Nathan Grubaugh, PhD
Associate Professor of Epidemiology (Microbial Diseases)Cards
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Education
Colorado State University, Microbiology (2016)
Johns Hopkins University, Biotechnology (2011)
Contact Info
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Education
Colorado State University, Microbiology (2016)
Johns Hopkins University, Biotechnology (2011)
Contact Info
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Education
Colorado State University, Microbiology (2016)
Johns Hopkins University, Biotechnology (2011)
Contact Info
About
Titles
Associate 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
- 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
Overview
Medical Subject Headings (MeSH)
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 Ko, MD
Akiko Iwasaki, PhD
Chaney Kalinich, MPH
Rebecca Earnest, MPH
Wade Schulz, MD, PhD
Disease Outbreaks
West Nile virus
Dengue Virus
Aedes
Chikungunya virus
Culex
Publications
2024
Genome-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 ResearchMeSH Keywords and ConceptsConceptsGenome-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 new lineage nomenclature to aid genomic surveillance of dengue virus
Hill V, Cleemput S, Pereira J, Gifford R, Fonseca V, Tegally H, Brito A, Ribeiro G, de Souza V, Brcko I, Ribeiro I, De Lima I, Slavov S, Sampaio S, Elias M, Tran V, Kien D, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau G, Gregianini T, Godinho F, Vogels C, Breban M, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara L, Faria N, Carrington C, Hanley K, Holmes E, Dumon W, Lima A, de Oliveira T, Grubaugh N. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLOS Biology 2024, 22: e3002834. PMID: 39283942, PMCID: PMC11426435, DOI: 10.1371/journal.pbio.3002834.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settingsNorth–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic
Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M. North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic. BMC Infectious Diseases 2024, 24: 751. PMID: 39075335, PMCID: PMC11288047, DOI: 10.1186/s12879-024-09658-6.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenome sequenceCombination of genome sequencingTrace transmission pathwaysDengue virusHistorical climatic patternsHigh climatic suitabilityCo-circulationDengue virus serotype 2Transmission pathwaysPhylogenetic analysisVirus transmission pathwaysBiodiversity hotspotHistorical climate dataVirus lineagesDominican RepublicImpacts of climate changeLineagesClimatic suitabilityClimate dataRising temperaturePathwaySerotype 2Subtropical regionsTransmission dynamicsImpact of climatic factorsSARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity
Peña-Hernández M, Alfajaro M, Filler R, Moriyama M, Keeler E, Ranglin Z, Kong Y, Mao T, Menasche B, Mankowski M, Zhao Z, Vogels C, Hahn A, Kalinich C, Zhang S, Huston N, Wan H, Araujo-Tavares R, Lindenbach B, Homer R, Pyle A, Martinez D, Grubaugh N, Israelow B, Iwasaki A, Wilen C. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity. Nature Microbiology 2024, 9: 2038-2050. PMID: 39075235, DOI: 10.1038/s41564-024-01765-z.Peer-Reviewed Original ResearchAltmetricConceptsBat coronavirusesRelatives of SARS-CoV-2Upper airwayUpper airways of miceEpithelial cellsHuman nasal epithelial cellsAirways of miceMajor histocompatibility complex class I.SARS-CoV-2Nasal epithelial cellsHistocompatibility complex class I.Human bronchial epithelial cellsGenetic similarityBronchial epithelial cellsInnate immune restrictionCoronavirus replicationFunctional characterizationMolecular cloningReduced pathogenesisImpaired replicationBat virusCoronavirus pathogenesisPandemic potentialHigh-risk familiesImmune restrictionCombining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US
Lopes R, Pham K, Klaassen F, Chitwood M, Hahn A, Redmond S, Swartwood N, Salomon J, Menzies N, Cohen T, Grubaugh N. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Reports 2024, 43: 114451. PMID: 38970788, DOI: 10.1016/j.celrep.2024.114451.Peer-Reviewed Original ResearchCitationsAltmetricDengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specificTravel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Taylor-Salmon E, Hill V, Paul L, Koch R, Breban M, Chaguza C, Sodeinde A, Warren J, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán J, Santiago G, Adams L, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman F, Galán J, Huits R, Hamer D, Vogels C, Morrison A, Michael S, Grubaugh N. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nature Communications 2024, 15: 3508. PMID: 38664380, PMCID: PMC11045810, DOI: 10.1038/s41467-024-47774-8.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsDengue virusDENV-3Rates of severe diseaseMosquito-borne viral diseasePublic health threatPattern of spreadSevere diseaseLocal surveillanceGenomic epidemiologyEpidemiological patternsVirus surveillanceSurveillanceHealth threatSerotypesDiseaseIncreased rateDengueViral diseasesVirusInfected travelersFrequent outbreaksResurgence of Dengue in the Era of Genomic Surveillance and Vaccines.
Huits R, Grubaugh N, Libman M, Hamer D. Resurgence of Dengue in the Era of Genomic Surveillance and Vaccines. Annals Of Internal Medicine 2024, 177: 670-671. PMID: 38498879, DOI: 10.7326/m24-0496.Peer-Reviewed Original ResearchCitationsAltmetricLow antibody levels associated with significantly increased rate of SARS‐CoV‐2 infection in a highly vaccinated population from the US National Basketball Association
Tai C, Haviland M, Kissler S, Lucia R, Merson M, Maragakis L, Ho D, Anderson D, DiFiori J, Grubaugh N, Grad Y, Mack C. Low antibody levels associated with significantly increased rate of SARS‐CoV‐2 infection in a highly vaccinated population from the US National Basketball Association. Journal Of Medical Virology 2024, 96: e29505. PMID: 38465748, DOI: 10.1002/jmv.29505.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAntibody levelsSARS-CoV-2 infectionSARS-CoV-2 antibody levelsPfizer-BioNTech mRNA vaccineHistory of SARS-CoV-2 infectionCox proportional hazards modelsLow antibody levelsProportional hazards modelRisk of infectionMRNA vaccinesRates of SARS-CoV-2 infectionAnalytic cohortPrimary seriesPfizer-BioNTechVaccine doseIncreased rate of SARS-CoV-2 infectionInterquartile rangeBooster schedulesHazards modelSerological testsInfectionSARS-CoV-2Vaccinated individualsAntibodiesAntibody testContribution of climate change to the spatial expansion of West Nile virus in Europe
Erazo D, Grant L, Ghisbain G, Marini G, Colón-González F, Wint W, Rizzoli A, Van Bortel W, Vogels C, Grubaugh N, Mengel M, Frieler K, Thiery W, Dellicour S. Contribution of climate change to the spatial expansion of West Nile virus in Europe. Nature Communications 2024, 15: 1196. PMID: 38331945, PMCID: PMC10853512, DOI: 10.1038/s41467-024-45290-3.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsWest Nile virusEcological niche modelsExpansion of West Nile virusClimate changeWNV circulationNiche modelsNile virusMosquito-borne pathogensEffects of climate changeHuman population changeSpatial expansionContributions of climate changeWest Nile virus circulationEnvironmental changesPublic health threatHuman populationLand-useHuman influencePotential driversRisk of exposureLong-term trendsPopulation densityPopulation changeHealth threatClimate
News & Links
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
- September 27, 2024Source: Yale News
New dengue virus naming system will help identify and track variants
- August 28, 2024
Presence of rare eastern equine encephalitis virus has Northeast towns on high alert
- August 28, 2024
Fauci illness highlights threat of West Nile Virus
- May 23, 2024Source: CIDRAP
International scientists propose additions to dengue virus classification system
Get In Touch
Contacts
Administrative Support
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