort-chain fatty acidsTyphoid fever patientsS. typhiGut microbiomeTyphoid feverShort-chain fatty acid metabolismInfection modelAsymptomatic household contactsHuman infection modelPotential functional roleGene clusterShotgun metagenomicsInvasive SalmonellaFever patientsBacterial diversityMicrobiota characteristicsAssociated with typhoid feverBackgroundTyphoid feverStool microbiomeBacterial speciesClade ADevelopment of clinical infectionSCFA metabolismIngestion of contaminated foodIntegrated 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 dataInfectionExploring RSV Transmission Patterns in Different Age Groups in the United States
Li K, Pitzer V, Weinberger D. Exploring RSV Transmission Patterns in Different Age Groups in the United States. The Journal Of Infectious Diseases 2025, 232: 700-708. PMID: 40308004, PMCID: PMC12455310, DOI: 10.1093/infdis/jiaf230.Peer-Reviewed Original ResearchThe Role of Viral Interference in Shaping RSV Epidemics Following the 2009 H1N1 Influenza Pandemic
Li K, Thindwa D, Weinberger D, Pitzer V. The Role of Viral Interference in Shaping RSV Epidemics Following the 2009 H1N1 Influenza Pandemic. Influenza And Other Respiratory Viruses 2025, 19: e70111. PMID: 40275825, PMCID: PMC12022500, DOI: 10.1111/irv.70111.Peer-Reviewed Original ResearchConceptsRespiratory syncytial virusRespiratory syncytial virus activityRespiratory syncytial virus epidemicsInfluenza pandemicViral interferenceLaboratory-confirmed RSV casesRSV epidemicsDecreased RSV infectionH1N1 influenza pandemicRSV infectionRSV seasonRSV casesSyncytial virusPandemic influenzaInfluenzaRSV activityCo-InfectionSurveillance dataEpidemicUnited StatesUS regionsH1N1The validity of test-negative design for assessment of typhoid conjugate vaccine protection: comparison of estimates by different study designs using data from a cluster-randomised controlled trial
Feng S, Zhang Y, Khanam F, Voysey M, Pitzer V, Qadri F, Clemens J, Pollard A, Liu X. The validity of test-negative design for assessment of typhoid conjugate vaccine protection: comparison of estimates by different study designs using data from a cluster-randomised controlled trial. The Lancet Global Health 2025, 13: e1122-e1131. PMID: 40252689, PMCID: PMC12095117, DOI: 10.1016/s2214-109x(25)00056-7.Peer-Reviewed Original ResearchConceptsTyphoid Conjugate VaccineCluster randomised controlled trialJapanese encephalitis vaccineAge-eligible childrenCohort designTest-negative controlsStudy designTyphoid feverVaccine effectivenessHealth care seeking behaviorNon-vaccineesIncreased riskBlood culture-confirmed typhoid feverSalmonella enterica serotype TyphiCase-control study designNon-typhoidal infectionsVaccine protectionBlood culture specimensExperimental study designMiddle-income countriesObservational study designPublic health challengeChildren aged 9 monthsIncreased risk of typhoid feverRisk of typhoid feverCost-effectiveness analysis of alternative infant and neonatal rotavirus vaccination schedules in Malawi
Wenger C, Asare E, Kwon J, Li X, Mwinjiwa E, Chinkhumba J, Jere K, Hungerford D, Cunliffe N, Paltiel A, Pitzer V. Cost-effectiveness analysis of alternative infant and neonatal rotavirus vaccination schedules in Malawi. PLOS Global Public Health 2025, 5: e0004341. PMID: 40209158, PMCID: PMC11984971, DOI: 10.1371/journal.pgph.0004341.Peer-Reviewed Original ResearchDose of RotarixNeonatal vaccinationThird doseDisability-adjusted life yearsRotavirus vaccination strategiesVaccination strategiesVaccination scheduleRV3-BB vaccineRotavirus vaccine scheduleModerate-to-severeCurrent rotavirus vaccinesProbabilistic sensitivity analysesRV3-BBPrevent rotavirusRotavirus casesRotavirus vaccineWTP thresholdAlternate infantsVaccine impactSevere diarrheaWeeks of ageRotarixVaccine effectivenessCost-effectiveness analysisCost-effectiveRelating In Vivo Respiratory Syncytial Virus Infection Kinetics to Host Infectiousness in Different Age Groups
Li K, Bont L, Weinberger D, Pitzer V. Relating In Vivo Respiratory Syncytial Virus Infection Kinetics to Host Infectiousness in Different Age Groups. The Journal Of Infectious Diseases 2025, 232: 691-699. PMID: 40085821, DOI: 10.1093/infdis/jiaf138.Peer-Reviewed Original ResearchRespiratory syncytial virusViral kineticsAge groupsHigher peak viral loadRespiratory syncytial virus infectionPeak viral loadRespiratory syncytial virus transmissionHousehold transmission studyAge-specific considerationsViral loadSyncytial virusPediatric populationViral infectionPublic health concernSecondary attack rateProcess of viral infectionGlobal estimates of rotavirus vaccine efficacy and effectiveness: a rapid review and meta-regression analysis
Prunas O, Asare E, Sajewski E, Li Y, Pithawala Z, Weinberger D, Warren J, Armah G, Cunliffe N, Iturriza-Gómara M, Lopman B, Pitzer V. Global estimates of rotavirus vaccine efficacy and effectiveness: a rapid review and meta-regression analysis. EClinicalMedicine 2025, 81: 103122. PMID: 40115174, PMCID: PMC11925534, DOI: 10.1016/j.eclinm.2025.103122.Peer-Reviewed Original ResearchRotavirus-associated gastroenteritisRotavirus vaccine efficacyPredicting vaccine efficacyVaccine efficacyVaccine effectivenessVaccine performanceNational rotavirus immunization programImpact of rotavirus vaccinationRotavirus immunization programAffecting young childrenBill &Meta-regression analysisRandomized Controlled TrialsSystematic review of studiesEstimates of vaccine effectivenessRotavirus morbidityMelinda Gates FoundationRotavirus vaccineCohort studyLicensed vaccinesVaccine trialsDecreased efficacyControlled TrialsCase-controlLow-income settingsEstimated Effectiveness of Nirsevimab Against Respiratory Syncytial Virus
Xu H, Aparicio C, Wats A, Araujo B, Pitzer V, Warren J, Shapiro E, Niccolai L, Weinberger D, Oliveira C. Estimated Effectiveness of Nirsevimab Against Respiratory Syncytial Virus. JAMA Network Open 2025, 8: e250380. PMID: 40063022, PMCID: PMC11894488, DOI: 10.1001/jamanetworkopen.2025.0380.Peer-Reviewed Original ResearchConceptsRSV-positive casesCase-control studyRSV infectionLRTI-associated hospitalizationsWeeks postimmunizationLong-acting monoclonal antibodiesTest-negative case-control studyClinical settingRespiratory syncytial virusMultivariate logistic regressionYale New Haven Health SystemRSV diseaseEmergency department dataState immunization registryRSV seasonSyncytial virusNirsevimabPolymerase chain reactionClinical trialsLRTIInfantsPotential confoundersMonoclonal antibodiesBroader outcomesDisease severityTime series data on typhoid fever incidence during outbreaks from 2000 to 2022
Koh D, Duong M, Kipshidze N, Pitzer V, Kim J. Time series data on typhoid fever incidence during outbreaks from 2000 to 2022. Scientific Data 2025, 12: 94. PMID: 39821093, PMCID: PMC11739417, DOI: 10.1038/s41597-024-04289-7.Peer-Reviewed Original Research
2024
Impact of dosing schedules on performance of rotavirus vaccines in Ghana
Asare E, Al-Mamun M, Armah G, Lopman B, Pitzer V. Impact of dosing schedules on performance of rotavirus vaccines in Ghana. Science Advances 2024, 10: eadn4176. PMID: 39661683, PMCID: PMC11633732, DOI: 10.1126/sciadv.adn4176.Peer-Reviewed Original ResearchConceptsVaccine dosing schedulesDosing scheduleDoses of RV1Median percentage reductionImprove vaccine performanceRotavirus vaccine impactThird doseRotavirus vaccineRotarix vaccineVaccine impactAdditional doseVaccine effectivenessVaccine performanceVaccineRotavirusRV1Percentage reductionChildrenRotarixImpact of rotavirus vaccination in Malawi from 2012 to 2022 compared to model predictions
Pitzer V, Ndeketa L, Asare E, Hungerford D, Lopman B, Jere K, Cunliffe N. Impact of rotavirus vaccination in Malawi from 2012 to 2022 compared to model predictions. Npj Vaccines 2024, 9: 227. PMID: 39562592, PMCID: PMC11576906, DOI: 10.1038/s41541-024-01008-6.Peer-Reviewed Original ResearchRotavirus-associated gastroenteritisRotavirus-negative childrenRotavirus-negative controlsImpact of rotavirus vaccinationVaccination coverageRotavirus vaccine impactAcute gastroenteritis casesNational immunization programPre-vaccination dataVaccine introductionRotavirus vaccineVaccine impactAcute gastroenteritisVaccine effectivenessGastroenteritis casesLow-income settingsImmunization programsVaccineModelling vaccination approaches for mpox containment and mitigation in the Democratic Republic of the Congo
Savinkina A, Kindrachuk J, Bogoch I, Rimoin A, Hoff N, Shaw S, Pitzer V, Mbala-Kingebeni P, Gonsalves G. Modelling vaccination approaches for mpox containment and mitigation in the Democratic Republic of the Congo. The Lancet Global Health 2024, 12: e1936-e1944. PMID: 39393385, DOI: 10.1016/s2214-109x(24)00384-x.Peer-Reviewed Original Research5-year vaccine protection following a single dose of Vi-tetanus toxoid conjugate vaccine in Bangladeshi children (TyVOID): a cluster randomised trial
Qadri F, Khanam F, Zhang Y, Biswas P, Voysey M, Mujadidi Y, Kelly S, Bhuiyan A, Rajib N, Hossen I, Rahman N, Islam S, Pitzer V, Kim Y, Clemens J, Pollard A, Liu X. 5-year vaccine protection following a single dose of Vi-tetanus toxoid conjugate vaccine in Bangladeshi children (TyVOID): a cluster randomised trial. The Lancet 2024, 404: 1419-1429. PMID: 39396349, DOI: 10.1016/s0140-6736(24)01494-6.Peer-Reviewed Original ResearchConceptsTyphoid Conjugate VaccineJapanese encephalitis vaccineVaccine effectivenessRandomised controlled trialsConjugate vaccineFollow-upTyphoid feverControlled TrialsVaccine protectionChildren aged 9 monthsIncreased risk of typhoid feverAnti-Vi IgGRisk of typhoid feverVaccine efficacy dataTest-negative designAged 9 monthsUnvaccinated individualsHigh-burden countriesIncidence rate ratiosAnalyses of vaccine effectivenessSingle-doseSingle doseDecay of antibodiesSubgroup analysisBooster doseCelebrating a body of work
Papin J, Mac Gabhann F, Pitzer V. Celebrating a body of work. PLOS Computational Biology 2024, 20: e1012441. PMID: 39325699, PMCID: PMC11426496, DOI: 10.1371/journal.pcbi.1012441.Peer-Reviewed Original ResearchGenome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections
Li K, Chaguza C, Stamp J, Chew Y, Chen N, Ferguson D, Pandya S, Kerantzas N, Schulz W, Initiative Y, Hahn A, Ogbunugafor C, Pitzer V, Crawford L, Weinberger D, Grubaugh N. Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology 2024, 20: e1012469. PMID: 39288189, PMCID: PMC11432881, DOI: 10.1371/journal.pcbi.1012469.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle-nucleotide polymorphismsAssociation studiesWhole-genome sequencingAmino acid changesSingle nucleotide polymorphismsPairs of substitutionsViral copiesEpistasis testsGenome sequenceGenetic variationSpike geneAcid changesViral genomeNucleotide polymorphismsSARS-CoV-2Detect interactionsHost factorsVirus copiesCopyInfection dynamicsRT-qPCRPolymorphismOmicron BASARS-CoV-2 infectionA low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva
Peno C, Lin T, Hislop M, Yolda-Carr D, Farjado K, York A, Pitzer V, Weinberger D, Bei A, Allicock O, Wyllie A. A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva. Microbiology Spectrum 2024, 12: e00591-24. PMID: 39028185, PMCID: PMC11370248, DOI: 10.1128/spectrum.00591-24.Peer-Reviewed Original ResearchDetection of pneumococciDetection of pneumococcal carriagePneumococcal carriageCarriage surveillanceLow-resource settingsChildren attending childcare centersCarriage of pneumococciDNA extractionSaliva samplesMolecular methodsCultural enrichmentImprove surveillance effortsQPCR-based protocolPneumococcal vaccineExtraction-free methodMolecular detectionNucleic acid extractionVaccination strategiesPneumococciCulture-enrichment methodExtraction-free protocolPurified DNASalivaPaired samplesCarriagePathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study
Dyson Z, Ashton P, Khanam F, Chirambo A, Shakya M, Meiring J, Tonks S, Karkey A, Msefula C, Clemens J, Dunstan S, Baker S, Dougan G, Pitzer V, Basnyat, Qadri F, Heyderman R, Gordon M, Pollard A, Holt K, Group S, Banda H, Biswas P, Bhuiyan A, Blohmke C, Darton T, Dolecek C, Dongol S, Mujadidi Y, Hill J, Hoang N, Jere T, Mbewe M, Msuku H, Nga T, Nkhata R, Rahman S, Rahman N, Saad N, Tan T, Thindwa D, Voysey M, Wachepa R. Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. The Lancet Microbe 2024, 5: 100841. PMID: 38996496, PMCID: PMC11300424, DOI: 10.1016/s2666-5247(24)00047-8.Peer-Reviewed Original ResearchParatyphi ASerovars TyphiPathogenic variantsAntimicrobial resistanceSalmonella enterica serovar TyphiEnteric feverAncestral state reconstructionS paratyphi ADeterminants of antimicrobial resistanceSingle-nucleotide variantsAntimicrobial resistance determinantsQuinolone-resistance mutationsAntimicrobial resistance transmissionCore genomePhylogenomic analysisAzithromycin resistance mutationsPhylogenetic analysisGenomic dataPopulation structurePathogen diversityS typhiTransmission of resistant strainsGenomic epidemiologyAntimicrobial resistant infectionsAge groups
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