Nathan Grubaugh, PhD
Associate 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
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
- 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 Ko, MD
Akiko Iwasaki, PhD
Rebecca Earnest, MPH
Wade Schulz, MD, PhD
Benjamin Goldman-Israelow, MD, PhD
Disease Outbreaks
West Nile virus
Dengue Virus
Aedes
Chikungunya virus
Culex
Publications
2025
Implications of successive blood feeding on Wolbachia-mediated dengue virus inhibition in Aedes aegypti mosquitoes
Johnson R, Breban M, Nolan B, Sodeinde A, Ott I, Ross P, Gu X, Grubaugh N, Perkins T, Brackney D, Vogels C. Implications of successive blood feeding on Wolbachia-mediated dengue virus inhibition in Aedes aegypti mosquitoes. Nature Communications 2025, 16: 6971. PMID: 40730791, PMCID: PMC12307751, DOI: 10.1038/s41467-025-62352-2.Peer-Reviewed Original ResearchCitationsAltmetricIntegrated 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 ResearchMeSH Keywords and ConceptsConceptsDominant 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 dataInfectionType 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort
Jayavelu N, Qi J, Milliren C, Ozonoff A, Liu S, Levy O, Baden L, Melamed E, McComsey G, Cairns C, Schaenman J, Shaw A, Hafler D, Corry D, Kheradmand F, Atkinson M, Brakenridge S, Higuita N, Metcalf J, Hough C, Messer W, Pulendran B, Nadeau K, Davis M, Geng L, Sesma A, Simon V, Krammer F, Bime C, Calfee C, Bosinger S, Eckalbar W, Steen H, Maecker H, Becker P, Augustine A, Holland S, Rosen L, Lee S, Vaysman T, Ozonoff A, Diray-Arce J, Chen J, Kho A, Milliren C, Hoch A, Chang A, McEnaney K, Barton B, Lentucci C, Murphy M, Saluvan M, Shaheen T, Liu S, Syphurs C, Albert M, Hayati A, Bryant R, Abraham J, Thomas S, Cooney M, Karoly M, Altman M, Jayavelu N, Presnell S, Kohr B, Jancsyk T, Arnett A, Peters B, Overton J, Vita R, Westendorf K, Overton J, Levy O, Steen H, van Zalm P, Fatou B, Smolen K, Viode A, van Haren S, Jha M, Stevenson D, Odumade O, Baden L, Mendez K, Lasky-Su J, Tong A, Rooks R, Desjardins M, Sherman A, Walsh S, Mitre X, Cauley J, Li X, Evans B, Montesano C, Licona J, Krauss J, Issa N, Chang J, Izaguirre N, Hutton S, Michelotti G, Wong K, Tebbutt S, Shannon C, Sekaly R, Fourati S, McComsey G, Harris P, Sieg S, Ribeiro S, Cairns C, Haddad E, Kutzler M, Bernui M, Cusimano G, Connors J, Woloszczuk K, Joyner D, Edwards C, Lee E, Lin E, Melnyk N, Powell D, Kim J, Goonewardene I, Simmons B, Smith C, Martens M, Croen B, Semenza N, Bell M, Furukawa S, McLin R, Tegos G, Rogowski B, Mege N, Ulring K, Schearer P, Sheidy J, Nagle C, Seyfert-Margolis V, Rouphael N, Bosinger S, Boddapati A, Tharp G, Pellegrini K, Johnson B, Panganiban B, Huerta C, Anderson E, Samaha H, Sevransky J, Bristow L, Beagle E, Cowan D, Hamilton S, Hodder T, Bechnak A, Cheng A, Mehta A, Ciric C, Spainhour C, Carter E, Scherer E, Usher J, Hellmeister K, Hussaini L, Hewitt L, Mcnair N, Ribeiro S, Wimalasena S, Fernandez-Sesma A, Simon V, Krammer F, Van Bakel H, Kim-Schulze S, Reiche A, Qi J, Lee B, Carreño J, Singh G, Raskin A, Tcheou J, Khalil Z, van de Guchte A, Farrugia K, Khan Z, Kelly G, Srivastava K, Eaker L, Bermúdez-González M, Mulder L, Beach K, Saksena M, Altman D, Kojic E, Sominsky L, Azad A, Bielak D, Kawabata H, Yellin T, Fried M, Sullivan L, Morris S, Kleiner G, Stadlbauer D, Dutta J, Xie H, Patel M, Nie K, Rahman A, Messer W, Hough C, Siegel S, Sullivan P, Lu Z, Brunton A, Strand M, Lyski Z, Coulter F, Micheleti C, Maecker H, Pulendran B, Nadeau K, Rosenberg-Hasson Y, Leipold M, Sigal N, Rogers A, Fernandes A, Manohar M, Do E, Chang I, Lee A, Blish C, Din H, Roque J, Geng L, Artandi M, Davis M, Ahuja N, Yang S, Chinthrajah S, Hagan T, Reed E, Schaenman J, Salehi-Rad R, Rivera A, Pickering H, Sen S, Elashoff D, Ward D, Brook J, Sanchez E, Llamas M, Perdomo C, Magyar C, Fulcher J, Erle D, Calfee C, Hendrickson C, Kangelaris K, Nguyen V, Lee D, Chak S, Ghale R, Gonzalez A, Jauregui A, Leroux C, Altamirano L, Rashid A, Willmore A, Woodruff P, Krummel M, Carrillo S, Ward A, Langelier C, Patel R, Wilson M, Dandekar R, Alvarenga B, Rajan J, Eckalbar W, Schroeder A, Fragiadakis G, Tsitsiklis A, Mick E, Guerrero Y, Love C, Maliskova L, Adkisson M, Leligdowicz A, Beagle A, Rao A, Sigman A, Samad B, Curiel C, Shaw C, Tietje-Ulrich G, Milush J, Singer J, Vasquez J, Tang K, Betancourt L, Santhosh L, Pierce L, Paz M, Matthay M, Thakur N, Rodriguez N, Sutter N, Jones N, Sinha P, Prasad P, Lota R, Rashid S, Asthana S, Bhide S, Lea T, Abe-Jones Y, Hafler D, Montgomery R, Shaw A, Kleinstein S, Gygi J, Pawar S, Konstorum A, Chen E, Cotsapas C, Wang X, Xu L, Dela Cruz C, Iwasaki A, Mohanty S, Nelson A, Zhao Y, Farhadian S, Asashima H, Chaudhary O, Coppi A, Fournier J, Muenker M, Nelson A, Raddassi K, Rainone M, Ruff W, Salahuddin S, Shulz W, Vijayakumar P, Wang H, Wunder E, Young H, Ko A, Wang X, Duchen D, Esserman D, Guan L, Brito A, Rothman J, Grubaugh N, Corry D, Kheradmand F, Song L, Nelson E, Metcalf J, Higuita N, Sinko L, Booth J, Drevets D, Brown B, Kraft M, Bime C, Mosier J, Erickson H, Schunk R, Kimura H, Conway M, Francisco D, Molzahn A, Wilson C, Schunk R, Hughes T, Sierra B, Atkinson M, Brakenridge S, Ungaro R, Manning B, Moldawer L, Oberhaus J, Guirgis F, Borresen B, Anderson M, Ehrlich L, Melamed E, Maguire C, Wylie D, Rousseau J, Hurley K, Geltman J, Siles N, Rogers J, Augustine A, Diray-Arce J, Haddad E, Sekaly R, Kraft M, Woodruff P, Erle D, Ehrlich L, Montgomery R, Becker P, Altman M, Fourati S. Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort. Journal Of Allergy And Clinical Immunology Global 2025, 4: 100515. PMID: 40709330, PMCID: PMC12284355, DOI: 10.1016/j.jacig.2025.100515.Peer-Reviewed Original ResearchCitationsConceptsT2 immune responseClinical outcomesVirus loadImmune responseSARS-CoV-2Primary siteSusceptibility to respiratory viral infectionsType 2 immune responsesAntibody titersCellular markersPrimary site of infectionSeverity of respiratory illnessRespiratory viral infectionsIL-13 levelsDegree of respiratory supportAssociated with less severe COVID-19Site of infectionLow virus loadSevere COVID-19Effects of SARS-CoV-2Severe coronavirus diseaseDiagnosis of asthmaRespiratory supportCoronavirus severe acute respiratory syndrome coronavirus 2Blood cytometryPhylogenetic insights into the transmission dynamics of arthropod-borne viruses
Hill V, Dellicour S, Giovanetti M, Grubaugh N. Phylogenetic insights into the transmission dynamics of arthropod-borne viruses. Nature Reviews Genetics 2025, 1-15. PMID: 40481331, PMCID: PMC12257617, DOI: 10.1038/s41576-025-00854-x.Peer-Reviewed Original ResearchCitationsAltmetricConceptsArthropod-borne virusesPhylogenetic insightsPhylogenetic modelsGenomic surveillanceAnimal populationsVertebrate hostsBluetongue virusArthropod vectorsHuman clinical dataEpidemiological dynamicsVeterinary healthClimate changeComplex transmission cyclesClinical dataVirusTransmission cycleTemporal patternsEpidemiological dataComplication surveillancePhylogeneticallyCrimean-Congo haemorrhagic feverEarly Release - Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States - Volume 31, Supplement—May 2025 - Emerging Infectious Diseases journal - CDC
Pham K, Chaguza C, Lopes R, Cohen T, Taylor-Salmon E, Wilkinson M, Katebi V, Grubaugh N, Hill V. Early Release - Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States - Volume 31, Supplement—May 2025 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2025, 31: s45-s56. PMID: 40359081, PMCID: PMC12078544, DOI: 10.3201/eid3113.240981.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsThe impact of orthopoxvirus vaccination and Mpox infection on cross-protective immunity: a multicohort observational study
Crandell J, Monteiro V, Pischel L, Fang Z, Conde L, Zhong Y, Lawres L, de Asis G, Maciel G, Zaleski A, Lira G, Higa L, Breban M, Vogels C, Caria J, Pinto A, Almeida V, Maltez F, Cordeiro R, Póvoas D, Grubaugh N, Aoun-Barakat L, Grifoni A, Sette A, Castineiras T, Chen S, Yildirim I, Vale A, Omer S, Lucas C. The impact of orthopoxvirus vaccination and Mpox infection on cross-protective immunity: a multicohort observational study. The Lancet Microbe 2025, 6: 101098. PMID: 40311645, DOI: 10.1016/j.lanmic.2025.101098.Peer-Reviewed Original ResearchCitationsAltmetricConceptsT cellsAntigenic distanceMpox virusBreadth of immune responsesSmallpox vaccineThird-generation smallpox vaccineImmune responseObservational studyCross-reactive immune responsesT cell cross-reactivityT cell memoryT cell responsesImmune memory responseVaccina virusCross-neutralising activityFc-mediated functionsMucosal humoral responsesVirus neutralisation titresCross-reactive responsesCross-protectionCross-protective immunityCowpox virusNeutralising antibody titresAntibody effector functionsEffector functionsDifferent Clinical Severity and Outcomes in a Cohort of Patients With Dengue With Warning Signs in an Endemic Latin American City
Gómez-Zambrano M, Torres-Hernández D, Murillo-Ortiz M, Hurtado I, Dávalos D, Cantor E, López P, Grubaugh N, López-Medina E. Different Clinical Severity and Outcomes in a Cohort of Patients With Dengue With Warning Signs in an Endemic Latin American City. Open Forum Infectious Diseases 2025, 12: ofaf227. PMID: 40271160, PMCID: PMC12015475, DOI: 10.1093/ofid/ofaf227.Peer-Reviewed Original ResearchCitationsAltmetricUnravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage
Pereira J, Slavov S, Brcko I, Ribeiro G, de Souza V, Ribeiro I, De Lima I, Borges G, de Lima Furtado K, da Silva Chagas S, da Costa P, Adelino T, de Melo Iani F, Alcantara L, Hill V, Grubaugh N, Sampaio S, Elias M, Giovanetti M, Lima A. Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage. Virus Evolution 2025, 11: veaf034. PMID: 40589497, PMCID: PMC12208352, DOI: 10.1093/ve/veaf034.Peer-Reviewed Original ResearchCitationsAltmetric
2024
Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development
Klontz E, Chowdhury N, Holbrook N, Solomon I, Telford S, Aliota M, Vogels C, Grubaugh N, Helgager J, Hughes H, Velez J, Piantadosi A, Chiu C, Lemieux J, Branda J. Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development. Viruses 2024, 16: 1653. PMID: 39599768, PMCID: PMC11599074, DOI: 10.3390/v16111653.Peer-Reviewed Original ResearchCitationsConceptsGenome sequenceDiversity of genomic sequencesHuman infectionsPCR assay designVirus genome sequencesAssay designIn silico analysisBiology of infectionViral genomic dataGenetic diversityGenomic dataSensitivity of PCRGenomeCladePCR assayHuman diseasesVirulent strainsPCR designPowassan virusSequenceImmunocompromised patientsPCRTick-borne virusesAssay developmentClinical diagnosticsEarly Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC
Grubaugh N, Torres-Hernández D, Murillo-Ortiz M, Dávalos D, Lopez P, Hurtado I, Breban M, Bourgikos E, Hill V, López-Medina E. Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 2391-2395. PMID: 39378873, PMCID: PMC11521178, DOI: 10.3201/eid3011.241031.Peer-Reviewed Original ResearchCitationsAltmetric
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- 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).
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