papers

key publications

Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic

Cell

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Nature

Tracking virus outbreaks in the twenty-first century

Nature Microbiology

Genomic insights into Zika virus emergence and spread

Cell

Ebola virus glycoprotein with increased infectivity dominated the 2013-2016 epidemic

Cell

Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas

PLOS NTD

Arbovirus coinfection and co-transmission: A neglected public health concern?

PLOS Biology

Misperceived risks of Zika-related microcephaly in India

Trends in Microbiology

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Genome Biology

Multiplexed PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Nature Protocols

Mosquitoes transmit unique West Nile virus populations during each feeding episode

Cell Reports

Genetic drift during systemic arbovirus infection of mosquito vectors leads to decreased relative fitness during host switching

Cell Host & Microbe

research topics

Epidemiology

Evolution & Ecology

Pathogenesis & Immunology

Methods development

Zika virus

West Nile virus

Other virus

Plasmodium

all publications

2019

Grubaugh ND*, Saraf S*, Gangavarapu K*, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH for the GeoSentinel Surveillance Network, Gardner LM, Perkins AT, Baele G, Khan K, Morrison A, Isern S, Michael SM, Andersen KG
Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic 
Cell 
178, 1057–1071 (2019)

paperbioRxivblog postNew York Timesdata

Scroggs SL, Grubaugh ND, Sena JA, Sundararajan A, Schilkey FD, Smith DR,Ebel GD, Hanley KA
Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts
mSphere 4(3), e00291-19 (2019)

paper

Rückert C, Prasad AN, Garcia-Luna SM, Robinson A, Grubaugh ND, Weger-Lucarelli J, Ebel GD
Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infection
Insect Biochemistry and Molecular Biology 109, 13-23 (2019)

paper

Grubaugh ND, Ishtiaq F, Setoh YX, Ko AI
Misperceived Risks of Zika-related Microcephaly in India
Trends in Microbiology 27(5), 381-383 (2019)

paper

Ladner JT, Grubaugh ND, Pybus OG, Andersen KG
Precision epidemiology for infectious disease control
Nature Medicine 25, 206-211 (2019)

paperread cube

Vogels CBF*, Rückert C*, Cavany SM*, Perkins TA, Ebel GD, Grubaugh ND
Arbovirus coinfection and co-transmission: A neglected public health concern?
PLOS Biology 17(1), e3000130 (2019)

paperdata

Grubaugh ND*, Gangavarapu K*, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology 20:8 (2019)

paperbioRxivread cubedata & code

Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG
Tracking virus outbreaks in the twenty-first century
Nature Microbiology 4, 10–19 (2019)

paperread cube

2018

Grubaugh ND
Cause to remain alert: On Zika virus
The Hindu November 10 (2018)

op-ed

Weger-Lucarelli J, Rückert C, Grubaugh ND, Misencik MJ, Armstrong PM, Stenglein PM, Ebel GD, Brackney D
Adventitious viruses persistently infect three commonly used mosquito cell lines
Virology 521, 175-180 (2018)

paperbioRxiv

Magnani DM, Roger TF, Maness NJ, Grubaugh ND, Beutler N, Bailey VK, Gonzalez-Nieto L, Gutman ML, Pedreno-Lopez N, Kwal JM, Ricciardi MJ, Myers TA, Julander JG, Bohm RP, Gilbert MH, Schiro F, Aye PP, Blair RV, Martins MA, Falkenstein KP, Kaur A, Curry CL, Kallas EG, Desrosiers RC, Goldshmidt-Clermont PJ, Whitehead SS, Andersen KG, Bonaldo MC, Lackner AA, Panganiban AT, Burton DR, Watkins DI
Fetal demise and failed antibody therapy during Zika virus infection of pregnant macaques
Nature Communications 9(1624), (2018)

paper

Ma S, Cahalan S, LaMonte G, Grubaugh ND, Zeng W, Murthy SE, Paytas E, Gamini R, Lukacs V, Whitwam T, Loud M, Lohia R, Berry L, Khan SM, Janse CJ, Bandell M, Schmedt C, Wengelnik K, Su AI, Honore E, Winzeler EA, Andersen KG, Patapoutian A
Common PIEZO1 allele in African populations causes RBC dehydration and attenuates Plasmodium infection
Cell 173(2), 1-13 (2018)

paperbioRxivblog post

Grubaugh ND, Faria NR, Andersen KG, Pybus OG
Genomic insights into Zika virus emergence and spread
Cell 172(6), 1160-1162 (2018)

paper

Gardner LM, Bóta A, Gangavarapu K, Kraemer MUG, Grubaugh ND
Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas
PLOS Neglected Tropical Diseases 12(1), e0006194 (2018)

paper

2017

Ricciardi MJ, Magnani DM, Grifoni A, Kwon Y-C, Gutman MJ, Grubaugh ND, Gangavarapu K, Sharkey M, Silveira CGT, Bailey VK, Pedreno-Lopez N, Gonzalez-Nieto L, Maxwell HS, Domingues A, Martins MA, Pham J, Weiskopf D, Altman J, Kallas EG, Andersen KG, Stevenson M, Lichtenberger P, Choe H, Whitehead SS, Sette A, Watkins DI
Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naïve individual during the 2016 outbreak in Miami, FL
PLOS Neglected Tropical Diseases 11(12), e0006000 (2017)

paper

Black A, Potter B, Dudas G, Feldstein L, Grubaugh ND, Andersen KG, Ellis BR, Ellis EM, Bedford T
Genetic characterization of the Zika virus epidemic in the US Virgin Islands
bioRxiv 113100 (2017)

bioRxiv

Magnani DM, Rogers TF, Beutler N, Ricciardi MJ, Bailey VK, Gonzalez-Nieto L, Briney B, Sok D, Le K, Strubel A, Gutman MJ, Pedreño-Lopez N, Grubaugh ND, Silveira CGT, Maxwell HS, Domingues A, Martins MA, Lee DE, Okwuazi EE, Jean S, Strobert EA, Chahroudi A, Silvestri G, Vanderford TH, Kallas EG, Desrosiers RC, Bonaldo MC, Whitehead SS, Burton DR, Watkins DI
Neutralizing human monoclonal antibodies prevent Zika virus infection in macaques
Science Translational Medicine 9(410), eaan8184 (2017)

paper

Fauver JR, Gendernalik A, Weger-Lucarelli, Grubaugh ND, Brackney DE, Foy BD, Ebel GD
The use of xenosurveillance to detect human bacteria, parasites, and viruses in mosquito bloodmeals
The American Journal of Tropical Medicine Hygiene 97(2), 324-329 (2017)

paper

Grubaugh ND*, Ladner JT*, Kraemer MUG*, Dudas G*, Tan AL*, Gangavarapu K*, Wiley MR*, White S*, Theze J, Magnani DM, Prieto K, Reyes D, Bingham A, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Lou C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC, Lichtenberger PN, Ricciardi M, Bailey VK, Watkins DI, Cone MR, Kopp EW, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Nature 545(7656), 401-405 (2017)

paperbioRxivpreview

Faria NR, Quick J, Morales I, Theze J, Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Ragwhani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chis CY, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, Franca RF, Magalhaes T, Marques ET, Jaenish T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Moura Neto JP, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman N, Pybus OG
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Nature 545(7656), 406-410 (2017)

paperbioRxiv

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Park DJ, Lou CY, Barnes KG, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Gelvez Ramirez RM, Miranda Montoya, MC, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar Centeno LA, Mattar S, Lorenzana I, Cerbino-Neto J, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael S, Bozza F, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC
Zika virus evolution and spread in the Americas
Nature 545(7656), 411-415 (2017)

paperbioRxiv

Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lexis-Ximenez LL, Jesus JG, Giovanetti M, Hill S, Black A, Bedford T, Carrol MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria N, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Nature Protocols 12(6), 1261-1276 (2017)

paperbioRxivprotocols

Grubaugh ND, Andersen KG
Experimental evolution to study virus emergence
Cell 169(1), 1-3 (2017)

paper

Grubaugh ND, Fauver JR, Rückert C, Weger-Lucarelli J, Garcia-Luna S, Murrieta RA, Gendernalik A, Smith DR, Brackney DE, Ebel GD
Mosquitoes transmit unique West Nile virus populations during each feeding episode
Cell Reports 19(4), 709-718 (2017)

2016

Grubaugh ND*, Rückert C*, Armstrong PM, Bransfield A, Anderson JF, Ebel GD, Brackney DE
Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution
Virus Evolution 2(2), vew033 (2016)

paper

Fauver JR, Grubaugh ND, Krajacich BJ, Weger-Lucarelli J, Lakin SM, Fakoli LS, Bolay FK, Diclaro JW, Dabire KR, Foy BD, Brackney DE, Ebel GE, Stenglein MD
West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegavirueses, and totiviruses
Virology 498, 288-299 (2016)

paper

Diehl WE*, Lin AE*, Grubaugh ND*, Carvalho LM*, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J
Ebola virus glycoprotein with increased infectivity dominated the 2013–2016 epidemic
Cell 167(4), 1088-1098, e6 (2016)

paper

Grubaugh ND, Ebel GD
Dynamics of West Nile virus evolution in mosquito vectors
Current Opinion in Virology 21, 132-138 (2016)

paper

Grubaugh ND, Weger-Lucarelli J, Murrieta RA, Fauver JR, Garcia-Luna SM, Prasad AN, Black WC, Ebel GD
Genetic drift during systemic arbovirus infection of mosquito vectors leads to decreased relative fitness during host switching
Cell Host & Microbe 19(4), 481-492 (2016)

paper

Misencik MJ, Grubaugh ND, Andreadis TG, Ebel GD, Armstrong PM
Isolation of a novel insect-specific Flavivirus from Culiseta melanura in the Northeastern United States
Vector-Borne and Zoonotic Diseases 16(3), 181-190 (2016)

paper

Grubaugh ND, Massey A, Shives KD, Stenglein MD, Ebel GD, Beckham JD
West Nile virus population structure, injury, and interferon-stimulated gene expression in the brain from a fatal case of encephalitis
Open Forum Infectious Diseases 3(1), ofv182 (2016)

paper

2015

Fauver JR, Pecher L, Schurich JA, Bolling BG, Calhoon M, Grubaugh ND, Burkhalter KL, Eisen L, Andre BG, Nasci RS, LeBailly A, Ebel GD, Moore CG
Temporal and spatial variability of entomological risk indices for West Nile virus infection in Northern Colorado: 2006-2013
Journal of Medical Entomology tjv234 (2015)

paper

Grubaugh ND*, Smith DR*, Brackney DE, Bosco-Lauth, AM, Fauver JR, Campbell CL, Felix TA, Romo H, Duggal NK, Dietrich EA, Eike T, Beane JE, Bowen RA, Black WC, Brault AC, Ebel GD
Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness
PLOS Pathogens 11(5), e100487 (2015)

paper

Grubaugh ND, Sharma S, Krajacich BJ, Fakoli III LS, Bolay FK, Diclaro II JW, Johnson WE, Ebel GD, Foy BD, Brackney DE
Xenosurveillance: a novel mosquito-based approach for examining the human-pathogen landscape
PLOS Neglected Tropical Diseases 9(3), e0003628 (2015)

paper

Krajacich BJ, Slade JR, Mulligan RF, LaBrecque B, Alout H, Grubaugh ND, Meyers JI, Fakoli III LS, Bolay FK, Brackney DE, Burton TA, Seaman JA, Diclaro II JW, Dabire RK, Foy BD
Sampling host-seeking anthropophilic mosquito vectors in West Africa: comparisons of an active human-baited tent-trap against gold standard methods
The American Journal of Tropical Medicine Hygiene 92(2), 415-421 (2015)

paper

2014

Alout H, Krajacich BJ, Meyers JI, Grubaugh ND, Brackney DE, Kobylinski KC, Diclaro II JW, Bolay FK, Fakoli III LS, Diabate A, Dabire RK, Bougma RW, Foy BD
Evaluation of ivermectin mass drug administration for malaria transmission control across different West African environments
Malaria 13(1), 417 (2014)

paper

2013

Grubaugh ND, McMenamy SS, Turell MJ, Lee JS
Multi-gene detection and identification of mosquito-borne RNA viruses using an oligonucleotide microarray
PLOS Neglected Tropical Diseases 7(8), e2349 (2013)

paper

Grubaugh ND, Petz LN, Melanson VR, McMenamy SS, Turell MJ, Long LS, Pisarcik SE, Kengluecha A, Jaichapor B, O’Guinn ML, Lee JS
Evaluation of a field-portable DNA microarray platform and nucleic acid amplification strategies for the detection of arboviruses, arthropods, and bloodmeals
The American Journal of Tropical Medicine Hygiene 88(2), 245-253 (2013)

paper

Lee JS, Grubaugh ND, Kondig JP, Turell MJ, Kim HC, Klein TA, O’Guinn ML
Isolation and genomic characterization of Chaoyang virus strain ROK144 from Aedes vexans nipponii from the Republic of Korea
Virology 495(2), 220-224 (2013)

paper

*co-first or co-senior author