Nathan Grubaugh, PhD
Professor of Epidemiology (Microbial Diseases)Cards
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
Education
Colorado State University, Microbiology (2016)
Johns Hopkins University, Biotechnology (2011)
Western Michigan University, Biomedical Sciences (2005)
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
Education
Colorado State University, Microbiology (2016)
Johns Hopkins University, Biotechnology (2011)
Western Michigan University, Biomedical Sciences (2005)
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
Education
Colorado State University, Microbiology (2016)
Johns Hopkins University, Biotechnology (2011)
Western Michigan University, Biomedical Sciences (2005)
About
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Titles
Professor of Epidemiology (Microbial Diseases)
Affiliated Faculty, Yale Institute for Global Health
Biography
Nathan Grubaugh joined the faculty at Yale School of Public Health in 2018. Before going to graduate school, he spent ~7 years working in the biotech industry developing early phase vaccine candidates. He earned his MS in biotechnology from Johns Hopkins University (2011) while conducting research at the NIH and the US Army Research Institute of Infectious Diseases (focus on mosquito-borne virus surveillance). Dr. Grubaugh earned his PhD in microbiology from Colorado State University in 2016 (focus on West Nile virus evolution), and went on to be a postdoctoral fellow at The Scripps Research Institute to study the 2015-2017 Zika virus epidemic. Now at Yale, the Grubaugh Lab uses genomics and phylogenetics to uncover the epidemiological, ecological, and evolutionary determinants of virus outbreaks. They primarily focus on mosquito- and tick-borne viruses, like dengue, West Nile, and Powassan, that are increasingly spreading into new areas and have high outbreak potential. The Grubaugh Lab is diverse and multidisciplinary, including expertise in molecular biology, phylogenetics, statistics, and mathematical modeling. His lab was critical during the COVID-19 response, from designing and evaluating diagnostics (such as SalivaDirect) to establishing the Yale SARS-CoV-2 Genomic Surveillance Initiative to track emerging variants. Expanding on this work, the lab is an academic partner for the Pathogen Genomics Centers of Excellence to foster and improve innovation and technical capacity in pathogen genomics, molecular epidemiology, and bioinformatics to better prevent, control, and respond to microbial threats of public health importance. Read more about their team and work at grubaughlab.com.
Appointments
Epidemiology of Microbial Diseases
Associate Professor on TermPrimaryDepartment of Ecology & Evolutionary Biology
Assistant ProfessorSecondary
Other Departments & Organizations
- Center for Infection and Immunity
- Center for RNA Science and Medicine
- Department of Ecology & Evolutionary Biology
- Epidemiology of Microbial Diseases
- Microbiology
- Public Health Modeling
- Virology Laboratories
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Institute for Global Health
- Yale School of Public Health
- YSPH Global Health Concentration
Education & Training
- Postdoctoral Fellow
- The Scripps Research Institute (2018)
- PhD
- Colorado State University, Microbiology (2016)
- MS
- Johns Hopkins University, Biotechnology (2011)
- BS
- Western Michigan University, Biomedical Sciences (2005)
Research
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Overview
Medical Research Interests
Public Health Interests
ORCID
0000-0003-2031-1933- View Lab Website
Grubaugh Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Chantal Vogels, PhD
Albert Icksang Ko, MD
Akiko Iwasaki, PhD
Wade Schulz, MD, PhD
M. Catherine Muenker, MS
Shelli Farhadian, MD, PhD
Disease Outbreaks
Dengue Virus
West Nile virus
Aedes
Chikungunya virus
Culex
Publications
2026
Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.
Vargas D, Albornoz L, Peña-Morales M, Ortiz Rojas H, Breban M, Grubaugh N, Hahn A. Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection. Journal Of Virology 2026, e0222425. PMID: 42262131, DOI: 10.1128/jvi.02224-25.Peer-Reviewed Original ResearchAltmetricConceptsIntra-host single-nucleotide variantsSARS-CoV-2 diversityAllele-frequency distributionsPolymorphic sitesAllele frequenciesImmunocompromised patientsNon-synonymous changesWhole-genome sequencingSingle-nucleotide variantsS regionIntra-host diversityWithin-host diversityImmunocompromised individualsImmunocompetent individualsImmunocompromised hostsDiverse viral populationsLineage-specific effectsAcute infectionImmune statusEvolutionary potentialNon-synonymousViral lineagesDiversity metricsViral populationsMutational signaturesUtilizing virus genomic surveillance to predict vaccine effectiveness
Kwon J, Li K, Warren J, Pandya S, Hahn A, Initiative Y, Pitzer V, Weinberger D, Grubaugh N. Utilizing virus genomic surveillance to predict vaccine effectiveness. PLOS Computational Biology 2026, 22: e1014329. PMID: 42189851, PMCID: PMC13258143, DOI: 10.1371/journal.pcbi.1014329.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsAmino acid distancesWhole-genome sequencingAmino acid substitutionsGenetic distanceAcid substitutionsSpike geneGenomic surveillanceGenomic surveillance dataSequence(s)Genome sequenceGenomic informationPathogen diversitySequence informationVirus sequencesVaccine effectivenessAminoGenesSARS-CoV-2SequencePathogenic featuresVaccine protectionPathogensVariantsTest-negative controlsMRNA-based vaccinesExpert Recommendations to Strengthen Chikungunya Outbreak Surveillance and Reporting for Traveler Health Protection.
Payne D, Bagamian K, Goad J, Grubaugh N, Johansson M, Kraemer M, Leshem E, Norman F, Rodríguez-Morales A, Salje H, Thomas S, Weaver S, Laytner L, Sturgis R, Scheele S, Hamer D. Expert Recommendations to Strengthen Chikungunya Outbreak Surveillance and Reporting for Traveler Health Protection. American Journal Of Tropical Medicine And Hygiene 2026 PMID: 42190647, DOI: 10.4269/ajtmh.26-0117.Peer-Reviewed Original ResearchConceptsLocal health care contextInadequate awarenessHealth care settingsHealth care contextExpert recommendationsReporting resourcesHealth care workersExpert panel discussionCare contextCare settingsHealth professionalsHealth protectionCare workersExpert panelCase definitionDiagnostic capacityDiagnostic testsHealth burdenSurveillance dataChikungunya virusHealthInfection riskRisk communicationRiskOutbreak reportsEpidemiología genómica del dengue 2 y 3: introducciones y exportaciones de linajes en Colombia
Miranda Regino J, Rivero Herrera R, Tique Salleg V, Echeverri de la Hoz D, Damodaran L, Paternina Berrio D, Santos Vega M, Torres D, Davalos D, López Medina E, Breban M, Arrieta Bernate G, Hill V, Grubaugh N, Mattar Velilla S. Epidemiología genómica del dengue 2 y 3: introducciones y exportaciones de linajes en Colombia. Salud Uninorte 2026, 01: 201-202. DOI: 10.14482/sun.01.813.445.Peer-Reviewed Original ResearchEvolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology
Bourgikos E, Dellicour S, Lemey P, Feriancek N, Bransfield A, Breban M, Misencik M, Petruff T, Shepard J, Andreadis T, Anderson J, Ngo K, Maffei J, Dupuis A, Rich S, Xu G, Sakolsky G, Price K, Metzger M, Suchard M, Lopes R, Gámbaro F, Carlson C, Baele G, Ciota A, Vogels C, Hill V, Armstrong P, Grubaugh N. Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology. Current Biology 2026, 36: 2343-2356.e7. PMID: 42025175, DOI: 10.1016/j.cub.2026.03.076.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsEvolutionary historyEcological driversMosquito-Borne VirusesPrimary introductionJamestown Canyon virusEvolutionary stasisPhylogenetic analysisPhylogeographic reconstructionLineage AEcological knowledgeRNA virusesPhylodynamic methodsJCV sequencesMosquito surveillance dataMid-1900sTick-borne virusesNortheast United StatesMid-1800sMosquito eggsNorth AmericaComplex transmission cyclesSequenceVirusTransmission cycleMosquitoesReal-world effectiveness of perinatal RSV immunoprophylaxis: protocol for a test-negative case–control study
Llorente C, Wats A, Araujo B, Ganem J, Oliva I, Xu H, Brodsky N, Lucas C, Aronson P, Grubaugh N, Breban M, Redmond S, Shapiro E, Niccolai L, Weinberger D, Oliveira C. Real-world effectiveness of perinatal RSV immunoprophylaxis: protocol for a test-negative case–control study. BMJ Open 2026, 16: e114524. PMID: 41856594, PMCID: PMC13007147, DOI: 10.1136/bmjopen-2025-114524.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsRespiratory syncytial virusAcute respiratory illnessTest-negative case-control studyCase-control studyLong-acting monoclonal antibodiesSingle-cell immune profilingRSV-negative infantsImmune-escape mutationsConvalescent blood samplesRSV-positive specimensPrelicensure clinical trialsMultivariate logistic regressionWritten Informed ConsentHuman Investigation CommitteeMaternal vaccinationState immunization registryImmune profileBreakthrough infectionSyncytial virusClinical trialsNational InstituteVaccine effectivenessPotential confoundersControlled TrialsInfantsQuantifying the spatiotemporal dynamics of the first two epidemic waves of SARS-CoV-2 infections in the United States.
Lopes R, Lan Y, Chitwood M, Klaassen F, Salomon J, Menzies N, Warren J, Grubaugh N, Cohen T, Swartwood N. Quantifying the spatiotemporal dynamics of the first two epidemic waves of SARS-CoV-2 infections in the United States. PLOS Computational Biology 2026, 22: e1013983. PMID: 41779806, PMCID: PMC12959703, DOI: 10.1371/journal.pcbi.1013983.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsUnexpected diversification of DENV2 genotype III in Colombia: New Insights and application of the globalized nomenclature.
Calvo E, Madroñero L, Hernández L, Arturo J, Pinzón H, Delgado F, Velandia-Romero M, Hill V, Grubaugh N, Castellanos J. Unexpected diversification of DENV2 genotype III in Colombia: New Insights and application of the globalized nomenclature. PLOS ONE 2026, 21: e0343528. PMID: 41734239, PMCID: PMC12931762, DOI: 10.1371/journal.pone.0343528.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsMinor lineageEvolutionary dynamicsGenotype IIIIntegration of genomic dataNon-synonymous substitutionsEvolutionary relationshipsWhole genomePhylogenetic analysisGenomic dataCoding sequenceGenomic identityDENV-2Typing toolDominant lineageGenomic surveillanceVirus lineagesGenomeViral virulenceDengue virus lineagesLineagesLineage definitionDengue virus serotypesFunctional implicationsGlobal nomenclatureVector competenceA tiled amplicon protocol for culture-free whole-genome sequencing of M. tuberculosis from clinical specimens
Kalinich C, Gonzalez F, Osmaston A, Breban M, Distefano I, Leon C, Coronel J, Tan G, Crudu V, Ciobanu N, Codreanu A, Solano W, Ráez J, Sheen P, Zimic M, Allicock O, Chaguza C, Wyllie A, Brandt M, Weinberger D, Sobkowiak B, Cohen T, Grandjean L, Grubaugh N, Redmond S. A tiled amplicon protocol for culture-free whole-genome sequencing of M. tuberculosis from clinical specimens. Journal Of Clinical Microbiology 2026, 64: e01823-25. PMID: 41660836, PMCID: PMC12977623, DOI: 10.1128/jcm.01823-25.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsWhole-genome sequencingComprehensive drug susceptibility testingAmplicon panelDrug susceptibility testingSusceptibility testingWhole-genome sequences of M. tuberculosisClinical specimensSARS-CoV-2 sequencesNear-full genomesSlow-growing bacteriumAmplicon sequencing panelsBacterial genomesDrug resistanceBacterial sequencesSequence dataAmplicon sequencingAssociated with drug resistanceClinically relevant mutationsGenomic epidemiologySequencing methodsGenomePublic health laboratoriesRelevant mutationsSequencing panelClinical decision-makingGenomic epidemiology of dengue virus 2 and 3 reveals repeated introductions and exportations of several lineages in Colombia
Rivero R, Tique-Salleg V, Echeverri-De la Hoz D, Damodaran L, Paternina D, Santos-Vega M, Torres-Hernández D, Davalos D, López-Medina E, Breban M, Arrieta G, Miranda J, Hill V, Grubaugh N, Mattar S. Genomic epidemiology of dengue virus 2 and 3 reveals repeated introductions and exportations of several lineages in Colombia. Cell Reports 2026, 45: 116844. PMID: 41546866, DOI: 10.1016/j.celrep.2025.116844.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenomic epidemiologyComplete genome sequenceMultiple independent introductionsGenome sequencePhylogeographic reconstructionDengue virus 2DENV-2Emergent lineagesGenomic surveillanceIndependent introductionsDynamics of dengue virusLineagesDENV-3III lineagesSpatiotemporal dynamicsViral trafficDengue virusViral diseasesMosquito-borne viral diseaseVirus 2Critical roleGlobal health burdenAntigenic profileAntigenic spaceHealth burden
Clinical Trials
Current Trials
Volunteers Needed for HIV & Health Study (HARC Plus)
IRB ID1502015318RoleSub InvestigatorPrimary Completion Date06/01/2025Recruiting Participants
News & Links
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Media
- The Grubaugh Lab uses genomics to investigate how mosquito-borne viruses, like Zika, dengue, and chikungunya, spread (genomic epidemiology), cause disease (functional evolution), and adapt to new environments (experimental evolution).
News
- January 09, 2026Source: Yale News
SARS-CoV-2 Is on the Decline in Animals, Study Finds
- July 21, 2025
New YSPH Pilot Grants Support Innovative Interdisciplinary Research
- May 27, 2025Source: Yale News
Yale Planetary Solutions Announces a New ‘Constellation’ of Grants
- May 23, 2025
EMD Student Spotlight series: Afeez Sodeinde
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Locations
LEPH 608
Academic Office
60 College Street
New Haven, CT 06510
Business Office
203.737.5869LEPH 603
Lab
60 College Street
New Haven, CT 06510