papers

key publications

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

medRxiv

Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity

Nature

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages

medRxiv

Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated individuals

medRxiv

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Cell

Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil

Nature Communications

SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity

Med

Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2

New England Journal of Medicine

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

Cell

Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain

PLOS Pathogens

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

Cell

Tracking virus outbreaks in the twenty-first century

Nature Microbiology

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

Genome Biology

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

PLOS NTD

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

Nature

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

Cell

research topics

Epidemiology

Evolution
& Ecology

Pathogenesis & Immunology

Methods
development

Zika &
dengue virus

West Nile &
Powassan virus

SARS-CoV-2

Other viruses/
microbes

pre-prints

Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL, New England Variant Investigation Team, Tewhey R*, Adams MD*, Park DJ*, Lemieux JE*, Grubaugh ND*
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
medRxiv 21264641 (2021)

medRxivgithub

Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Hill SC, Danish Covid-19 Genome Consortium, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxamn S, Suchard MA, Grubaugh ND*, Baele G*, Faria NR*
Global disparities in SARS-CoV-2 genomic surveillance
medRxiv 21262393 (2021)

medRxiv

Baaijens JA*, Zulli A*, Ott IM*, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli K, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB, Yale SARS-CoV-2 Genomic Surveillance Initiative, Hanage WP, Grubaugh ND*, Peccia J*, Baym M*
Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
medRxiv 21262938 (2021)

medRxiv

Petrone ME*, Rothman JE*, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St. George K, Adams MD, Grubaugh ND
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages
medRxiv 21259859 (2021)

medRxiv

Alpert T, Vogels CBF, Breban MI, Petrone ME, Yale IMPACT Research Team, Wyllie AL, Grubaugh ND, Fauver JR
Sequencing SARS-CoV-2 genomes from saliva

medRxiv 21259289 (2021)

medRxiv

Lee M*, Sallah YH*, Petrone ME*, Ringer M, Cosentino D, Vogels CBF, Fauver JR, Alpert T, Grubaugh ND, Gupta S
COVID-19 Outcomes and Genomic characterization of SARS-CoV-2 isolated from Veterans in New England States
medRxiv 21256222 (2021)

medRxiv

Kissler SM*, Fauver JR*, Mack C*, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Ho DD, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Grubaugh ND*, Grad YH*
Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated individuals
medRxiv 21251535 (2021)

medRxiv

Allicock OM*, Petrone ME*, Yolda-Carr D*, Breban MI, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL
Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics
medRxiv
21250946 (2021)

medRxiv

George S, Chattopadhyay Pal A, Gagnon J, Timalsina S, Singh P, Vydyam P, Munshi M, Chiu JE, Renard I, Harden CA, Ott IM, Watkins AE, Vogels CBF, Lu P, Tokuyama M, Venkataraman A, Casanovas-Massana A, Wyllie AL, Rao C, Campbell M, Farhadian SF, Grubaugh ND, Dela Cruz CS, Ko AI, Yale IMPACT Research Team, Berna Perez A, Akaho E, Moledina DG, Testani J, John AR, Ledizet M, Ben Mamoun C
Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 patients
medRxiv 21250637 (2021)

medRxiv

Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T,  Eun Oh J, Park A, Casanovas-Massana A, Vogels CBF, Muenker MC, Zell J, Fournier JB, Campbell M, Chiorazzi M, Fuentes ER, Yale IMPACT Team, Grubaugh ND, Farhadian S, Dela Cruz CS, Ko AI, Schulz WL, Ring A, Ma S, Omer S, Wyllie AL, Iwasaki A
Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality
medRxiv 21249236 (2021)

medRxiv

Pagano N, Laurent-Rolle M, Hsu JC, Yale IMPACT Research Team, Vogels CBF, Grubaugh ND, Manuelidis L
Detection of long SARS-CoV-2 nucleocapsid sequences in peripheral blood monocytes collected soon after hospital admission
bioRxiv 423113 (2020)

bioRxiv

Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Brickman Raredon MS, Hoehn K, Wang G, Wang Z, Deiuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Minasyan M, Yale IMPACT Research Team, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS
Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19
medRxiv 20153437 (2020)

medRxivdata

Moore AJ, Nakahata MI, Kalinich CC, Nyhan K, Bromberg DJ, Shi X, Ko AI, Grubaugh ND, Casanovas-Massana A, Wyllie AL
The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis
medRxiv 20144543 (2020)

medRxiv

Cheemarla NR, Brito AF, Fauver JR, Alpert T, Vogels CBF, Omer SB, Ko AI, Grubaugh ND, Landry ML, Foxman EF
Host response-based screening to identify undiagnosed cases of COVID-19 and expand testing capacity
medRxiv 20109306 (2020)

medRxiv

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

peer-reviewed publications

2021

Mao T, Israelow B, Lucas C, Vogels CBF, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Yale SARS-CoV-2 Genomic Surveillance Initiative, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A
A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice
Journal of Experimental Medicine 219(1):e20211818 (2021)

paperbioRxiv

Santiago GA*, Kalinich CC*, Cruz-López F, González GL, Flores B, Hentoff A, Charriez KN, Fauver JR, Adams LE, Sharp TM, Black A, Bedford T, Ellis E, Ellis B, Waterman SH, Paz-Bailey G, Grubaugh ND*, Muñoz-Jordán JL*
Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016–2017
Emerging Infectious Diseases 27(11), (2021)

paper

Klein J*, Brito AF*, Trubin P*, Lu P*, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Yale IMPACT Research Team, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B*, Iwasaki A*, Azar MM*
Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient
Journal of Infectious Diseases jiab553 (2021)

papermedRxiv

Lucas C*, Vogels CBF*, Yildirim I*, Rothman J, Lu P, Monteiro V, Gelhausen JR, Campbell M, Silva J, Tabachikova A, Munker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Yale SARS-CoV-2 Genomic Surveillance Initiative, Shaw AC, Ko AI, Omer SA*, Grubaugh ND*, Iwasaki A*
Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity

Nature
In-Press Preview (2021)

papermedRxiv

Bart SM, Flaherty E, Alpert T, Carlson S, Fasulo L, Earnest R, White EB, Dickens N, Brito AF, Grubaugh ND, Hadler JL, Sosa LE
Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020
Emerging Infectious Diseases (27(10) (2021)

paper

Cevik M, Grubaugh ND, Iwasaki A, Openshaw P
COVID-19 vaccines: Keeping pace with SARS-CoV-2 variants
Cell In-Press Preview (2021)

paper

Mack CD, Tai C, Sikka R, Grad YH, Maragakis LL, Grubaugh ND, Anderson DJ, Ho D, Merson M, Samant RM, Fauver JR, Barrett J, Sims L, DiFiori J
SARS-CoV-2 Reinfection: A Case Series from a 12-Month Longitudinal Occupational Cohort
Clinical Infectious Diseases ciab738 (2021)

paper

Beddingfield BJ, Hartnett JN, Wilson RB, Kulakosky PC, Andersen KG, Robles-Sikisaka R, Grubaugh ND, Aybar A, Nunez M-Z, Fermin CD,  Garry RF
Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay
Viruses 13(9), 1771 (2021)

paper

Mytle N, Leyrer S, Inglefield JR, Harris AM, Hickey TE, Minang J, Lu H, Ma Z, Andersen H, Grubaugh ND, Guina T, Skiadopoulos MH, Lacy MJ
Influenza Antigens NP and M2 Confer Cross Protection to BALB/c Mice against Lethal Challenge with H1N1, Pandemic H1N1 or H5N1 Influenza A Viruses
Viruses 13(9), 1708 (2021)

paper

Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos Jr G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG
Emergence of an early SARS-CoV-2 epidemic in the United States
Cell 184(19) P4939-4952.E15 (2021)

papermedRxiv

Kissler SM*, Fauver JR*, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho D, Grubaugh ND*, Grad YH* 
Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies 
PLOS Biology 19(7): e3001333 (2021)

papermedRxivdatatwitter thread

Wang EY*, Mao T*, Klein J*, Dai Y*, Huck JD, Liu F, Zheng NS, Zhou T, Israelow B, Wong P, Lucas C, Silva J, Eun Oh J, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Yale IMPACT Team, Dela Cruz CS, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A*, Ring AM* 
Diverse Functional Autoantibodies in Patients with COVID-19
Nature
 595, 283–288 (2021)

papermedRxiv

Novelli G, Biancolella M, Mehrian-Shai R, Colona VL, Brito AF, Grubaugh ND, Vasiliou V, Luzzatto L, Reichardt JKV
COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy
Human Genomics 15, 27 (2021) 

paper

Brito AF*, Machado LC*, Oidtman RJ*Siconelli MJL*, Tran QM, Fauver JR, Carvalho RDO, Dezordi FZ, Pereira MR, Castro-Jorge LA, Minto ECM, Passos LMR, Kalinich CC, Petrone ME, Allen E, Espana GC, Huang AT, Cummings DAT, Baele G, Franca RFO, Fonseca BAL*, Perkins TA*, Wallau GL*, Grubaugh ND
Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
Nature Communications 12:2619, (2021)

papermedRxivdatatwitter thread

Vogels CBF*, Breban MI*, Ott IMAlpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ, Network for Genomic Surveillance in South Africa, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JF*, Grubaugh ND*
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

PLOS Biology 
19(5): e3001236, (2021)

papermedRxivprotocol

Lucas C*, Klein J*, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B,  Vogels CBF, Muenker MC, Chang C-H, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Yale IMPACT Research Team, Wyllie AL, Campbell M, Lee A, Chun HJ, Grubaugh ND, Schulz WL, Farhadian S, Dela Cruz C, Ring AI, Shaw A, Wisnewski AV, Yildirim I, Ko AI, Omer S, Iwasaki A 
Delayed production of neutralizing antibodies correlates with fatal COVID-19
Nature Medicine
 27, 1178–1186 (2021)

papermedRxiv

Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano CM, Tang Z, Pope SD,  Song E, Vogels CBF,  Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Yale IMPACT Team, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF
Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface
Med
2(5) P591-610.E10 (2021)

papermedRxiv

Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman N, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JS, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF
Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Cell Reports Medicine
 2(5) 100288 (2021)

paperbioRxiv



Alpert T*, Brito AF*, Lasek-Nesselquist E*, Rothman J*, Valesano AL*, MacKay MJ*, Petrone ME, Breban MI, Watkins AE, Vogels CBF, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Cong L, Peaper DR, Landry ML, Cook PW, Fauver JR*, Mason CE*, Lauring AS*, St. George K*, MacCannell DR*, Grubaugh ND*  
Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States
Cell 184(10), P2595-2604.E13 (2021)

papermedRxivjournal cover

Brito AF, Baele G, Nahata KD, Grubaugh ND, Pinney JW
Intrahost speciations and host switches played an important role in the evolution of herpesviruses
Virus Evolution veab025 (2021)

paper

Ott IM*, Strine MS*, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CBF, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Yale IMPACT Research Team, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND*, Wilen CB*, Wyllie AL*
Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva
Emerging Infectious Diseases
27 (2021)

papermedRxiv

Watkins AE, Fenichel EI, Weinberger DM, Vogels CBF, Brackney DE, Casanovas-Massana A, Campbell M, Fournier J, Bermejo S, Datta R, Yale IMPACT Research Team, Dela Cruz CS, Farhadian SF, Iwasaki A, Ko AI, Grubaugh ND*, Wyllie AL*
Increasing SARS-CoV-2 Testing Capacity with Pooled Saliva Samples 
Emerging Infectious Diseases 27 (2021)

papermedRxivgithub

Peters J, Alhasana S, Vogels, CBF, Grubaugh ND, Farhadian S, Longbrakea EE
MOG-associated encephalitis following SARS-COV-2 infection
Multiple Sclerosis and Related Disorders 50 (2021)

paper

Weiss JJ, Attuquayefio TN, White EB, Li F, Herz RS, White TL, Campbell M, Geng B, Datta R, Wyllie AL, Grubaugh ND, Casanovas-Massana A, Muenker MC, Handoko R, Iwasaki A, Yale IMPACT Research Team, Martinello RA, Ko AI, Small DM, Farhadian SF
Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection
PLoS ONE e0248025 (2021)

papermedRxiv

Grubaugh ND, Hodcroft EB, Fauver JR, Phelan AL, Cevik M
Public health actions to control new SARS-CoV-2 variants
Cell 184(5), 1127-1132 (2021)

paper

Petrone ME*, Earnest R*, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND*, Tapia L*  
Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Nature Communications 12:151, (2021)

papermedRxiv

Vogels CBF*, Watkins AE*, Harden CA*, Brackney DE*, Shafer J, Wang J, Caraballo C, Kalinich CCOtt IMFauver JR, Kudo E, Lu P, Venkataraman A, Tokuyama M, Moore AJ, Muenker MC, Casanovas-Massana A, Fournier J, Bermejo S, Campbell M, Datta R, Nelson A, Yale IMPACT Research Team, Dela Cruz CS, Ko AI, Iwasaki A, Krumholz HM, Matheus JD, Hui P, Liu C, Farhadian S, Sikka R, Wyllie AL*, Grubaugh ND*
SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity

Med
 2 (3), 263-280 (2021)

papermedRxivwebsiteprotocol

2020

Petrone M 
Virus genomics as a clinical and epidemiological tool 

EBioMedicine
62, 103141 (2020)

paper

Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P 
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework 
Nature Communications 11:5620, (2020)

paperbioRxivgithub

Kalinich CC*, Jensen CG*, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF,  Fauver JR, Grubaugh ND*, Brito AF*
Real-time public health communication of local SARS-CoV-2 genomic epidemiology
PLOS Biology 3000869 (2020)  

paperWebsitedata

Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Sanchez-San Martin C, Li T, Martyn C, Oliveira GM, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY,  Van Rompay KA, Coffey LL
Two sides of a coin: a Zika virus mutation selected in pregnant rhesus macaques promotes fetal infection in mice but at a cost of reduced fitness in nonpregnant macaques and diminished transmissibility by vectors
Journal of Virology
 94(24), e01605-20 (2020)

paperbioRxiv

Grubaugh ND, Hanage WP, Rasmussen AL 
Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear
Cell
  182(4), 794-795 (2020)

paper

Lucas C, Wong P, Klein J, Castro T, Silva J, Sundaram M, Ellingson M, Mao T, Oh J, Israelow B, Tokuyama M, Lu P, Venkataraman A, Park A, Mohanty S, Wang H, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott I, Moore M, Muenker C, Fournier J, Campbell M, Odio C,  Casanovas-Massana A, Yale IMPACT Research Team, Herbst R, Shaw A, Medzhitov R, Schulz WL, Grubaugh NG, Dela Cruz C, Farhadian S, Ko AI, Omer S, Iwasaki A
Longitudinal immunological analyses reveal inflammatory misfiring in severe COVID-19 patients
Nature 584, 463–469 (2020)

papermedRxiv

Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Yale IMPACT Research Team, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND*, Iwasaki A*
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
PLOS Biology 18(10), e3000867 (2020)

paperbioRxiv

Takahashi T*, Ellingson M*, Wong P*, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh J, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang E, Casanovas A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore A, Yale IMPACT Research Team, Shaw A, Fournier J, Odio C, Farhadian S, Dela Cruz C, Grubaugh ND, Schultz W, Ko AI, Ring A, Omer S, Iwasaki A
Sex differences in immune responses to SARS-CoV-2 that underlie disease outcomes
Nature 588, 315–320 (2020)

papermedRxiv

Peccia J*, Zulli A*, Brackney DE*, Grubaugh ND, Kaplan EH, Casanovas-Massana A, AKo AI, Malik AA, Wang D, Wang M, Weinberger DM, Arnold W, Omer SB
Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics 
Nature Biotechnology 38, 1164–1167 (2020)

papermedRxiv



Hosier H*, Farhadian S*, Morotti R, Deshmukh U, Lu-Culligans A, Campbell K, Yasumoto Y, Vogels CBF, Casanovas-Massana A, Vijayakumar P, Geng B, Odio C, Fournier J, Brito AF, Fauver JR, Liu F, Alpert T, Tal R, Szigeti-Buck K, Perincheri S, Larsen C, Gariepy A, Aguilar G, Fardelmann K, Harigopal M, Taylor H, Pettker C, Wyllie AL, Dela Cruz C, Ring A, Grubaugh ND, Ko AI, Horvath T, Iwasaki A, Reddy U, Lipkind H
SARS-CoV-2 Infection of the Placenta 
Journal of Clinical Investigation 130(9), 4947-4953 (2020)

papermedRxiv

Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Dela Cruz C, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Aoun Barakat L
Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19
BMC Neurology 248(20), (2020)

paperpre-print

Mavian C, Pond SK, Marini S, Magalis BF, Vandamme A-F, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NV, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Tsan-Yuk Lam T, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T,  Bento AI, Schmidt HA, Martin D, Hadfield J, Faria NR, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
PNAS 117(23), 12522-12523 (2020)

paper

Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Lu-Culligan A, Klein J, Venkataraman A, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman O-E, Wong P, Yang Y, Bermejo S, Odio C, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND*, Ko AI*
Saliva or nasopharyngeal swab specimens for detection of SARS-CoV-2
New England Journal of Medicine
 383, 1283-1286 (2020)

papermedRxivTwitter thread

Iwasaki A, Grubaugh ND
Why does Japan have so few cases of COVID19? 
EMBO Molecular Medicine 12, e12481 (2020)

paper

Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Muenker AC, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takehashi T, Taura M, Tokuyama M, Venkataraman A, Weizman O, Wong P, Yang Y, Cheemarla NR, White E, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz C, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND
Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR primer-probe sets 
Nature Microbiology 5, 1299–1305 (2020)

papermedRxiv

Fauver JR*, Petrone ME*, Hodcroft EB*, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J,  Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NL, Neugebauer KM, Greninger AL, Jerome KR, Roychoundhury P, Xie H, Shrestha L, Huang M-L, Pitzer VE, Iwasaki A, Omer SB, Khan K,  Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND  
Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States
Cell
  181(5), 990-996 (2020)

papergithubnextstraintwitter threadmedRxiv

Grubaugh ND, Petrone ME, Holmes EC
We shouldn’t worry when a virus mutates during disease outbreaks
Nature Microbiology 5, 529–530 (2020)

papertwitter thread

Pollett S, Faver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND 
Genomic epidemiology as a public health tool to combat mosquito-borne virus outbreaks

Journal of Infectious Diseases Supp 3, S308–S318 (2020)

paper

2019

Hadfield J*, Brito AF*, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND
Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain 

PLOS Pathogens
15(10): e1008042 (2019)

papernextstrainnarrativegithubblogtwitter thread



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(5), 1057-1071 (2019)

papergithubbioRxivvideo abstractblogtwitter threadNIH Director’s blogNew York Times

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)

papergithub

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)

paperbioRxivgithubread cube

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

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

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

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)

paperbioRxivgithubpreviewThe Atlantickpbs

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)

paper



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)

paperThe Atlantic

Grubaugh ND, Andersen KG
Navigating the Zika panic
F1000 5:1914 (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

op-eds

Grubaugh ND
What you need to know about the UK COVID-19 variant found in New Haven County
New Haven Independent January 12 (2021)

What You Need To Know About The UK COVID-19 Variant Found In New Haven County
January 12 (2021)op-ed

Petrone ME, Grubaugh ND
Coronavirus mutations: Much ado about nothing

CNN health, March 7 (2020)

op-ed

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

op-ed

protocols

Vogels CBF, Fauver JR, Grubaugh ND
Multiplexed RT-qPCR to screen for SARS-COV-2 B.1.1.7, B.1.351, and P.1 variants of concern
protocols.io br9vm966 (2021)

protocol

Ott IM, Vogels CBF, Grubaugh NG, Wyllie AL
Saliva Collection and RNA Extraction for SARS-CoV-2 Detection
protocols.io bg3pjymn (2020)

protocol

Vogels CBF, Brackney DEB, Kalinich CC, Ott IM, Grubaugh NG*, Wyllie AL* 
SalivaDirect: RNA extraction-free SARS-CoV-2 diagnostics
protocols.io bhfej3je (2020)

protocol

Vogels CBFFauver JR, Ott IM, Grubaugh ND
Generation of SARS-COV-2 RNA transcript standards for qRT-PCR detection assays 
Protocols.io bdv6i69e (2020)

protocol

*co-first or co-senior author