2024
Impact 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 infectionWorkshop on the design and use of clinical trials with multiple endpoints, with a focus on prevention of RSV
Prunas O, Willemsen J, Warren J, Bont L, Schwartz J, Atwell J, Begier E, Dean N, Hirsch I, Karron R, Klugman K, Kramer R, Leidman E, Link-Gelles R, Nair H, Panozzo C, Pelfrene E, Simões E, Smith P, Srikantiah P, Sundaram M, Thindwa D, Vaughn D, Wilson E, Zar H, Pitzer V, Weinberger D. Workshop on the design and use of clinical trials with multiple endpoints, with a focus on prevention of RSV. Vaccine X 2024, 19: 100509. DOI: 10.1016/j.jvacx.2024.100509.Peer-Reviewed Original ResearchRespiratory syncytial virusRandomized controlled trialsPreventive therapyPrevention of respiratory syncytial virusTrial designSuccess of randomized controlled trialsVaccine trial designDesign randomized controlled trialClinical trial designEstimates of vaccine efficacyPrimary endpointSyncytial virusClinical trialsVaccine efficacyControlled trialsMeta-regression modelsSelection of primary endpointsEndpointSequential trial designTherapyMultiple endpointsA 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 groupsGlobal patterns of rebound to normal RSV dynamics following COVID-19 suppression
Thindwa D, Li K, Cooper-Wootton D, Zheng Z, Pitzer V, Weinberger D. Global patterns of rebound to normal RSV dynamics following COVID-19 suppression. BMC Infectious Diseases 2024, 24: 635. PMID: 38918718, PMCID: PMC11201371, DOI: 10.1186/s12879-024-09509-4.Peer-Reviewed Original ResearchExpanded Programme on Immunization at 50 years: its legacy and future
Wahl B, Pitzer V. Expanded Programme on Immunization at 50 years: its legacy and future. The Lancet 2024, 403: 2265-2267. PMID: 38796196, DOI: 10.1016/s0140-6736(24)00982-6.Peer-Reviewed Original ResearchEstimating the health effects of COVID-19-related immunisation disruptions in 112 countries during 2020–30: a modelling study
Hartner A, Li X, Echeverria-Londono S, Roth J, Abbas K, Auzenbergs M, de Villiers M, Ferrari M, Fraser K, Fu H, Hallett T, Hinsley W, Jit M, Karachaliou A, Moore S, Nayagam S, Papadopoulos T, Perkins T, Portnoy A, Minh Q, Vynnycky E, Winter A, Burrows H, Chen C, Clapham H, Deshpande A, Hauryski S, Huber J, Jean K, Kim C, Kim J, Koh J, Lopman B, Pitzer V, Tam Y, Lambach P, Sim S, Woodruff K, Ferguson N, Trotter C, Gaythorpe K. Estimating the health effects of COVID-19-related immunisation disruptions in 112 countries during 2020–30: a modelling study. The Lancet Global Health 2024, 12: e563-e571. PMID: 38485425, PMCID: PMC10951961, DOI: 10.1016/s2214-109x(23)00603-4.Peer-Reviewed Original ResearchConceptsCatch-up activitiesVaccine-preventable disease burdenCatch-upVaccine Impact Modelling ConsortiumImmunisation servicesMiddle-income countriesEffectiveness of HPV vaccinationVaccine effectivenessAffected cohortBill & Melinda Gates FoundationImmunisation coverageLow-incomeLong-term effectsWHO-UNICEFDisease burdenVaccination coverageCalendar yearImmunisation effortsMelinda Gates FoundationMitigation measuresCountriesYears of vaccinationYellow fever vaccineMapping the incidence rate of typhoid fever in sub-Saharan Africa
Kim J, Choi J, Kim C, Pak G, Parajulee P, Haselbeck A, Park E, Mogasale V, Jeon H, Browne A, Owusu-Dabo E, Rakotozandrindrainy R, Bassiahi A, Teferi M, Lunguya-Metila O, Dolecek C, Pitzer V, Crump J, Hay S, Marks F. Mapping the incidence rate of typhoid fever in sub-Saharan Africa. PLOS Neglected Tropical Diseases 2024, 18: e0011902. PMID: 38408128, PMCID: PMC10965079, DOI: 10.1371/journal.pntd.0011902.Peer-Reviewed Original ResearchIncidence rateSub-Saharan AfricaRate of typhoid feverTyphoid feverIncidence rate of typhoid feverIncidence rate estimatesEffective intervention programsEstimated incidence ratePublic health problemSub-SaharanHigh-incidence countriesLow-incidence countriesHealth conditionsIntervention programsDisease riskHealth problemsTarget resourcesGeospatial variationAge classesDisease incidenceEnvironmental conditionsPublished articlesSub-national heterogeneityGeospatial covariatesCultures of bloodReport from the World Health Organization’s immunization and vaccines related implementation research advisory committee (IVIR-AC) meeting, Geneva, 11–13 September 2023
Lambach P, Orenstein W, Silal S, Sbarra A, Koh M, Aggarwal R, Farooqui H, Flasche S, Hogan A, Kim S, Leask J, Luz P, Lyimo D, Moss W, Pitzer V, Wang X, Wu J. Report from the World Health Organization’s immunization and vaccines related implementation research advisory committee (IVIR-AC) meeting, Geneva, 11–13 September 2023. Vaccine 2024, 42: 1424-1434. PMID: 38326131, PMCID: PMC10953699, DOI: 10.1016/j.vaccine.2024.02.014.Peer-Reviewed Original Research
2023
Typhoid fever
Meiring J, Khanam F, Basnyat B, Charles R, Crump J, Debellut F, Holt K, Kariuki S, Mugisha E, Neuzil K, Parry C, Pitzer V, Pollard A, Qadri F, Gordon M. Typhoid fever. Nature Reviews Disease Primers 2023, 9: 71. PMID: 38097589, DOI: 10.1038/s41572-023-00480-z.Peer-Reviewed Original ResearchConceptsTyphoid feverUndifferentiated febrile illnessInvasive bacterial diseaseEffective vaccination programsFecal-oral routeNovel diagnostic modalitiesFebrile illnessBloodstream infectionsVaccination programBlood culturesClinical trialsImmunological protectionHigh burdenCausative organismDiagnostic modalitiesGlobal burdenDisease pathogenesisFeverHuman infectionsIntestinal epitheliumYoung adultsCulture testingSalmonella enterica subspSerovar TyphiAntimicrobial resistanceSurvey of white-footed mice (Peromyscus leucopus) in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses
Earnest R, Hahn A, Feriancek N, Brandt M, Filler R, Zhao Z, Breban M, Vogels C, Chen N, Koch R, Porzucek A, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber H, Cantoni J, Pitzer V, Olarte Castillo X, Goodman L, Wilen C, Linske M, Williams S, Grubaugh N. Survey of white-footed mice (Peromyscus leucopus) in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses. Npj Viruses 2023, 1: 10. DOI: 10.1038/s44298-023-00010-4.Peer-Reviewed Original ResearchIncorporating Data from Multiple Endpoints in the Analysis of Clinical Trials: Example from RSV Vaccines
Prunas O, Willemsen J, Bont L, Pitzer V, Warren J, Weinberger D. Incorporating Data from Multiple Endpoints in the Analysis of Clinical Trials: Example from RSV Vaccines. Epidemiology 2023, 35: 103-112. PMID: 37793120, DOI: 10.1097/ede.0000000000001680.Peer-Reviewed Original ResearchIncorporating Efficacy Data from Initial Trials Into Subsequent Evaluations: Application to Vaccines Against Respiratory Syncytial Virus
Warren J, Sundaram M, Pitzer V, Omer S, Weinberger D. Incorporating Efficacy Data from Initial Trials Into Subsequent Evaluations: Application to Vaccines Against Respiratory Syncytial Virus. Epidemiology 2023, 35: 130-136. PMID: 37963353, PMCID: PMC10842163, DOI: 10.1097/ede.0000000000001690.Peer-Reviewed Original ResearchFloods and Diarrhea Risk in Young Children in Low- and Middle-Income Countries
Wang P, Asare E, Pitzer V, Dubrow R, Chen K. Floods and Diarrhea Risk in Young Children in Low- and Middle-Income Countries. JAMA Pediatrics 2023, 177: 1206-1214. PMID: 37782513, PMCID: PMC10546297, DOI: 10.1001/jamapediatrics.2023.3964.Peer-Reviewed Original ResearchConceptsMiddle-income countriesDiarrhea riskOdds ratioMAIN OUTCOMEMixed-effects logistic regression modelRisk of diarrheaCross-sectional studyHigher odds ratioPrevalence of diarrheaLogistic regression modelsHealth survey programUnexposed childrenEffect modificationChild healthDiarrhea prevalenceSurvey clustersSignificant associationHygiene practicesFourth weekWeeksStrong associationRandom interceptYoung childrenChildrenDiarrheaAssessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi
Walker J, Chaguza C, Grubaugh N, Carey M, Baker S, Khan K, Bogoch I, Pitzer V. Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi. Nature Communications 2023, 14: 6502. PMID: 37845201, PMCID: PMC10579367, DOI: 10.1038/s41467-023-42353-9.Peer-Reviewed Original ResearchConceptsXDR S. TyphiS. typhiDrug-resistant Salmonella enterica serovar TyphiDrug-resistant Salmonella TyphiTyphoid outbreakMajor public health threatResistant Salmonella typhiPublic health activitiesTyphoid fever incidencePublic health threatSalmonella enterica serovar TyphiXDR typhoidEnterica serovar TyphiH58 haplotypeHigh riskOnward transmissionTyphoid feverSignificant associationHealth activitiesFever incidenceHealth threatFuture outbreaksSerovar TyphiSalmonella typhiTyphiThe blossoming of methods and software in computational biology
Mac Gabhann F, Pitzer V, Papin J. The blossoming of methods and software in computational biology. PLOS Computational Biology 2023, 19: e1011390. PMID: 37590323, PMCID: PMC10434930, DOI: 10.1371/journal.pcbi.1011390.Peer-Reviewed Original Research