2025
Topography and environmental deficiencies are associated with chikungunya virus exposure in urban informal settlements in Salvador, Brazil
Travis C, Argibay H, Pellizzaro M, de Oliveira D, Santana R, Palma F, Lustosa R, Santana J, Souza F, López Y, Reis M, Ko A, Diggle P, Ribeiro G, Begon M, Costa F, Khalil H, Eyre M. Topography and environmental deficiencies are associated with chikungunya virus exposure in urban informal settlements in Salvador, Brazil. PLOS Neglected Tropical Diseases 2025, 19: e0013477. PMID: 40911655, PMCID: PMC12440227, DOI: 10.1371/journal.pntd.0013477.Peer-Reviewed Original ResearchConceptsUrban informal settlementsPublic health burdenLow-income communitiesInformal settlementsGlobal public health burdenBinomial mixed-effects modelDegree of urbanisationHealth burdenMixed-effects modelsCHIKV seroprevalenceEnvironmental deficienciesReduced riskAssociated with seropositivityRisk factorsUrban communitiesMale sexBrazilian citiesRiskHouseholdsCommunityCHIKV seropositivityIndividualsEnvironmental factorsExposure patternsDomains individualsNational and sub-national sero-epidemiology of immunoglobulin G against SARS-CoV-2 in Iran in 2021
Azangou-Khyavy M, Ghasemi E, Ebrahimi N, Rashidi M, Abbasi-Kangevari M, Ahmadi N, Khanali J, Kazemi A, Dilmaghani-Marand A, Farzi Y, Yoosefi M, Abdolhamidi E, Moghimi M, Nasserinejad M, Fattahi N, Azadnajafabad S, Alipour-Daroei A, Rezaee K, Djalalinia S, Rezaei N, Jamshidi H, Farzadfar F. National and sub-national sero-epidemiology of immunoglobulin G against SARS-CoV-2 in Iran in 2021. PLOS ONE 2025, 20: e0313795. PMID: 40743259, PMCID: PMC12312912, DOI: 10.1371/journal.pone.0313795.Peer-Reviewed Original ResearchConceptsPopulation-based cross-sectional studyCross-sectional studySARS-CoV-2Population-based seroprevalence studyAge-standardized seroprevalenceIntervening factorsInfection rateSeroprevalence of IgGN antigenPCR test resultsRisk of infectionCOVID-19 infectionProtective factorsSymptomatic casesELISA kitsInfectionImmunoglobulin GSeroprevalence studySerological samplesPulmonary function and comparative SARS-CoV-2 RBD-specific IgG antibody response among the COVID-19 recovered group
Siddik A, Faisal A, khan A, Alam M, Nayeem J, Kulsum U, Mukta S, Kawser Z, Hasan I, Azad K, Hossain M, Kar S, Sultana N, Alam R, Mustafa A, Habib M, Ryan E, Qadri F, Hassan M. Pulmonary function and comparative SARS-CoV-2 RBD-specific IgG antibody response among the COVID-19 recovered group. PLOS ONE 2025, 20: e0318959. PMID: 40644485, PMCID: PMC12250562, DOI: 10.1371/journal.pone.0318959.Peer-Reviewed Original ResearchConceptsForced Vital CapacityPulmonary function testsDose of vaccineIgG antibody responsesPulmonary functionAntibody titersInfection historyBooster doseFollow-upRecovered groupAntibody responseLong-term pulmonary consequencesProspective case control studyPulmonary function abnormalitiesControl groupAbnormal pulmonary functionCase-control studyLong-term respiratory healthHigh IgG antibody titersIgG antibody titersForced expiratory volumeAsymptomatic COVID-19Pulmonary function measurementsManifestations of long COVIDThird doseSARS-CoV-2 induced immune perturbations in infants vary with disease severity and differ from adults’ responses
Nehar-Belaid D, Mejías A, Xu Z, Marches R, Yerrabelli R, Chen G, Mertz S, Ye F, Sánchez P, Tsang J, Aydillo T, Miorin L, Cupic A, García-Sastre A, Ucar D, Banchereau J, Pascual V, Ramilo O. SARS-CoV-2 induced immune perturbations in infants vary with disease severity and differ from adults’ responses. Nature Communications 2025, 16: 4562. PMID: 40379618, PMCID: PMC12084365, DOI: 10.1038/s41467-025-59411-z.Peer-Reviewed Original ResearchConceptsResponse to SARS-CoV-2Infected infantsT cellsSARS-CoV-2B cellsCytotoxic CD8+ T cellsImmune profile of childrenISG signatureNaive CD4+ T cellsCD8+ T cellsCD4+ T cellsImmune response to SARS-CoV-2Anti-IFN autoantibodiesAntibody response to SARS-CoV-2Transitional B cellsEarly life immunityCD14+ monocytesIncreased serum concentrationsInflammasome-related moleculesInterferon-stimulated genesImmune profileImmune perturbationsSerum concentrationsInflammatory cytokinesImmune responseImpact of COVID‐19 Vaccination and Infection on Anti‐Triple‐Knockout (TKO) Pig Antibody Production: A Study in Patients With End‐Stage Liver Disease and Liver Transplant Recipients
Wang L, Zhuang L, Li T, Hara H, Cooper D, Leng J, Pan D, Zheng S, Wang Y, Xu X, Wei Q. Impact of COVID‐19 Vaccination and Infection on Anti‐Triple‐Knockout (TKO) Pig Antibody Production: A Study in Patients With End‐Stage Liver Disease and Liver Transplant Recipients. Xenotransplantation 2025, 32: e70050. PMID: 40375623, DOI: 10.1111/xen.70050.Peer-Reviewed Original ResearchConceptsEnd-stage liver diseaseEnd-stage liver disease patientsLT recipientsLiver transplantationCOVID-19 vaccineAntibody productionLiver diseaseAntibody levelsImpact of COVID-19 vaccinationTKO pig cellsLiver transplant recipientsAnti-pig antibody levelsActive COVID-19 infectionSARS-CoV-2 IgGTransplant recipientsCOVID-19 infectionEffectiveness of COVID-19 vaccinesHealthy controlsIgG levelsXenotransplant recipientsPig cellsHealthy individualsIgG antibodiesPatientsEnd-stageImpact of memory T cells on SARS-CoV-2 vaccine response in hematopoietic stem cell transplant
VanOudenhove J, Liu Y, Nelakanti R, Kim D, Busarello E, Ovalle N, Qi Z, Mamillapalli P, Siddon A, Bai Z, Axtmayer A, Corso C, Kothari S, Foss F, Isufi I, Tebaldi T, Gowda L, Fan R, Seropian S, Halene S. Impact of memory T cells on SARS-CoV-2 vaccine response in hematopoietic stem cell transplant. PLOS ONE 2025, 20: e0320744. PMID: 40294012, PMCID: PMC12036906, DOI: 10.1371/journal.pone.0320744.Peer-Reviewed Original ResearchConceptsHematopoietic stem cell transplantationMemory T cellsStem cell transplantationCell transplantationT cellsSARS-CoV-2Hematopoietic stem cell transplant recipientsAntigen-specific T-cell activationSARS-CoV-2 mRNA vaccinesSARS-CoV-2 vaccine responsesSevere diseaseAnti-spike IgGT cell activationAdaptive immune responsesRobust antibody responsesPost-vaccination responseSARS-CoV-2 infectionMRNA vaccine seriesSingle-cell RNAMyeloablative chemotherapyCellular responsesImmune profileVaccine responseCOVID-19 infectionMRNA vaccinesCoVimmune COVID-19 Immunity Calculator: Web Application Development and Validation Study
Slotkin R, Kyriakides T, Yu V, Chen X, Kundu A, Gupta S. CoVimmune COVID-19 Immunity Calculator: Web Application Development and Validation Study. JMIR Formative Research 2025, 9: e59467. PMID: 40262279, PMCID: PMC12040297, DOI: 10.2196/59467.Peer-Reviewed Original ResearchMeSH KeywordsAdultAntibodies, NeutralizingAntibodies, ViralCOVID-19COVID-19 VaccinesFemaleHumansImmunoglobulin GInternetMaleMiddle AgedSARS-CoV-2Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction
Wang M, Patsenker J, Li H, Kluger Y, Kleinstein S. Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. PLOS Computational Biology 2025, 21: e1012153. PMID: 40163503, PMCID: PMC12013870, DOI: 10.1371/journal.pcbi.1012153.Peer-Reviewed Original ResearchConceptsSupervised fine-tuningImmune responseMolecular basis of antigen recognitionSARS-CoV-2 spike proteinLanguage modelSARS-CoV-2 vaccinesAdaptive immune responsesSpecific predictionsMolecular basisSpike proteinAntibody-based therapeuticsFine-tuningAntibody-antigen specificitySpecific to antigensInfluenza hemagglutininVaccine designAntigen recognitionModel embeddingsImmune functionLanguage model embeddingsSARS-CoV-2AntibodiesAntigenInfluenzaVaccineSpike specific IgG3 and nucleocapsid IgG response in serum serve as distinguishing immunological markers between SARS-CoV-2 infection and vaccination
Akhtar M, Islam M, Khaton F, Rahman F, Sami T, Tauheed I, Ahmed T, Akter A, Khan I, Khan Z, Kumar Biswas P, Ryan E, Banu S, Shirin T, Chowdhury F, Khan A, Bhuiyan T, Qadri F. Spike specific IgG3 and nucleocapsid IgG response in serum serve as distinguishing immunological markers between SARS-CoV-2 infection and vaccination. Frontiers In Immunology 2025, 16: 1518915. PMID: 40213555, PMCID: PMC11983542, DOI: 10.3389/fimmu.2025.1518915.Peer-Reviewed Original ResearchConceptsCOVID-19 patientsSARS-CoV-2 infectionIgG responsesCOVID-19 vaccinated individualsCOVID-19 vaccineReceptor-binding domainSARS-CoV-2RBD-specific IgG responsesIgG subclass antibody responsesSpecific IgG responsesEarly phase of infectionSubclass antibody responsesNatural infectionPhase of infectionDays of infectionBreakthrough infectionImmunological markersVaccine recipientsNucleocapsid IgGSpike receptor-binding domainAntibody responseIgG subclassesImmunological responseIgG3 subclassPatientsPost-transfusion activation of coagulation pathways during severe COVID-19 correlates with COVID-19 convalescent plasma antibody profiles
Weiss S, Lin H, Acosta E, Komarova N, Chen P, Wodarz D, Baine I, Duerr R, Wajnberg A, Gervais A, Bastard P, Casanova J, Arinsburg S, Swartz T, Aberg J, Bouvier N, Liu S, Alvarez R, Chen B. Post-transfusion activation of coagulation pathways during severe COVID-19 correlates with COVID-19 convalescent plasma antibody profiles. Journal Of Clinical Investigation 2025, 135: e181136. PMID: 40091845, PMCID: PMC11910229, DOI: 10.1172/jci181136.Peer-Reviewed Original ResearchConceptsCOVID-19 convalescent plasmaCOVID-19 convalescent plasma unitsActivation of coagulation pathwaysSevere COVID-19Post-transfusionAntibody profilesEffectiveness of COVID-19 convalescent plasmaSevere SARS-CoV-2 infectionCoagulation pathwayD-dimer levelsHospitalized COVID-19 patientsHigher-riskCCP recipientsSARS-CoV-2 infectionTreat severe COVID-19SARS-CoV-2 spikeCOVID-19 patientsAntibody therapyD-dimerD-dimer trendsConvalescent plasmaSevere diseaseBetacoronavirus OC43Higher mortalityIn vitro assaysCharacterising the SARS-CoV-2 nucleocapsid (N) protein antibody response
Noble C, McDonald E, Nicholson S, Biering-Sørensen S, Pittet L, Byrne A, Croda J, Dalcolmo M, Lacerda M, Lucas M, Lynn D, Aymerich C, Richmond P, Warris A, Curtis N, Messina N, Group T. Characterising the SARS-CoV-2 nucleocapsid (N) protein antibody response. Journal Of Infection 2025, 90: 106436. PMID: 39922387, DOI: 10.1016/j.jinf.2025.106436.Peer-Reviewed Original ResearchConceptsAntibody indexAntibody responseSpike-based vaccinesSeroconversion ratesSARS-CoV-2 virus vaccineCourse of COVID-19SARS-CoV-2Severe COVID-19 symptomsResponse to natural infectionInternational randomised controlled trialRandomised controlled trialsIncomplete courseCoronaVac vaccineVirus vaccineControlled TrialsCoronaVacCOVID-19 symptomsProtein antibodiesVaccineAnti-NCOVID-19Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients
Pickering H, Schaenman J, Phan H, Maguire C, Tsitsiklis A, Rouphael N, Higuita N, Atkinson M, Brakenridge S, Fung M, Messer W, Salehi-rad R, Altman M, Becker P, Bosinger S, Eckalbar W, Hoch A, Doni Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein S, Krammer F, Maecker H, Ozonoff A, Diray-Arce J, Shaw A, Baden L, Levy O, Reed E, Langelier C. Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients. Nature Communications 2025, 16: 586. PMID: 39794319, PMCID: PMC11723965, DOI: 10.1038/s41467-025-55823-z.Peer-Reviewed Original ResearchConceptsSolid organ transplant recipientsOrgan transplant recipientsTransplant recipientsInduction of pro-inflammatory genesSenescent T cellsTransitional B cellsImpaired viral clearanceImmune response to infectionAnti-spike IgG levelsNon-transplanted controlsFeatures of COVID-19Innate Immune Signaling PathwaysResponse to infectionPro-inflammatory genesSerum chemokinesViral clearanceImmune dysregulationT cellsImmune signaling pathwaysB cellsImmune featuresSex-matchedIgG levelsSevere diseaseTransplantationSystem vaccinology analysis of predictors and mechanisms of antibody response durability to multiple vaccines in humans
Cortese M, Hagan T, Rouphael N, Wu S, Xie X, Kazmin D, Wimmers F, Gupta S, van der Most R, Coccia M, Aranuchalam P, Nakaya H, Wang Y, Coyle E, Horiuchi S, Wu H, Bower M, Mehta A, Gunthel C, Bosinger S, Kotliarov Y, Cheung F, Schwartzberg P, Germain R, Tsang J, Li S, Albrecht R, Ueno H, Subramaniam S, Mulligan M, Khurana S, Golding H, Pulendran B. System vaccinology analysis of predictors and mechanisms of antibody response durability to multiple vaccines in humans. Nature Immunology 2025, 26: 116-130. PMID: 39747435, PMCID: PMC12158788, DOI: 10.1038/s41590-024-02036-z.Peer-Reviewed Original ResearchConceptsHuman bone marrow plasma cellsResponse longevityBone marrow plasma cellsAntibody responseVaccine-induced antibody responsesAntibody response magnitudesH5N1 influenza vaccineMIF-CD74 axisInvestigate immune responsesBlood transcriptional signaturesAS03-adjuvantedInfluenza vaccineMegakaryocyte activityResponse durabilityAnalysis of predictorsPlasma cellsVaccine durabilityImmune responseDay 7Transcriptional signaturePromote survivalCell-cell interactionsAntibodiesPlateletVaccine
2024
Booster COVID-19 mRNA vaccination ameliorates impaired B-cell but not T-cell responses in older adults
Kometani K, Yorimitsu T, Jo N, Yamaguchi E, Kikuchi O, Fukahori M, Sawada T, Tsujimoto Y, Sunami A, Li M, Ito T, Pretemer Y, Gao Y, Hidaka Y, Yamamoto M, Kaku N, Nakagama Y, Kido Y, Grifoni A, Sette A, Nagao M, Morita S, Nakajima T, Muto M, Hamazaki Y. Booster COVID-19 mRNA vaccination ameliorates impaired B-cell but not T-cell responses in older adults. Frontiers In Immunology 2024, 15: 1455334. PMID: 39717779, PMCID: PMC11663736, DOI: 10.3389/fimmu.2024.1455334.Peer-Reviewed Original ResearchMeSH KeywordsAdultAge FactorsAgedAged, 80 and overAntibodies, ViralB-LymphocytesCD8-Positive T-LymphocytesCOVID-19COVID-19 VaccinesFemaleHumansImmunity, HumoralImmunization, SecondaryImmunoglobulin GImmunologic MemoryMaleMemory B CellsMiddle AgedmRNA VaccinesSARS-CoV-2Spike Glycoprotein, CoronavirusYoung AdultConceptsB cell responsesT cell responsesB cellsT cellsBooster vaccinationT cell-mediated cellular immunityCD8<sup>+</sup> T cell responsesCytotoxic CD8<sup>+</sup> T cell responsesReduced PD-1 expressionMemory T cell activationMemory B cell responsesCOVID-19 mRNA booster vaccinationPD-1 expressionCOVID-19 mRNA vaccinesMemory T cellsImpaired humoral immunityImpaired B cellYoung adultsT cell activationMRNA booster vaccinationEnhanced IgG responseSpike-specificCellular immunityMRNA vaccinesAge-associated differencesA B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses
Yang Y, Treger R, Hernandez-Bird J, Lu P, Mao T, Iwasaki A. A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses. Science Immunology 2024, 9: eadd6608-eadd6608. PMID: 39514636, PMCID: PMC11962862, DOI: 10.1126/sciimmunol.add6608.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, ViralB-LymphocytesEndogenous RetrovirusesImmunoglobulin MMiceMice, Inbred C57BLPolysaccharidesConceptsB-1 cellsB cell-deficient miceEndogenous retrovirusesEnveloped virusesNatural IgM antibodiesGermline-encoded antibodiesNaive miceInnate antiviral mechanismsGenetic invadersB cellsVertebrate genomesNatural antibody repertoireRepertoire profilingSurface antigensInfectious endogenous retrovirusIgM antibodiesSelf-proteinsComplement pathwayAntibody repertoireAntibodiesMiceRetrovirusesVirusSensor stimulationGlycoproteinPerformance of rapid antigen tests to detect SARS-CoV-2 variant diversity and correlation with viral culture positivity: implication for diagnostic development and future public health strategies
Goux H, Green J, Wilson A, Sozhamannan S, Richard S, Colombo R, Lindholm D, Jones M, Agan B, Larson D, Saunders D, Mody R, Cox J, Deans R, Walish J, Fries A, Simons M, Pollett S, Smith D. Performance of rapid antigen tests to detect SARS-CoV-2 variant diversity and correlation with viral culture positivity: implication for diagnostic development and future public health strategies. MBio 2024, 15: e02737-24. PMID: 39480114, PMCID: PMC11633148, DOI: 10.1128/mbio.02737-24.Peer-Reviewed Original ResearchConceptsPerformance of Ag-RDTSARS-CoV-2 variantsAg-RDTs resultsRapid diagnostic testsAntigen-based rapid diagnostic testAg-RDTCulture-based resultsSARS-CoV-2Culture positivityDiagnostic testsPerformance of rapid antigen testsAg-RDT sensitivityApparent trade-offPCR-positive infectionsViral culture positivityN proteinRapid antigen testModerate to high sensitivityVariant diversityAntigen-based testsRisk of transmissionVirus-positiveMolecular assaysAntigen testRespiratory pathogensStructure and inhibition of SARS-CoV-2 spike refolding in membranes
Grunst M, Qin Z, Dodero-Rojas E, Ding S, Prévost J, Chen Y, Hu Y, Pazgier M, Wu S, Xie X, Finzi A, Onuchic J, Whitford P, Mothes W, Li W. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science 2024, 385: 757-765. PMID: 39146425, PMCID: PMC11449073, DOI: 10.1126/science.adn5658.Peer-Reviewed Original ResearchMeSH KeywordsAngiotensin-Converting Enzyme 2Antibodies, NeutralizingAntibodies, ViralBetacoronavirusCell MembraneCOVID-19Cryoelectron MicroscopyElectron Microscope TomographyHumansMolecular Dynamics SimulationPeptidyl-Dipeptidase AProtein DomainsProtein MultimerizationProtein RefoldingSARS-CoV-2Spike Glycoprotein, CoronavirusVirus InternalizationHigh silent prevalence of human herpesvirus 1 (HSV-1) infection affecting the indigenous reservation of the municipality of Dourados, Central-West Brazil
de Oliveira Bonfim F, Villar L, Croda J, Pereira J, Guimarães A, da Silva S, Maymone Gonçalves C, Leonardo L, de Rezende Romeira G, Cesar G, Weis-Torres S, de Oliveira Landgraf de Castro V, Horta M, Simionatto S, Motta-Castro A, de Paula V. High silent prevalence of human herpesvirus 1 (HSV-1) infection affecting the indigenous reservation of the municipality of Dourados, Central-West Brazil. BMC Infectious Diseases 2024, 24: 700. PMID: 39020287, PMCID: PMC11253429, DOI: 10.1186/s12879-024-09497-5.Peer-Reviewed Original ResearchConceptsAnti-HSV-1 antibodiesHSV-1 DNAAnti-HSV-1HSV-1Viral loadReal-time PCRDetection of HSV-1 DNAHSV-1 viral loadSeroprevalence of HSV-1HSV-1 transmissionControl of HSV-1 infectionHSV-1 infectionAdult Brazilian populationIgM-positive samplesNeonatal infectionHerpetic keratitisGenital wartsUrethral dischargeHerpes encephalitisHuman herpesvirus 1IgM antibodiesRisk factorsSevere diseaseUrinary problemsHuman alphaherpesvirusComparative Analysis of Viral Load and Cytokines during SARS-CoV-2 Infection between Pregnant and Non-Pregnant Women
Liu D, Li H, Li X, Rodriguez G, Pietz H, Fiel R, Konadu E, Singh V, Loo F, Rodgers W. Comparative Analysis of Viral Load and Cytokines during SARS-CoV-2 Infection between Pregnant and Non-Pregnant Women. International Journal Of Molecular Sciences 2024, 25: 7731. PMID: 39062978, PMCID: PMC11277191, DOI: 10.3390/ijms25147731.Peer-Reviewed Original ResearchConceptsNon-pregnant womenSARS-CoV-2 infectionResponse to SARS-CoV-2 infectionPregnant womenViral loadNeutralizing antibodiesImmune response to SARS-CoV-2 infectionAnalysis of viral loadSARS-CoV-2Retrospective cohort studyIgG neutralizing antibodiesCytokine expression patternsMultiplex reverse transcription polymerase chain reactionAnti-N protein IgGExpression of leptinDifferential cytokine expressionEnhanced antibody productionReverse transcription polymerase chain reactionVulnerability of pregnant womenCytokine array assayTranscription polymerase chain reactionCytokine profileIncidence of SARS-CoV-2 infectionImmune modulationPolymerase chain reactionMaturation of germinal center B cells after influenza virus vaccination in humans
McIntire K, Meng H, Lin T, Kim W, Moore N, Han J, McMahon M, Wang M, Malladi S, Mohammed B, Zhou J, Schmitz A, Hoehn K, Carreño J, Yellin T, Suessen T, Middleton W, Teefey S, Presti R, Krammer F, Turner J, Ward A, Wilson I, Kleinstein S, Ellebedy A. Maturation of germinal center B cells after influenza virus vaccination in humans. Journal Of Experimental Medicine 2024, 221: e20240668. PMID: 38935072, PMCID: PMC11211068, DOI: 10.1084/jem.20240668.Peer-Reviewed Original ResearchConceptsB cellsInfluenza vaccineGerminal centersAntigen-specific GC B cellsResponse to seasonal influenza vaccinationLong-lived bone marrow plasma cellsResponse to influenza vaccinationBone marrow plasma cellsGerminal center B cellsGC B cell clonesInfluenza virus vaccineMaturation of B cellsMarrow plasma cellsSeasonal influenza vaccineMemory B cellsHemagglutinin (HAB cell clonesGC B cellsInfluenza hemagglutinin (HAH5 HANeedle aspirationLymphoid structuresLymph nodesPlasma cellsGC reaction
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